From c7e34e5cc9fa3607fc268eb12b7a61e2b71edb7c Mon Sep 17 00:00:00 2001 From: James Seager Date: Thu, 4 Apr 2024 14:26:34 +0100 Subject: [PATCH] Make full release --- patterns/definitions.owl | 4 +- phipo-base.json | 650 +- phipo-base.obo | 258 +- phipo-base.owl | 394 +- phipo-full.json | 10126 ++++++++++------------- phipo-full.obo | 3992 ++++----- phipo-full.owl | 10328 ++++++++++-------------- phipo-simple-non-classified.json | 650 +- phipo-simple-non-classified.obo | 258 +- phipo-simple-non-classified.owl | 394 +- phipo-simple.json | 914 ++- phipo-simple.obo | 40 +- phipo-simple.owl | 450 +- phipo.json | 10126 ++++++++++------------- phipo.obo | 3994 ++++----- phipo.owl | 10328 ++++++++++-------------- src/ontology/imports/chebi_import.owl | 33 +- src/ontology/imports/cl_import.owl | 131 +- src/ontology/imports/go_import.owl | 4 +- src/ontology/imports/ido_import.owl | 4 +- src/ontology/imports/pato_import.owl | 4137 ++++------ src/ontology/imports/ro_import.owl | 74 +- src/ontology/imports/so_import.owl | 4 +- src/patterns/definitions.owl | 4 +- 24 files changed, 25515 insertions(+), 31782 deletions(-) diff --git a/patterns/definitions.owl b/patterns/definitions.owl index beb2447..67a0a07 100644 --- a/patterns/definitions.owl +++ b/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-01-31") + +Annotation(owl:versionInfo "2024-04-04") Declaration(Class()) Declaration(Class()) diff --git a/phipo-base.json b/phipo-base.json index a2d8d30..1417df2 100644 --- a/phipo-base.json +++ b/phipo-base.json @@ -22,9 +22,9 @@ "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-01-31" + "val" : "2024-04-04" } ], - "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-01-31/phipo-base.json" + "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-04-04/phipo-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/PHIPO_0000001", @@ -27243,6 +27243,538 @@ "val" : "single_species_phenotype" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001411", + "lbl" : "resistance to dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001412", + "lbl" : "sensitive to dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001413", + "lbl" : "normal growth on dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001414", + "lbl" : "resistance to thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001415", + "lbl" : "sensitive to thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001416", + "lbl" : "normal growth on thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001417", + "lbl" : "resistance to penflufen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001418", + "lbl" : "sensitive to penflufen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001419", + "lbl" : "normal growth on penflufen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001420", + "lbl" : "resistance to flutolanil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001421", + "lbl" : "sensitive to flutolanil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001422", + "lbl" : "normal growth on flutolanil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001423", + "lbl" : "resistance to imazalil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-12T10:06:39Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001424", + "lbl" : "sensitive to imazalil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-12T10:06:39Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001425", + "lbl" : "normal growth on imazalil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-12T10:06:39Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001426", + "lbl" : "normal growth on fludioxonil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-28T09:44:54Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001427", + "lbl" : "abnormal hyphal branching", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A single species cell morphology phenotype in which fungal hyphae branching is abnormal." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-04T15:00:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001428", + "lbl" : "normal growth on brefeldin A", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-12T15:12:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001429", + "lbl" : "normal growth on fluconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-12T15:14:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001430", + "lbl" : "resistance to ipconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001431", + "lbl" : "sensitive to ipconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001432", + "lbl" : "normal growth on ipconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001433", + "lbl" : "resistance to cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001434", + "lbl" : "sensitive to cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001435", + "lbl" : "normal growth on cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001436", + "lbl" : "normal growth on caspofungin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001437", + "lbl" : "normal growth on terbinafine", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001438", + "lbl" : "normal growth on bifonazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/PHIPO_0000001", @@ -30723,7 +31255,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001153", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001205" + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001427" }, { "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001154", "pred" : "is_a", @@ -31664,6 +32196,118 @@ "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001410", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001411", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001412", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001413", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001414", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001415", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001416", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001417", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001418", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001419", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001420", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001421", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001422", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001423", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001424", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001425", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001426", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001427", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001205" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001428", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001429", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001431", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001432", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001433", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001434", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001435", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001436", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001437", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001438", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" } ] } ] } \ No newline at end of file diff --git a/phipo-base.obo b/phipo-base.obo index d6d29de..f858866 100644 --- a/phipo-base.obo +++ b/phipo-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: phipo/releases/2024-01-31/phipo-base.owl +data-version: phipo/releases/2024-04-04/phipo-base.owl ontology: phipo/phipo-base property_value: created:by "alaynecuzick" xsd:string property_value: creation:date "2018-07-09T13:43:00Z" xsd:string @@ -7,7 +7,7 @@ property_value: http://purl.org/dc/elements/1.1/description "Ontology of species property_value: http://purl.org/dc/elements/1.1/title "Pathogen Host Interactions Phenotype Ontology" xsd:string property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/3.0/" xsd:string -property_value: owl:versionInfo "2024-01-31" xsd:string +property_value: owl:versionInfo "2024-04-04" xsd:string [Term] id: PHIPO:0000001 @@ -10157,7 +10157,7 @@ namespace: single_species_phenotype def: "A single species cell morphology phenotype in which fungal hyphae form an increased number of branches." [] synonym: "increased branching of hyphae" EXACT [] synonym: "increased hyphal branching" EXACT [] -is_a: PHIPO:0001205 ! abnormal filament morphology +is_a: PHIPO:0001427 ! abnormal hyphal branching created_by: alaynecuzick creation_date: 2020-03-04T14:33:49Z @@ -12596,6 +12596,258 @@ is_a: PHIPO:0001308 ! normal growth on chemical created_by: alaynecuzick creation_date: 2024-01-30T14:16:53Z +[Term] +id: PHIPO:0001411 +name: resistance to dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001412 +name: sensitive to dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001413 +name: normal growth on dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001414 +name: resistance to thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001415 +name: sensitive to thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001416 +name: normal growth on thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001417 +name: resistance to penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001418 +name: sensitive to penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001419 +name: normal growth on penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001420 +name: resistance to flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001421 +name: sensitive to flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001422 +name: normal growth on flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001423 +name: resistance to imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001424 +name: sensitive to imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001425 +name: normal growth on imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001426 +name: normal growth on fludioxonil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-28T09:44:54Z + +[Term] +id: PHIPO:0001427 +name: abnormal hyphal branching +namespace: single_species_phenotype +def: "A single species cell morphology phenotype in which fungal hyphae branching is abnormal." [] +is_a: PHIPO:0001205 ! abnormal filament morphology +created_by: alaynecuzick +creation_date: 2024-03-04T15:00:58Z + +[Term] +id: PHIPO:0001428 +name: normal growth on brefeldin A +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-12T15:12:17Z + +[Term] +id: PHIPO:0001429 +name: normal growth on fluconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-12T15:14:22Z + +[Term] +id: PHIPO:0001430 +name: resistance to ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001431 +name: sensitive to ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001432 +name: normal growth on ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001433 +name: resistance to cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001434 +name: sensitive to cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001435 +name: normal growth on cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001436 +name: normal growth on caspofungin +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + +[Term] +id: PHIPO:0001437 +name: normal growth on terbinafine +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + +[Term] +id: PHIPO:0001438 +name: normal growth on bifonazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + [Typedef] id: PHIPO:0000304 name: qualifier diff --git a/phipo-base.owl b/phipo-base.owl index 5ced72c..7c13763 100644 --- a/phipo-base.owl +++ b/phipo-base.owl @@ -21,14 +21,14 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + alaynecuzick 2018-07-09T13:43:00Z Ontology of species-neutral phenotypes observed in pathogen-host interactions. Pathogen Host Interactions Phenotype Ontology https://creativecommons.org/licenses/by/3.0/ - 2024-01-31 + 2024-04-04 @@ -28580,7 +28580,7 @@ - + A single species cell morphology phenotype in which fungal hyphae form an increased number of branches. alaynecuzick 2020-03-04T14:33:49Z @@ -32111,6 +32111,394 @@ occurs to a lesser extent than normal. PHIPO:0001410 normal growth on iprovalicarb + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001411 + resistance to dalfopristin + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001412 + sensitive to dalfopristin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001413 + normal growth on dalfopristin + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001414 + resistance to thifluzamide + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001415 + sensitive to thifluzamide + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001416 + normal growth on thifluzamide + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001417 + resistance to penflufen + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001418 + sensitive to penflufen + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001419 + normal growth on penflufen + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001420 + resistance to flutolanil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001421 + sensitive to flutolanil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001422 + normal growth on flutolanil + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001423 + resistance to imazalil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001424 + sensitive to imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001425 + normal growth on imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-28T09:44:54Z + single_species_phenotype + normal growth on fludioxonil + + + + + + + + + A single species cell morphology phenotype in which fungal hyphae branching is abnormal. + alaynecuzick + 2024-03-04T15:00:58Z + single_species_phenotype + abnormal hyphal branching + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:12:17Z + single_species_phenotype + normal growth on brefeldin A + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:14:22Z + single_species_phenotype + normal growth on fluconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001430 + resistance to ipconazole + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001431 + sensitive to ipconazole + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001432 + normal growth on ipconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001433 + resistance to cyprodinil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001434 + sensitive to cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001435 + normal growth on cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001436 + normal growth on caspofungin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001437 + normal growth on terbinafine + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001438 + normal growth on bifonazole + diff --git a/phipo-full.json b/phipo-full.json index 5a59eab..69e5297 100644 --- a/phipo-full.json +++ b/phipo-full.json @@ -19,9 +19,9 @@ "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-01-31" + "val" : "2024-04-04" } ], - "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-01-31/phipo-full.json" + "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-04-04/phipo-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", @@ -741,6 +741,12 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/OBOFoundry/COB/issues/65" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -938,9 +944,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -1006,9 +1009,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -1096,18 +1096,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -1131,9 +1125,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -1187,18 +1178,9 @@ "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -15033,6 +15015,49 @@ "val" : "chebi_ontology" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CHEBI_228364", + "lbl" : "NMR chemical shift reference compound", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "NMR chemical shift reference compounds", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR chemical shift standard", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR chemical shift standards", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR internal standard", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR internal standards", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR reference standard", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR reference standards", + "xrefs" : [ "ChEBI" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "chebi_ontology" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CHEBI_22888", "lbl" : "biphenyls", @@ -36198,13 +36223,35 @@ "lbl" : "alpha-amino-acid residue", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "An amino-acid residue derived from an alpha-amino acid." + }, "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "alpha-amino-acid residues", "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "an alpha-amino acid residue", + "xrefs" : [ "UniProt" ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/chebi/charge", + "val" : "0" + }, { + "pred" : "http://purl.obolibrary.org/obo/chebi/formula", + "val" : "C2H2NOR" + }, { + "pred" : "http://purl.obolibrary.org/obo/chebi/mass", + "val" : "56.043" + }, { + "pred" : "http://purl.obolibrary.org/obo/chebi/monoisotopicmass", + "val" : "56.01364" + }, { + "pred" : "http://purl.obolibrary.org/obo/chebi/smiles", + "val" : "*-NC([*])C(-*)=O" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "chebi_ontology" } ] @@ -86884,11 +86931,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs" : [ "CARO:mah" ] + "val" : "A material entity that has a plasma membrane and results from cellular division." }, - "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "comments" : [ "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.", "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).", "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -86913,6 +86959,96 @@ "val" : "http://purl.obolibrary.org/obo/cl.owl" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000151", + "lbl" : "secretory cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell that specializes in controlled release of one or more substances.", + "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "BTO:0003659" + }, { + "val" : "FMA:86916" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000154", + "lbl" : "protein secreting cell", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000225", + "lbl" : "anucleate cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell that lacks a nucleus.", + "xrefs" : [ "FB:ma" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "non-nucleated cell" + } ], + "xrefs" : [ { + "val" : "FMA:68647" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000226", + "lbl" : "single nucleate cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell with a single nucleus.", + "xrefs" : [ "FB:ma", "GOC:tfm" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000227", + "lbl" : "binucleate cell", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000228", + "lbl" : "multinucleate cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell with more than one nucleus.", + "xrefs" : [ "FB:ma" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "syncitium" + }, { + "pred" : "hasExactSynonym", + "val" : "syncytial cell" + }, { + "pred" : "hasExactSynonym", + "val" : "syncytium" + } ], + "xrefs" : [ { + "val" : "AEO:0000203" + }, { + "val" : "WBbt:0008074" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000255", + "lbl" : "eukaryotic cell", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "MESH:D005057" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000521", + "lbl" : "fungal cell", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/CL_0001061", "lbl" : "abnormal cell", @@ -86923,6 +87059,7 @@ "xrefs" : [ "GOC:add", "GOC:cg", "GOC:wdd" ] }, "comments" : [ "https://github.com/obophenotype/cell-ontology/issues/448" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913" } ], @@ -86935,22 +87072,37 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CL_0017505", - "lbl" : "increased nucleus size", + "id" : "http://purl.obolibrary.org/obo/CL_0002242", + "lbl" : "nucleate cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.", + "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "xrefs" : [ { + "val" : "FMA:67513" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-12-23T10:53:24Z" + "val" : "2010-09-07T03:32:33Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0011115", + "lbl" : "precursor cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell that, by division or terminal differentiation, can give rise to other cell types.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + } }, { "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", "lbl" : "results_in_fission_of", @@ -87073,59 +87225,32 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0000740", - "lbl" : "nuclear membrane fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The joining of 2 or more lipid bilayer membranes that surround the nucleus.", - "xrefs" : [ "GOC:elh" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0000741", - "lbl" : "karyogamy", + "id" : "http://purl.obolibrary.org/obo/GO_0001677", + "lbl" : "formation of translation initiation ternary complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei.", - "xrefs" : [ "GOC:elh" ] + "val" : "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).", + "xrefs" : [ "GOC:hjd" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "nuclear fusion" - }, { - "pred" : "hasExactSynonym", - "val" : "nuclear fusion during karyogamy" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Karyogamy" + "val" : "translation initiation ternary complex assembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007335" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0001677", - "lbl" : "formation of translation initiation ternary complex", + "id" : "http://purl.obolibrary.org/obo/GO_0001700", + "lbl" : "embryonic development via the syncytial blastoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).", - "xrefs" : [ "GOC:hjd" ] + "val" : "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster.", + "xrefs" : [ "GOC:go_curators", "GOC:mtg_sensu" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "translation initiation ternary complex assembly" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -87301,7 +87426,7 @@ "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -87538,7 +87663,7 @@ "xrefs" : [ "GOC:ai", "GOC:dgf" ] }, "comments" : [ "Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "carrier" @@ -87556,50 +87681,6 @@ "val" : "molecular_function" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005319", - "lbl" : "lipid transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Enables the directed movement of lipids into, out of or within a cell, or between cells.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "lipophorin" - }, { - "pred" : "hasRelatedSynonym", - "val" : "apolipoprotein" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-1369028" - }, { - "val" : "Reactome:R-HSA-1369052" - }, { - "val" : "Reactome:R-HSA-174786" - }, { - "val" : "Reactome:R-HSA-5682285" - }, { - "val" : "Reactome:R-HSA-5682311" - }, { - "val" : "Reactome:R-HSA-5683672" - }, { - "val" : "Reactome:R-HSA-5683714" - }, { - "val" : "Reactome:R-HSA-5688397" - }, { - "val" : "Reactome:R-HSA-6801250" - }, { - "val" : "Reactome:R-HSA-8848053" - }, { - "val" : "Reactome:R-HSA-8866329" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0005488", "lbl" : "binding", @@ -87660,7 +87741,7 @@ "val" : "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -87697,7 +87778,7 @@ "xrefs" : [ "GOC:go_curators" ] }, "comments" : [ "Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "extracellular" @@ -87807,7 +87888,7 @@ "val" : "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.", "xrefs" : [ "ISBN:0198547684" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "xrefs" : [ { "val" : "Wikipedia:Cytoplasm" } ], @@ -87902,7 +87983,7 @@ "val" : "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.", "xrefs" : [ "ISBN:0716731363" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "juxtamembrane" @@ -88078,31 +88159,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0006401", - "lbl" : "RNA catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RNA breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "RNA catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "RNA degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006403", "lbl" : "RNA localization", @@ -88135,7 +88191,7 @@ "val" : "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "protein anabolism" @@ -88385,7 +88441,7 @@ "val" : "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.", "xrefs" : [ "ISBN:0198506732" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular amino acid metabolic process" @@ -88458,7 +88514,7 @@ "val" : "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.", "xrefs" : [ "GOC:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "lipid metabolism" @@ -88637,7 +88693,7 @@ "xrefs" : [ "GOC:dos", "GOC:dph", "GOC:jl", "GOC:mah" ] }, "comments" : [ "Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "single-organism transport" @@ -88729,21 +88785,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0006869", - "lbl" : "lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006886", "lbl" : "intracellular protein transport", @@ -88753,7 +88794,7 @@ "val" : "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "copper-induced intracellular protein transport", @@ -88767,37 +88808,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0006887", - "lbl" : "exocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", - "xrefs" : [ "GOC:mah", "ISBN:0716731363", "PMID:22323285" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "vesicle exocytosis" - }, { - "pred" : "hasRelatedSynonym", - "val" : "nonselective vesicle exocytosis" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Exocytosis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016195" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006897", "lbl" : "endocytosis", @@ -88893,20 +88903,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0006906", - "lbl" : "vesicle fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Fusion of the membrane of a transport vesicle with its target membrane.", - "xrefs" : [ "GOC:jid" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006914", "lbl" : "autophagy", @@ -89195,33 +89191,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0007039", - "lbl" : "protein catabolic process in the vacuole", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.", - "xrefs" : [ "GOC:mah", "GOC:vw" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar protein breakdown" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar protein catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar protein catabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar protein degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007049", "lbl" : "cell cycle", @@ -89351,6 +89320,25 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0007275", + "lbl" : "multicellular organism development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", + "xrefs" : [ "GOC:dph", "GOC:ems", "GOC:isa_complete", "GOC:tb" ] + }, + "comments" : [ "Note that this term was 'developmental process'." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_plant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/21234" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0008061", "lbl" : "chitin binding", @@ -89430,7 +89418,7 @@ "definition" : { "val" : "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -89900,53 +89888,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009057", - "lbl" : "macromolecule catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "biopolymer catabolic process", - "xrefs" : [ "GOC:mtg_chebi_dec09" ] - }, { - "pred" : "hasExactSynonym", - "val" : "macromolecule breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "macromolecule catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "macromolecule degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organismal macromolecule catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cellular macromolecule catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cellular macromolecule catabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cellular macromolecule degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043285" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044266" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009058", "lbl" : "biosynthetic process", @@ -90025,7 +89966,10 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "http://amigo.geneontology.org/amigo/term/GO:0070589" + "val" : "https://github.com/geneontology/go-ontology/issues/15249" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/25418" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0043284" @@ -90034,36 +89978,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009063", - "lbl" : "amino acid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "amino acid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "amino acid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "amino acid degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular amino acid catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/17904" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009066", "lbl" : "aspartate family amino acid metabolic process", @@ -90245,30 +90159,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009310", - "lbl" : "amine catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.", - "xrefs" : [ "GOC:jl", "ISBN:0198506732" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "amine breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "amine catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "amine degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009403", "lbl" : "toxin biosynthetic process", @@ -90408,6 +90298,70 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0009790", + "lbl" : "embryo development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", + "xrefs" : [ "GOC:go_curators", "GOC:isa_complete", "GOC:mtg_sensu" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_plant" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "embryogenesis and morphogenesis" + }, { + "pred" : "hasExactSynonym", + "val" : "embryogenesis" + }, { + "pred" : "hasExactSynonym", + "val" : "embryonal development" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Embryogenesis" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0009795" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0009791", + "lbl" : "post-embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.", + "xrefs" : [ "GOC:go_curators" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_plant" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0009792", + "lbl" : "embryo development ending in birth or egg hatching", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.", + "xrefs" : [ "GOC:go_curators", "GOC:isa_complete", "GOC:mtg_sensu" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "embryogenesis" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009847", "lbl" : "spore germination", @@ -90630,105 +90584,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009894", - "lbl" : "regulation of catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009895", - "lbl" : "negative regulation of catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009896", - "lbl" : "positive regulation of catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009987", "lbl" : "cellular process", @@ -90830,7 +90685,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.", + "val" : "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.", "xrefs" : [ "GOC:txnOH-2018", "PMID:25934543", "PMID:31580950" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], @@ -90840,6 +90695,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22557" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/25419" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -91003,20 +90861,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0010567", - "lbl" : "regulation of ketone catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells.", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0010604", "lbl" : "positive regulation of macromolecule metabolic process", @@ -91149,19 +90993,28 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0010876", - "lbl" : "lipid localization", + "id" : "http://purl.obolibrary.org/obo/GO_0010720", + "lbl" : "positive regulation of cell development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any process in which a lipid is transported to, or maintained in, a specific location.", + "val" : "Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.", + "xrefs" : [ "GOC:BHF", "GOC:dph", "GOC:tb" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0010721", + "lbl" : "negative regulation of cell development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.", "xrefs" : [ "GOC:BHF", "GOC:dph", "GOC:tb" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "lipid localisation", - "xrefs" : [ "GOC:mah" ] - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -91286,23 +91139,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0012506", - "lbl" : "vesicle membrane", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The lipid bilayer surrounding any membrane-bounded vesicle in the cell.", - "xrefs" : [ "GOC:mah", "GOC:vesicle" ] - }, - "xrefs" : [ { - "val" : "NIF_Subcellular:sao1153182838" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0015031", "lbl" : "protein transport", @@ -91628,30 +91464,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016054", - "lbl" : "organic acid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic acid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "organic acid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic acid degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0016070", "lbl" : "RNA metabolic process", @@ -91661,7 +91473,7 @@ "val" : "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.", "xrefs" : [ "ISBN:0198506732" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "RNA metabolism" @@ -91862,7 +91674,7 @@ "val" : "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.", "xrefs" : [ "ISBN:0198506732" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "xrefs" : [ { "val" : "EC:2.-.-.-" }, { @@ -92329,20 +92141,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0017157", - "lbl" : "regulation of exocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of exocytosis.", - "xrefs" : [ "GOC:go_curators" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0018130", "lbl" : "heterocycle biosynthetic process", @@ -92416,24 +92214,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0019216", - "lbl" : "regulation of lipid metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid metabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0019219", "lbl" : "regulation of nucleobase-containing compound metabolic process", @@ -92536,36 +92316,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0019439", - "lbl" : "aromatic compound catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "aromatic compound breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "aromatic compound catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "aromatic compound degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "aromatic hydrocarbon catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "aromatic hydrocarbon catabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0019538", "lbl" : "protein metabolic process", @@ -93084,104 +92834,21 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030100", - "lbl" : "regulation of endocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of endocytosis.", - "xrefs" : [ "GOC:go_curators" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030133", - "lbl" : "transport vesicle", + "id" : "http://purl.obolibrary.org/obo/GO_0030154", + "lbl" : "cell differentiation", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.", - "xrefs" : [ "GOC:mah", "PMID:22160157" ] + "val" : "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.", + "xrefs" : [ "ISBN:0198506732" ] }, - "comments" : [ "Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "constitutive secretory pathway transport vesicle" - }, { - "pred" : "hasNarrowSynonym", - "val" : "Golgi to vacuole transport vesicle" - }, { - "pred" : "hasNarrowSynonym", - "val" : "Golgi-vacuole transport vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "secretory vesicle" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_plant" ], "xrefs" : [ { - "val" : "NIF_Subcellular:sao885490876" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030163", - "lbl" : "protein catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "This term refers to the breakdown of mature proteins. 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"val" : "multicellular organismal protein catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "pheromone catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "pheromone catabolism" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Protein_catabolism" + "val" : "Wikipedia:Cellular_differentiation" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044254" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044257" + "val" : "https://github.com/geneontology/go-ontology/issues/24390" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -93396,20 +93063,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030659", - "lbl" : "cytoplasmic vesicle membrane", - 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"meta" : { - "definition" : { - "val" : "A vesicle found in the cytoplasm of a cell.", - "xrefs" : [ "GOC:ai", "GOC:mah", "GOC:vesicles" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic membrane bounded vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic membrane-enclosed vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic, membrane-bounded vesicle" - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao180601769" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0031503", "lbl" : "protein-containing complex localization", @@ -93978,36 +93430,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031982", - "lbl" : "vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any small, fluid-filled, spherical organelle enclosed by membrane.", - "xrefs" : [ "GOC:mah", "GOC:pz", "GOC:vesicles" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "membrane-bounded vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "membrane-enclosed vesicle" - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao221389602" - }, { - "val" : "Wikipedia:Vesicle_(biology)" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032179", "lbl" : "germ tube", @@ -94110,162 +93532,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032365", - "lbl" : "intracellular lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of lipids within cells.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032368", - "lbl" : "regulation of lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032369", - "lbl" : "negative regulation of lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of lipid transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032370", - "lbl" : "positive regulation of lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "up regulation of lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of lipid transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032377", - "lbl" : "regulation of intracellular lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032378", - "lbl" : "negative regulation of intracellular lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of intracellular lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of intracellular lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of intracellular lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of intracellular lipid transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032379", - "lbl" : "positive regulation of intracellular lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "up regulation of intracellular lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of intracellular lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of intracellular lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of intracellular lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of intracellular lipid transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032386", "lbl" : "regulation of intracellular transport", @@ -94338,75 +93604,47 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032409", - "lbl" : "regulation of transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the activity of a transporter.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032410", - "lbl" : "negative regulation of transporter activity", + "id" : "http://purl.obolibrary.org/obo/GO_0032501", + "lbl" : "multicellular organismal process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any process that stops or reduces the activity of a transporter.", - "xrefs" : [ "GOC:mah" ] + "val" : "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.", + "xrefs" : [ "GOC:curators", "GOC:dph", "GOC:isa_complete", "GOC:tb" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "down regulation of transporter activity" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of transporter activity" + "val" : "organismal physiological process" }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of transporter activity" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of transporter activity" + "pred" : "hasRelatedSynonym", + "val" : "single-multicellular organism process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032411", - "lbl" : "positive regulation of transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the activity of a transporter.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "up regulation of transporter activity" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of transporter activity" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of transporter activity" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of transporter activity" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "jl" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-09-19T16:07:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044707" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0050874" }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of transporter activity" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -94511,20 +93749,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032871", - "lbl" : "regulation of karyogamy", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032879", "lbl" : "regulation of localization", @@ -94959,84 +94183,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0033241", - "lbl" : "regulation of amine catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of amine breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of amine catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of amine degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular amine catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0033242", - "lbl" : "negative regulation of amine catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amine breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amine catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amine degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular amine catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0033243", - "lbl" : "positive regulation of amine catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amine breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amine catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amine degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0033365", "lbl" : "protein localization to organelle", @@ -95085,7 +94231,7 @@ "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "down regulation of kinase activity" @@ -95116,7 +94262,7 @@ "val" : "Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "up regulation of kinase activity" @@ -95226,87 +94372,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0034251", - "lbl" : "regulation of amide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of amide breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of amide catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of amide degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular amide catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0034252", - "lbl" : "negative regulation of amide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amide breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amide catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular amide catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "negative regulation of amide degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0034253", - "lbl" : "positive regulation of amide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amide breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amide catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular amide catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "positive regulation of amide degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0034293", "lbl" : "sexual sporulation", @@ -95474,12 +94539,15 @@ "val" : "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular nitrogen compound metabolism" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/26424" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -95512,29 +94580,14 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0034655", - "lbl" : "nucleobase-containing compound catabolic process", + "id" : "http://purl.obolibrary.org/obo/GO_0035190", + "lbl" : "syncytial nuclear migration", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.", - "xrefs" : [ "GOC:mah" ] + "val" : "The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex.", + "xrefs" : [ "GOC:bf", "ISBN:0879694238", "PMID:8314839" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "nucleobase, nucleoside, nucleotide and nucleic acid degradation" - }, { - "pred" : "hasRelatedSynonym", - "val" : "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -95655,6 +94708,36 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0040019", + "lbl" : "positive regulation of embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the frequency, rate or extent of embryonic development.", + "xrefs" : [ "GOC:go_curators" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of embryonic development" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0040020", "lbl" : "regulation of meiotic nuclear division", @@ -95695,203 +94778,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0042176", - "lbl" : "regulation of protein catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.", - "xrefs" : [ "GOC:go_curators", "GOC:jl" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of protein breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of protein catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of protein degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of cyclin breakdown", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of cyclin catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of cyclin catabolism", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of cyclin degradation", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of degradation of cyclin", - "xrefs" : [ "GOC:obol" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2014-08-21T15:05:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1903362" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:2000598" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0042177", - "lbl" : "negative regulation of protein catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process.", - "xrefs" : [ "GOC:TermGenie", "GOC:kmv", "GOC:obol", "GO_REF:0000058", "PMID:24785082" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down regulation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down regulation of protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of protein breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of protein catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of protein degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of protein catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1903363" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:2000599" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0042180", "lbl" : "cellular ketone metabolic process", @@ -95938,30 +94824,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0042182", - "lbl" : "ketone catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ketone breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "ketone catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "ketone degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0042325", "lbl" : "regulation of phosphorylation", @@ -96084,7 +94946,7 @@ "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite.", "xrefs" : [ "GOC:ai", "GOC:dph", "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "extracellular structure organisation" @@ -96107,7 +94969,7 @@ "val" : "Any process that activates or increases the activity of an enzyme.", "xrefs" : [ "GOC:ebc", "GOC:jl", "GOC:tb", "GOC:vw" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "positive regulation of enzyme activity", @@ -96163,7 +95025,7 @@ "val" : "Any process that stops or reduces the activity of an enzyme.", "xrefs" : [ "GOC:ebc", "GOC:jl", "GOC:tb", "GOC:vw" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "down regulation of enzyme activity" @@ -96277,30 +95139,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0043171", - "lbl" : "peptide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.", - "xrefs" : [ "GOC:jl" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "peptide breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "peptide catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "peptide degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043207", "lbl" : "response to external biotic stimulus", @@ -96324,7 +95162,7 @@ "val" : "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "xrefs" : [ { "val" : "NIF_Subcellular:sao1539965131" }, { @@ -96703,7 +95541,7 @@ "val" : "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", "xrefs" : [ "GOC:bf" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -96745,24 +95583,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0043605", - "lbl" : "amide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.", - "xrefs" : [ "GOC:curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular amide catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043933", "lbl" : "protein-containing complex organization", @@ -97016,7 +95836,7 @@ "val" : "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.", "xrefs" : [ "GO:jl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" @@ -97037,7 +95857,7 @@ "val" : "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.", "xrefs" : [ "GO:jl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" @@ -97277,30 +96097,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044270", - "lbl" : "cellular nitrogen compound catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.", - "xrefs" : [ "GOC:jl", "ISBN:0198506732" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "nitrogen compound breakdown" - }, { - "pred" : "hasBroadSynonym", - "val" : "nitrogen compound catabolism" - }, { - "pred" : "hasBroadSynonym", - "val" : "nitrogen compound degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044271", "lbl" : "cellular nitrogen compound biosynthetic process", @@ -97354,31 +96150,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044282", - "lbl" : "small molecule catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.", - "xrefs" : [ "GOC:curators", "GOC:vw" ] - }, - "comments" : [ "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "small molecule catabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-01-26T12:06:10Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044283", "lbl" : "small molecule biosynthetic process", @@ -97389,7 +96160,7 @@ "xrefs" : [ "GOC:curators", "GOC:pde", "GOC:vw" ] }, "comments" : [ "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "small molecule biosynthesis" @@ -97721,30 +96492,6 @@ "val" : "molecular_function" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045026", - "lbl" : "plasma membrane fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.", - "xrefs" : [ "GOC:elh", "GOC:mtg_muscle" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cell fusion" - }, { - "pred" : "hasBroadSynonym", - "val" : "cell-cell fusion" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045087", "lbl" : "innate immune response", @@ -97824,6 +96571,77 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045595", + "lbl" : "regulation of cell differentiation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.", + "xrefs" : [ "GOC:go_curators" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045596", + "lbl" : "negative regulation of cell differentiation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.", + "xrefs" : [ "GOC:go_curators" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "down regulation of cell differentiation" + }, { + "pred" : "hasExactSynonym", + "val" : "down-regulation of cell differentiation" + }, { + "pred" : "hasExactSynonym", + "val" : "downregulation of cell differentiation" + }, { + "pred" : "hasNarrowSynonym", + "val" : "inhibition of cell differentiation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045597", + "lbl" : "positive regulation of cell differentiation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the frequency, rate or extent of cell differentiation.", + "xrefs" : [ "GOC:go_curators" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of cell differentiation" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of cell differentiation" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of cell differentiation" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of cell differentiation" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of cell differentiation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045727", "lbl" : "positive regulation of translation", @@ -97897,152 +96715,6 @@ "val" : "biological_process" } ] } - 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"val" : "positive regulation of cyclin degradation", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation of degradation of cyclin", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of protein catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1903364" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:2000600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045763", "lbl" : "negative regulation of cellular amino acid metabolic process", @@ -98179,126 +96851,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045806", - 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}, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of lipid metabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045834", - "lbl" : "positive regulation of lipid metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid metabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of lipid metabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of lipid metabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of lipid metabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045835", "lbl" : "negative regulation of meiotic nuclear division", @@ -98476,63 +97028,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045920", - "lbl" : "negative regulation of exocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis.", - 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"val" : "upregulation of exocytosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of exocytosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of exocytosis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045934", "lbl" : "negative regulation of nucleobase-containing compound metabolic process", @@ -98725,26 +97220,26 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046112", - "lbl" : "nucleobase biosynthetic process", + "id" : "http://purl.obolibrary.org/obo/GO_0045992", + "lbl" : "negative regulation of embryonic development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.", - "xrefs" : [ "GOC:ai" ] + "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development.", + "xrefs" : [ "GOC:go_curators" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "nucleobase anabolism" + "val" : "down regulation of embryonic development" }, { "pred" : "hasExactSynonym", - "val" : "nucleobase biosynthesis" + "val" : "down-regulation of embryonic development" }, { "pred" : "hasExactSynonym", - "val" : "nucleobase formation" + "val" : "downregulation of embryonic development" }, { - "pred" : "hasExactSynonym", - "val" : "nucleobase synthesis" + "pred" : "hasNarrowSynonym", + "val" : "inhibition of embryonic development" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -98752,23 +97247,40 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046113", - "lbl" : "nucleobase catabolic process", + "id" : "http://purl.obolibrary.org/obo/GO_0045995", + "lbl" : "regulation of embryonic development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.", + "val" : "Any process that modulates the frequency, rate or extent of embryonic development.", + "xrefs" : [ "GOC:go_curators" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0046112", + "lbl" : "nucleobase biosynthetic process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.", "xrefs" : [ "GOC:ai" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "nucleobase breakdown" + "val" : "nucleobase anabolism" }, { "pred" : "hasExactSynonym", - "val" : "nucleobase catabolism" + "val" : "nucleobase biosynthesis" + }, { + "pred" : "hasExactSynonym", + "val" : "nucleobase formation" }, { "pred" : "hasExactSynonym", - "val" : "nucleobase degradation" + "val" : "nucleobase synthesis" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -98859,30 +97371,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046395", - "lbl" : "carboxylic acid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "carboxylic acid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "carboxylic acid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "carboxylic acid degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0046483", "lbl" : "heterocycle metabolic process", @@ -98902,107 +97390,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046700", - "lbl" : "heterocycle catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heterocycle breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "heterocycle catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "heterocycle degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046889", - "lbl" : "positive regulation of lipid biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid formation" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid synthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipogenesis", - "xrefs" : [ "GOC:sl" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of lipid biosynthetic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of lipid biosynthetic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of lipid biosynthetic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046890", - "lbl" : "regulation of lipid biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid formation" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid synthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipogenesis", - "xrefs" : [ "GOC:sl" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0046903", "lbl" : "secretion", @@ -99113,12 +97500,12 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0048284", - "lbl" : "organelle fusion", + "id" : "http://purl.obolibrary.org/obo/GO_0048285", + "lbl" : "organelle fission", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The creation of a single organelle from two or more organelles.", + "val" : "The creation of two or more organelles by division of one organelle.", "xrefs" : [ "GOC:jid" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -99128,35 +97515,51 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0048285", - "lbl" : "organelle fission", + "id" : "http://purl.obolibrary.org/obo/GO_0048468", + "lbl" : "cell development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The creation of two or more organelles by division of one organelle.", - "xrefs" : [ "GOC:jid" ] + "val" : "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place.", + "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "terminal differentiation", + "xrefs" : [ "GOC:dph", "GOC:tb" ] + } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/24390" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0048288", - "lbl" : "nuclear membrane fusion involved in karyogamy", + "id" : "http://purl.obolibrary.org/obo/GO_0048513", + "lbl" : "animal organ development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei.", - "xrefs" : [ "GOC:jid" ] + "val" : "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.", + "xrefs" : [ "GOC:dph", "GOC:jid" ] }, "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "nuclear membrane fusion during karyogamy", - "xrefs" : [ "GOC:dph", "GOC:tb" ] + "pred" : "hasExactSynonym", + "val" : "development of an organ" + }, { + "pred" : "hasExactSynonym", + "val" : "organogenesis" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Organogenesis" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/25943" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -99303,6 +97706,77 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0048580", + "lbl" : "regulation of post-embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.", + "xrefs" : [ "GOC:jid" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0048581", + "lbl" : "negative regulation of post-embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.", + "xrefs" : [ "GOC:jid" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "down regulation of post-embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "down-regulation of post-embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "downregulation of post-embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "inhibition of post-embryonic development" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0048582", + "lbl" : "positive regulation of post-embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.", + "xrefs" : [ "GOC:jid" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of post-embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of post-embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of post-embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of post-embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of post-embryonic development" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0048589", "lbl" : "developmental growth", @@ -99504,7 +97978,7 @@ "val" : "Any process that modulates the activity of an enzyme.", "xrefs" : [ "GOC:ai", "GOC:ebc", "GOC:vw" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "regulation of enzyme activity" @@ -99520,6 +97994,20 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0050793", + "lbl" : "regulation of developmental process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", + "xrefs" : [ "GOC:go_curators" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0050794", "lbl" : "regulation of cellular process", @@ -99565,105 +98053,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0050994", - "lbl" : "regulation of lipid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0050995", - "lbl" : "negative regulation of lipid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of lipid catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0050996", - "lbl" : "positive regulation of lipid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of lipid catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of lipid catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of lipid catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051046", "lbl" : "regulation of secretion", @@ -99807,49 +98196,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051055", - "lbl" : "negative regulation of lipid biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid formation" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid synthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipogenesis", - "xrefs" : [ "GOC:sl" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of lipid biosynthetic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051078", "lbl" : "meiotic nuclear membrane disassembly", @@ -99904,6 +98250,63 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051093", + "lbl" : "negative regulation of developmental process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", + "xrefs" : [ "GOC:ai" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "down regulation of developmental process" + }, { + "pred" : "hasExactSynonym", + "val" : "down-regulation of developmental process" + }, { + "pred" : "hasExactSynonym", + "val" : "downregulation of developmental process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "inhibition of developmental process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051094", + "lbl" : "positive regulation of developmental process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", + "xrefs" : [ "GOC:ai" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of developmental process" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of developmental process" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of developmental process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of developmental process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of developmental process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051128", "lbl" : "regulation of cellular component organization", @@ -100309,6 +98712,77 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051239", + "lbl" : "regulation of multicellular organismal process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.", + "xrefs" : [ "GOC:ai", "GOC:dph", "GOC:tb" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051240", + "lbl" : "positive regulation of multicellular organismal process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.", + "xrefs" : [ "GOC:ai" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of multicellular organismal process" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of multicellular organismal process" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of multicellular organismal process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of multicellular organismal process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of multicellular organismal process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051241", + "lbl" : "negative regulation of multicellular organismal process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.", + "xrefs" : [ "GOC:ai" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "down regulation of multicellular organismal process" + }, { + "pred" : "hasExactSynonym", + "val" : "down-regulation of multicellular organismal process" + }, { + "pred" : "hasExactSynonym", + "val" : "downregulation of multicellular organismal process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "inhibition of multicellular organismal process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051246", "lbl" : "regulation of protein metabolic process", @@ -100612,7 +99086,7 @@ "xrefs" : [ "GOC:ai" ] }, "comments" : [ "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "transferase regulator" @@ -100632,7 +99106,7 @@ "xrefs" : [ "GOC:ai" ] }, "comments" : [ "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "transferase activator" @@ -100667,7 +99141,7 @@ "xrefs" : [ "GOC:ai" ] }, "comments" : [ "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "down regulation of transferase activity" @@ -100794,30 +99268,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051469", - "lbl" : "vesicle fusion with vacuole", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "heterotypic vacuole fusion (non-autophagic)" - }, { - "pred" : "hasRelatedSynonym", - "val" : "heterotypic vacuole fusion, non-autophagic" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042146" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051640", "lbl" : "organelle localization", @@ -100920,31 +99370,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051648", - "lbl" : "vesicle localization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cytoplasmic vesicle localization" - }, { - "pred" : "hasExactSynonym", - "val" : "establishment and maintenance of vesicle localization" - }, { - "pred" : "hasExactSynonym", - "val" : "vesicle localisation", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051649", "lbl" : "establishment of localization in cell", @@ -100977,25 +99402,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051650", - "lbl" : "establishment of vesicle localization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of a vesicle to a specific location.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "establishment of vesicle localisation", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051656", "lbl" : "establishment of organelle localization", @@ -101484,7 +99890,7 @@ "val" : "The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.", "xrefs" : [ "GOC:vw" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nucleobase, nucleoside and nucleotide metabolism" @@ -101511,6 +99917,20 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0060284", + "lbl" : "regulation of cell development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.", + "xrefs" : [ "GOC:dph", "GOC:tb" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0060341", "lbl" : "regulation of cellular localization", @@ -101555,26 +99975,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0060627", - "lbl" : "regulation of vesicle-mediated transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-05-18T02:29:43Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0061024", "lbl" : "membrane organization", @@ -101584,7 +99984,7 @@ "val" : "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.", "xrefs" : [ "GOC:dph", "GOC:tb" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular membrane organisation" @@ -101620,43 +100020,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0061025", - "lbl" : "membrane fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The membrane organization process that joins two lipid bilayers to form a single membrane.", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular membrane fusion" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism membrane fusion" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Lipid_bilayer_fusion" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-02-08T02:48:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006944" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044801" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0061650", "lbl" : "ubiquitin-like protein conjugating enzyme activity", @@ -101976,7 +100339,7 @@ "val" : "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.", "xrefs" : [ "GOC:jl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular protein complex assembly" @@ -102047,7 +100410,7 @@ "val" : "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.", "xrefs" : [ "GOC:isa_complete" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "regulation of a molecular function" @@ -102122,28 +100485,6 @@ } ], "deprecated" : true } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0070382", - "lbl" : "exocytic vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.", - "xrefs" : [ "GOC:kad", "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "exocytic constitutive secretory pathway transport vesicle" - }, { - "pred" : "hasExactSynonym", - "val" : "exocytotic vesicle", - "xrefs" : [ "GOC:kad" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0070727", "lbl" : "cellular macromolecule localization", @@ -102592,7 +100933,7 @@ "val" : "A process in which a protein is transported to, or maintained in, a specific location in a membrane.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "protein localisation in membrane", @@ -102942,26 +101283,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0090174", - "lbl" : "organelle membrane fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The joining of two lipid bilayers to form a single organelle membrane.", - "xrefs" : [ "GOC:ascb_2009", "GOC:dph", "GOC:tb" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-12-11T11:44:58Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0090304", "lbl" : "nucleic acid metabolic process", @@ -102972,6 +101293,9 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/26133" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "tb" }, { @@ -103163,46 +101487,6 @@ "val" : "molecular_function" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0097576", - "lbl" : "vacuole fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole.", - "xrefs" : [ "GOC:pr", "GOC:vw", "Wikipedia:Vacuole" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2014-02-28T09:49:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0097708", - "lbl" : "intracellular vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any vesicle that is part of the intracellular region.", - "xrefs" : [ "GOC:vesicles" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2016-03-29T17:39:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0098542", "lbl" : "defense response to other organism", @@ -103348,49 +101632,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0098876", - "lbl" : "vesicle-mediated transport to the plasma membrane", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis.", - "xrefs" : [ "GOC:dos" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099500", - "lbl" : "vesicle fusion to plasma membrane", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "ISBN:0071120009", "PMID:18618940" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099503", - "lbl" : "secretory vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.", - "xrefs" : [ "GOC:dos" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0099568", "lbl" : "cytoplasmic region", @@ -103512,69 +101753,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0110112", - "lbl" : "regulation of lipid transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate, or extent of lipid transporter activity.", - "xrefs" : [ "GOC:BHF", "GOC:BHF_miRNA", "GOC:rph", "PMID:27365390" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-07-06T18:53:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0110113", - "lbl" : "positive regulation of lipid transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that increases the frequency, rate, or extent of lipid transporter activity.", - "xrefs" : [ "GOC:BHF", "GOC:BHF_miRNA", "GOC:rph", "PMID:27365390" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-07-06T19:14:13Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0110114", - "lbl" : "negative regulation of lipid transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that decreases the frequency, rate, or extent of lipid transporter activity.", - "xrefs" : [ "GOC:BHF", "GOC:BHF_miRNA", "GOC:rph", "PMID:27365390" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-07-06T19:21:44Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", "lbl" : "cellular anatomical entity", @@ -103704,27 +101882,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140029", - "lbl" : "exocytic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The cellular processes that contribute to exocytosis.", - "xrefs" : [ "Wikipedia:Exocytosis" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-15T13:20:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140096", "lbl" : "catalytic activity, acting on a protein", @@ -103734,7 +101891,7 @@ "val" : "Catalytic activity that acts to modify a protein.", "xrefs" : [ "GOC:molecular_function_refactoring", "GOC:pdt" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14225" @@ -103758,7 +101915,7 @@ "val" : "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.", "xrefs" : [ "GOC:molecular_function_refactoring", "GOC:pdt" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14225" @@ -103797,42 +101954,6 @@ "val" : "molecular_function" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140318", - "lbl" : "protein transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Directly binding to a specific protein and delivering it to a specific cellular location.", - "xrefs" : [ "PMID:18706423" ] - }, - "comments" : [ "Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "protein carrier activity" - }, { - "pred" : "hasRelatedSynonym", - "val" : "protein transport chaperone" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-9662747" - }, { - "val" : "Reactome:R-HSA-9662818" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/17073" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2019-04-01T10:41:38Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140352", "lbl" : "export from cell", @@ -103857,54 +101978,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140353", - "lbl" : "lipid export from cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of a lipid from a cell, into the extracellular region.", - "xrefs" : [ "GOC:pg" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "lipid efflux" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - 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This may occur via transport across the plasma membrane or via endocytosis.", - "xrefs" : [ "GOC:pg" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "lipid uptake" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2019-05-22T11:38:15Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140513", "lbl" : "nuclear protein-containing complex", @@ -104560,39 +102633,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901361", - "lbl" : "organic cyclic compound catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.", - "xrefs" : [ 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Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001412", + "lbl" : "sensitive to dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001413", + "lbl" : "normal growth on dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001414", + "lbl" : "resistance to thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001415", + "lbl" : "sensitive to thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001416", + "lbl" : "normal growth on thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001417", + "lbl" : "resistance to penflufen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001418", + "lbl" : "sensitive to penflufen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. 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Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001434", + "lbl" : "sensitive to cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001435", + "lbl" : "normal growth on cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001436", + "lbl" : "normal growth on caspofungin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001437", + "lbl" : "normal growth on terbinafine", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001438", + "lbl" : "normal growth on bifonazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000000001", "lbl" : "protein", @@ -137772,6 +136512,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "bearer_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -137803,9 +136546,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "participates_in" @@ -137840,9 +136580,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" @@ -137950,9 +136687,6 @@ "definition" : { "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, - "xrefs" : [ { - "val" : "RO:0000086" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple has quality this red color" @@ -137962,12 +136696,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_quality" } ] } }, { @@ -138023,9 +136751,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -138052,9 +136777,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -138078,9 +136800,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -138095,9 +136814,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -138114,9 +136830,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -138127,13 +136840,10 @@ "lbl" : "directly regulated by", "type" : "PROPERTY", "meta" : { - "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.", "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -138146,14 +136856,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -138166,14 +136873,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -138186,20 +136890,50 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002086", "lbl" : "ends after", @@ -138230,9 +136964,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "immediately_preceded_by" @@ -138327,9 +137058,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -138343,9 +137071,6 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" @@ -138364,12 +137089,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -138385,9 +137104,6 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -138403,12 +137119,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -138441,9 +137151,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -138596,9 +137303,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -138624,9 +137328,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -138668,9 +137369,6 @@ "val" : "inverse of starts with" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -138683,12 +137381,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" } ] } }, { @@ -138721,9 +137413,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -138738,9 +137427,6 @@ "val" : "inverse of ends with" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -138750,12 +137436,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" } ] } }, { @@ -138785,9 +137465,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -138910,6 +137587,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -138945,9 +137625,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" @@ -138984,9 +137661,41 @@ "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -139106,6 +137815,35 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002315" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002320", "lbl" : "evolutionarily related to", @@ -139203,21 +137941,12 @@ "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" } ] } }, { @@ -139253,9 +137982,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "enables part of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" @@ -139443,18 +138169,9 @@ "val" : "inverse of has input" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" } ] } }, { @@ -139475,9 +138192,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -139781,7 +138495,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -139992,6 +138706,88 @@ "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", "lbl" : "existence ends during or before", @@ -140001,18 +138797,9 @@ "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" } ] } }, { @@ -140481,9 +139268,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -140510,9 +139294,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -140551,7 +139332,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -140578,7 +139359,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -140629,9 +139410,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:30Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" @@ -140675,9 +139453,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:14Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" @@ -140701,9 +139476,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:22Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" @@ -140760,29 +139532,6 @@ "val" : "https://orcid.org/0000-0003-4639-4431" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012008", - "lbl" : "results in fusion of", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0012008" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-02-26T07:28:29Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fusion_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012011", "lbl" : "indirectly causally upstream of", @@ -140794,9 +139543,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0003-1813-6857" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -140813,9 +139559,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0003-1813-6857" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -140898,9 +139641,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-11-08T12:00:00Z" } ] } }, { @@ -141004,6 +139744,9 @@ "xrefs" : [ "span:ProcessualEntity" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "BFO:0000003" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" @@ -141091,6 +139834,95 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000066", + "lbl" : "fully formed stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "adult stage" + }, { + "pred" : "hasExactSynonym", + "val" : "fully formed animal stage" + }, { + "pred" : "hasExactSynonym", + "val" : "juvenile-adult stage" + } ], + "xrefs" : [ { + "val" : "BTO:0001043" + }, { + "val" : "BilaDO:0000004" + }, { + "val" : "EFO:0001272" + }, { + "val" : "FBdv:00005369" + }, { + "val" : "WBls:0000041" + }, { + "val" : "XtroDO:0000084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/566" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000068", + "lbl" : "embryo stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A life cycle stage that starts with fertilization and ends with the fully formed embryo.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "embryogenesis" + } ], + "xrefs" : [ { + "val" : "BilaDO:0000002" + }, { + "val" : "EV:0300001" + }, { + "val" : "FBdv:00005289" + }, { + "val" : "FMA:72652" + }, { + "val" : "HsapDv:0000002" + }, { + "val" : "MmusDv:0000002" + }, { + "val" : "OGES:000000" + }, { + "val" : "OGES:000022" + }, { + "val" : "SCTID:296280003" + }, { + "val" : "WBls:0000003" + }, { + "val" : "WBls:0000092" + }, { + "val" : "WBls:0000102" + }, { + "val" : "XAO:1000012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000071", "lbl" : "death stage", @@ -141127,6 +139959,51 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000092", + "lbl" : "post-embryonic stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Stage succeeding embryo, including mature structure.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "postembryonic stage" + }, { + "pred" : "hasNarrowSynonym", + "val" : "post-hatching stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "postembryonic" + } ], + "xrefs" : [ { + "val" : "BilaDO:0000003" + }, { + "val" : "OGES:000010" + }, { + "val" : "OGES:000014" + }, { + "val" : "OGES:000024" + }, { + "val" : "WBls:0000022" + }, { + "val" : "WBls:0000093" + }, { + "val" : "WBls:0000103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", + "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/344" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000104", "lbl" : "life cycle", @@ -141247,6 +140124,118 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000106", + "lbl" : "zygote stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A stage at which the organism is a single cell produced by means of sexual reproduction.", + "xrefs" : [ "Wikipedia:Zygote" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "1-cell stage" + }, { + "pred" : "hasExactSynonym", + "val" : "fertilized egg stage", + "xrefs" : [ "BTO:0000854" ] + }, { + "pred" : "hasExactSynonym", + "val" : "one cell stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "fertilized egg stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "one-cell stage", + "xrefs" : [ "VHOG:0000745" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "zygote", + "xrefs" : [ "VHOG:0000745" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "zygotum", + "xrefs" : [ "Wikipedia:Zygote" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000106" + }, { + "val" : "BilaDO:0000005" + }, { + "val" : "EFO:0001322" + }, { + "val" : "EHDAA:27" + }, { + "val" : "FBdv:00005288" + }, { + "val" : "IDOMAL:0000302" + }, { + "val" : "NCIT:C12601" + }, { + "val" : "PdumDv:0000100" + }, { + "val" : "VHOG:0000745" + }, { + "val" : "Wikipedia:Zygote" + }, { + "val" : "XAO:1000001" + }, { + "val" : "ZFS:0000001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", + "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/EMAPA_16033" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" + }, { + "val" : "BilaDO:0000010" + }, { + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/533" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", "lbl" : "material anatomical entity", @@ -141294,6 +140283,212 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000468", + "lbl" : "multicellular organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical structure that is an individual member of a species and consists of more than one cell.", + "xrefs" : [ "CARO:0000012", "Wikipedia:Multi-cellular_organism", "http://orcid.org/0000-0001-9114-8737" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "organism", + "xrefs" : [ "FBbt:00000001", "VHOG:0000671", "WBbt:0007833" ] + }, { + "pred" : "hasExactSynonym", + "val" : "multi-cellular organism", + "xrefs" : [ "CARO:0000012" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Koerper", + "xrefs" : [ "BTO:0001489" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "body", + "xrefs" : [ "AEO:0000103", "BIRNLEX:18", "FMA:256135", "NCIT:C13041" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole body", + "xrefs" : [ "BTO:0001489" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole organism", + "xrefs" : [ "FBbt:00000001" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010026" + }, { + "val" : "AEO:0000191" + }, { + "val" : "BILA:0000012" + }, { + "val" : "BIRNLEX:18" + }, { + "val" : "BSA:0000038" + }, { + "val" : "BTO:0000042" + }, { + "val" : "CARO:0000012" + }, { + "val" : "EFO:0002906" + }, { + "val" : "EHDAA2:0003103" + }, { + "val" : "EHDAA2:0003191" + }, { + "val" : "EHDAA:1" + }, { + "val" : "EMAPA:25765" + }, { + "val" : "EV:0100016" + }, { + "val" : "FBbt:00000001" + }, { + "val" : "FMA:256135" + }, { + "val" : "HAO:0000012" + }, { + "val" : "NCIT:C13041" + }, { + "val" : "SCTID:243928005" + }, { + "val" : "TADS:0000001" + }, { + "val" : "TAO:0001094" + }, { + "val" : "TGMA:0001832" + }, { + "val" : "VHOG:0000671" + }, { + "val" : "WBbt:0007833" + }, { + "val" : "Wikipedia:Multi-cellular_organism" + }, { + "val" : "XAO:0003004" + }, { + "val" : "ZFA:0001094" + }, { + "val" : "galen:Organism" + }, { + "val" : "ncithesaurus:Whole_Organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - split body and mc organism? body continues after death stage" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", + "val" : "organismal" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000922", + "lbl" : "embryo", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", + "xrefs" : [ "BTO:0000379", "FB:FBrf0039741", "FB:FBrf0041814", "GO:0009790", "Wikipedia:Embryo" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic organism", + "xrefs" : [ "BILA:0000056" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "developing organism", + "xrefs" : [ "BILA:0000056" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "developmental tissue" + } ], + "xrefs" : [ { + "val" : "AAO:0011035" + }, { + "val" : "AEO:0000169" + }, { + "val" : "BILA:0000056" + }, { + "val" : "BSA:0000039" + }, { + "val" : "BTO:0000379" + }, { + "val" : "CALOHA:TS-0229" + }, { + "val" : "EFO:0001367" + }, { + "val" : "EHDAA2:0000002" + }, { + "val" : "EHDAA2_RETIRED:0003236" + }, { + "val" : "EHDAA:38" + }, { + "val" : "EMAPA:16039" + }, { + "val" : "FBbt:00000052" + }, { + "val" : "FMA:69068" + }, { + "val" : "GAID:963" + }, { + "val" : "IDOMAL:0000646" + }, { + "val" : "MAT:0000226" + }, { + "val" : "MESH:D004622" + }, { + "val" : "MIAA:0000019" + }, { + "val" : "NCIT:C28147" + }, { + "val" : "OGEM:000001" + }, { + "val" : "SCTID:57991002" + }, { + "val" : "UMLS:C0013935" + }, { + "val" : "VHOG:0001766" + }, { + "val" : "Wikipedia:Embryo" + }, { + "val" : "XAO:0000113" + }, { + "val" : "ZFA:0000103" + }, { + "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", + "val" : "embryonic" + }, { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", + "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/503" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", "lbl" : "anatomical entity", @@ -141308,6 +140503,8 @@ "val" : "AAO:0010841" }, { "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" }, { "val" : "BILA:0000000" }, { @@ -141353,6 +140550,80 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009953", + "lbl" : "post-embryonic organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multicellular organism that existence_starts_with a post-embryonic stage.", + "xrefs" : [ "OBOL:automatic" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "postnatal organism" + }, { + "pred" : "hasNarrowSynonym", + "val" : "TS28 mouse", + "xrefs" : [ "MA:0002405" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "post-hatching organism", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "post-natal organism", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "postnatal mouse", + "xrefs" : [ "MA:0002405" ] + } ], + "xrefs" : [ { + "val" : "MA:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/667" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "lbl" : "multicellular anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] + } ], + "xrefs" : [ { + "val" : "CARO:0010000" + }, { + "val" : "FBbt:00100313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "lbl" : "obsolete decreased_in_magnitude_relative_to", @@ -141437,81 +140708,13 @@ } ] } }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "lbl" : "created by", + "type" : "PROPERTY" }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "lbl" : "creation date", + "type" : "PROPERTY" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", @@ -141600,6 +140803,10 @@ "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" } ] } + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#id", + "lbl" : "id", + "type" : "PROPERTY" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", @@ -141640,7 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"http://purl.obolibrary.org/obo/CHEBI_33232" + }, { + "sub" : "http://purl.obolibrary.org/obo/CHEBI_228364", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CHEBI_51086" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_22888", "pred" : "is_a", @@ -144701,10 +143920,6 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_24431", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/CHEBI_24432", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_24432", "pred" : "is_a", @@ -145489,6 +144704,10 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_26078", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CHEBI_59698" + }, { + "sub" : "http://purl.obolibrary.org/obo/CHEBI_26078", + "pred" : "http://purl.obolibrary.org/obo/RO_0000087", + "obj" : "http://purl.obolibrary.org/obo/CHEBI_228364" }, { "sub" : 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"sub" : "http://purl.obolibrary.org/obo/CL_0000228", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001908" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000255", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000255", + "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000521", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000521", + "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001061", "pred" : "is_a", @@ -159206,13 +158481,21 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/PATO_0000460" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0017505", + "sub" : "http://purl.obolibrary.org/obo/CL_0002242", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0005634" + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0017505", + "sub" : "http://purl.obolibrary.org/obo/CL_0002242", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000586" + "obj" : "http://purl.obolibrary.org/obo/PATO_0002505" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011115", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011115", + "pred" : "http://purl.obolibrary.org/obo/RO_0002215", + "obj" : "http://purl.obolibrary.org/obo/GO_0030154" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000003", "pred" : "is_a", @@ -159253,34 +158536,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0000280", "pred" : 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: "http://purl.obolibrary.org/obo/GO_0000741", - "pred" : "http://purl.obolibrary.org/obo/RO_0012008", - "obj" : "http://purl.obolibrary.org/obo/GO_0005634" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0001677", "pred" : "is_a", @@ -159293,6 +158548,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0001677", "pred" : "http://purl.obolibrary.org/obo/RO_0002588", "obj" : "http://purl.obolibrary.org/obo/GO_0044207" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0001700", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009792" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0001700", + "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0002252", "pred" : "is_a", @@ -159405,24 +158668,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0005215", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0003674" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005319", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0005215" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005319", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GO_0006869", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source", - "val" : "GO_REF:0000090" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005319", - "pred" : "http://purl.obolibrary.org/obo/RO_0004009", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_18059" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005488", "pred" : "is_a", @@ -159559,22 +158804,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006139", "pred" : "http://purl.obolibrary.org/obo/RO_0004007", "obj" : "http://purl.obolibrary.org/obo/CHEBI_61120" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0006401", - "pred" : "is_a", - "obj" : 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"http://purl.obolibrary.org/obo/CHEBI_37022" + "obj" : "http://purl.obolibrary.org/obo/CHEBI_35238" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006521", "pred" : "is_a", @@ -159755,10 +158972,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006629", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0071704" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0006629", - "pred" : "http://purl.obolibrary.org/obo/RO_0004007", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_18059" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006714", "pred" : "is_a", @@ -159843,18 +159056,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006865", "pred" : "http://purl.obolibrary.org/obo/RO_0004009", "obj" : "http://purl.obolibrary.org/obo/CHEBI_33709" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0006869", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071702" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0006869", - "pred" : 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+ "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0003674" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", @@ -160155,10 +159328,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0008610", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_1901576" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0008610", - "pred" : "http://purl.obolibrary.org/obo/RO_0004008", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_18059" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008641", "pred" : "is_a", @@ -160171,10 +159340,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0008641", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0140657" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0008652", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0006520" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008652", "pred" : "is_a", @@ -160191,18 +159356,6 @@ "sub" : 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"http://purl.obolibrary.org/obo/RO_0002296", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0009791", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0032501" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0009791", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0007275" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0009792", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009790" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0009792", + "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009847", "pred" : "is_a", @@ -160431,38 +159584,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009893", "pred" : "http://purl.obolibrary.org/obo/RO_0002213", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : 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"http://purl.obolibrary.org/obo/GO_0006996" }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0010876", + "sub" : "http://purl.obolibrary.org/obo/GO_0010720", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0033036" + "obj" : "http://purl.obolibrary.org/obo/GO_0045597" }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0010876", - "pred" : "http://purl.obolibrary.org/obo/RO_0004009", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_18059" + "sub" : "http://purl.obolibrary.org/obo/GO_0010720", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0060284" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010720", + "pred" : "http://purl.obolibrary.org/obo/RO_0002213", + "obj" : "http://purl.obolibrary.org/obo/GO_0048468" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010721", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0045596" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010721", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0060284" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010721", + "pred" : "http://purl.obolibrary.org/obo/RO_0002212", + "obj" : "http://purl.obolibrary.org/obo/GO_0048468" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0010927", "pred" : "is_a", @@ -160747,14 +159872,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0012505", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/GO_0005886" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0012506", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0031090" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0012506", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GO_0031982" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0015031", "pred" : "is_a", @@ -160851,10 +159968,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0016042", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_1901575" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0016042", - "pred" : "http://purl.obolibrary.org/obo/RO_0004009", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_18059" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0016043", "pred" : "is_a", @@ -160867,10 +159980,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0016050", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0006996" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0016050", - "pred" : "http://purl.obolibrary.org/obo/RO_0002592", - "obj" : "http://purl.obolibrary.org/obo/GO_0031982" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0016053", "pred" : "is_a", @@ -160891,26 +160000,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0016053", "pred" : "http://purl.obolibrary.org/obo/RO_0004008", "obj" : "http://purl.obolibrary.org/obo/CHEBI_64709" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0016054", - "pred" : "is_a", - "obj" : 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"http://purl.obolibrary.org/obo/CL_0000151", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032940" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000154", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000151" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009306" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000225", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000460" + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001405" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0017505", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005634" ], + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000226", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000586" + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001407" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000280", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048285" ], + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000227", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001406" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000740", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0061025" ], + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000228", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031965" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001908" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000741", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048284" ], + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000521", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0001061", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000460" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002242", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0002505" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0011115", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0030154" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000280", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048285" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GOREL_0002004", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] }, { @@ -172538,13 +171181,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016887" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0005319", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005215" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0005938", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], @@ -172566,13 +171202,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_61120" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006401", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006412", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -172623,7 +171252,7 @@ "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_37022" + "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_35238" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006521", @@ -172632,13 +171261,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006629", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006725", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -172695,13 +171317,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33709" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006869", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006886", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -172712,20 +171327,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006887", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0070382" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006906", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0012506" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006996", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -172775,13 +171376,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002344", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007039", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0030163" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007097", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0046907" ], @@ -172789,6 +171383,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007275", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002295", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000468" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0008104", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], @@ -172810,13 +171411,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0008283" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0008610", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0008652", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -172824,13 +171418,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_37022" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009057", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33694" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009059", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -172838,13 +171425,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33694" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009063", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_37022" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009112", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -172874,11 +171454,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_32952" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009310", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009790", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_32952" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000922" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009889", @@ -172915,27 +171495,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0008152" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009894", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009056" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009895", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009056" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009896", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009056" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010256", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -173013,13 +171572,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0042181" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010567", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0042182" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010604", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173063,11 +171615,18 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0006996" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010876", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0033036" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010720", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0048468" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010721", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0048468" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010927", @@ -173090,13 +171649,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006817" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0012506", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0015031", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -173153,13 +171705,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_61120" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016042", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016043", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], @@ -173167,13 +171712,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005575" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016050", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016053", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -173181,13 +171719,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_64709" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016054", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_64709" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016070", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -173195,13 +171726,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016192", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0017148", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173209,13 +171733,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006412" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0017157", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0018130", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -173223,13 +171740,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_5686" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019216", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006629" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019219", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173258,13 +171768,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33655" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019439", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33655" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019538", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -173322,18 +171825,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_1990904" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030100", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006897" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030163", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030154", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048869" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002315", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000000" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030397", @@ -173342,13 +171838,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030659", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031410" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031090", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], @@ -173398,27 +171887,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0044249" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031329", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0044248" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031330", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0044248" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031331", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0044248" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031333", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173433,34 +171901,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0065003" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031338", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006906" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031339", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006906" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031340", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006906" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031410", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005737" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031503", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], @@ -173496,58 +171936,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0015931" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032365", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032368", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006869" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032369", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006869" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032370", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006869" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032377", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032365" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032378", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032365" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032379", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032365" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032386", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173569,27 +171957,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0046907" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032409", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005215" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032410", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005215" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032411", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005215" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032594", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0015031" ], @@ -173599,18 +171966,11 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032774", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009059" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032871", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0000741" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032879", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173695,27 +172055,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0009308" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033241", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009310" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033242", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009310" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033243", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009310" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033365", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008104" ], @@ -173758,27 +172097,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043603" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034251", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043605" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034252", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043605" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034253", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043605" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034293", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0043934" ], @@ -173801,11 +172119,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_61120" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034655", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035190", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007097" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_61120" + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000228" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035592", @@ -173815,32 +172133,25 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0040020", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0040019", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0140013" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009790" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042127", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0040020", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0008283" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0140013" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042176", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042127", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0030163" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042177", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0030163" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0008283" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042180", @@ -173856,13 +172167,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_17087" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042182", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_17087" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042325", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173933,13 +172237,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33694" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043171", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_16670" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043227", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0043226" ], @@ -174031,13 +172328,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_32988" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043605", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_32988" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043933", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -174084,7 +172374,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/GO_0044091", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0044085" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002234", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] }, { @@ -174101,13 +172391,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0003674" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045026", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045184", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], @@ -174116,74 +172399,60 @@ "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_36080" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045727", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045595", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006412" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045732", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0030163" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0030154" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045763", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045596", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0030154" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045764", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045597", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0030154" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045786", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007049" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045787", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045727", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007049" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0006412" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045806", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045763", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006897" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045807", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045764", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006897" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045833", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045786", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006629" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007049" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045834", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045787", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006629" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007049" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045835", @@ -174227,20 +172496,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006415" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045920", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045921", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045934", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -174284,31 +172539,31 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0006413" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046112", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045992", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18282" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009790" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046113", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045995", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18282" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009790" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046394", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046112", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_29067" + "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18282" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046395", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046394", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_29067" } ] }, { @@ -174318,27 +172573,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_5686" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046700", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_5686" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046889", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0008610" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046890", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0008610" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046907", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -174360,13 +172594,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016236" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048284", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048285", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], @@ -174375,11 +172602,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048288", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0000740" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048468", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0000741" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000000" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048518", @@ -174409,6 +172636,27 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0009987" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048580", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009791" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048581", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009791" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048582", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009791" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048589", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0040007" ], @@ -174416,6 +172664,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032502" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048856", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032502" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000061" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050657", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -174466,32 +172721,18 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0003824" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050794", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050793", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009987" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032502" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050994", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050794", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016042" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050995", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016042" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050996", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016042" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009987" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051046", @@ -174535,13 +172776,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006810" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051055", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0008610" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051078", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051081" ], @@ -174556,6 +172790,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", "fillerId" : "http://purl.obolibrary.org/obo/GO_0031965" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051093", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032502" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051094", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032502" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051128", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -174636,6 +172884,27 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0015031" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051239", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032501" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051240", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032501" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051241", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032501" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051246", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -174734,16 +173003,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0051321" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051469", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051640", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], @@ -174758,13 +173017,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051648", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051649", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], @@ -174772,13 +173024,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000000" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051650", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051656", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], @@ -174877,6 +173122,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043170" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060284", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0048468" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060341", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -174891,13 +173143,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0009653" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060627", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016192" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0061024", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -174905,13 +173150,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0061025", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0061024" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0061695", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], @@ -174985,13 +173223,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0045184" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0070382", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0030133" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0099500" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0070925", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -175121,13 +173352,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0090174", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0061025" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031090" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0090304", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -175170,20 +173394,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_28938" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0097576", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0097708", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098590", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], @@ -175225,36 +173435,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098876", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099500", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0061025" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0012506" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0098590" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099503", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0099500" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099568", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], @@ -175283,30 +173463,9 @@ "definedClassId" : "http://purl.obolibrary.org/obo/GO_0101025", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0044085" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002234", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/GO_0031965" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0110112", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005319" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0110113", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005319" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0110114", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005319" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140013", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0000280" ], @@ -175314,33 +173473,19 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0051321" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140029", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140096", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0003824" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002233", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140098", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0003824" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002233", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140318", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005215" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" + "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140352", @@ -175352,32 +173497,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140353", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002338", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140354", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002338", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140513", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], @@ -175396,7 +173515,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140640", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0003824" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002233", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33696" } ] }, { @@ -175455,13 +173574,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33832" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901361", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33832" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901362", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -175476,13 +173588,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_35352" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901565", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_35352" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901566", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -175490,13 +173595,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_35352" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901575", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_50860" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901576", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -175511,13 +173609,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_78608" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901606", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_78608" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901607", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -175546,13 +173637,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0070925" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1902369", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006401" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1902494", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], @@ -175658,13 +173742,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032940" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1903561", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1903729", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -175686,27 +173763,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0008104" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1904350", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007039" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1904351", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007039" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1904352", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007039" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1904375", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -175763,27 +173819,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0045184" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905153", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010324" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905154", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010324" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905155", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010324" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905475", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -175812,27 +173847,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905952", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010876" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905953", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010876" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905954", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010876" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1990234", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_1902494" ], @@ -175840,13 +173854,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016740" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1990351", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005215" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1990778", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008104" ], @@ -175861,6 +173868,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_2000026", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007275" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_2000241", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -176235,6 +174249,30 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000922", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000468" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002489", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000068" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002493", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000068" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0009953", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000468" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002489", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000092" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001993" + } ] } ], "domainRangeAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -176250,6 +174288,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -176263,12 +174305,28 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/GO_0001700", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" + }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005634", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0009792", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051321", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", @@ -176300,7 +174358,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -176308,7 +174366,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -176354,7 +174412,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002334", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -176449,6 +174508,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000086", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ], "propertyChainAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", @@ -176468,6 +174530,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] @@ -176498,9 +174563,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0002025" ] @@ -176654,12 +174716,30 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/RO_0002082" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] @@ -176675,12 +174755,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] } ] } ] } \ No newline at end of file diff --git a/phipo-full.obo b/phipo-full.obo index 35df9aa..89cd888 100644 --- a/phipo-full.obo +++ b/phipo-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: phipo/releases/2024-01-31/phipo-full.owl +data-version: phipo/releases/2024-04-04/phipo-full.owl subsetdef: 1_STAR "" subsetdef: 2_STAR "" subsetdef: 3_STAR "" @@ -7,6 +7,7 @@ subsetdef: abnormal_slim "" subsetdef: absent_slim "" subsetdef: attribute_slim "" subsetdef: cell_quality "" +subsetdef: cellxgene_subset "" subsetdef: common_anatomy "" subsetdef: disposition_slim "" subsetdef: efo_slim "" @@ -31,29 +32,33 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: mpath_slim "" -subsetdef: prokaryote_subset "" +subsetdef: pheno_slim "" subsetdef: relational_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" -subsetdef: term_scheduled_for_obsoletion "" +subsetdef: uberon_slim "" subsetdef: ubprop:upper_level "" subsetdef: upper_level "" subsetdef: value_slim "" +subsetdef: vertebrate_core "" synonymtypedef: blast_name "" synonymtypedef: BRAND_NAME "" -synonymtypedef: common_name "" +synonymtypedef: equivalent_name "" synonymtypedef: genbank_common_name "" +synonymtypedef: in_part "" synonymtypedef: INN "" synonymtypedef: IUPAC_NAME "" +synonymtypedef: OMO:0003003 "" +synonymtypedef: OMO:0003011 "" synonymtypedef: synonym "" ontology: phipo/phipo-full property_value: created:by "alaynecuzick" xsd:string property_value: creation:date "2018-07-09T13:43:00Z" xsd:string -property_value: dc-description "Ontology of species-neutral phenotypes observed in pathogen-host interactions." xsd:string -property_value: dc-title "Pathogen Host Interactions Phenotype Ontology" xsd:string -property_value: dcterms-license "https://creativecommons.org/licenses/by/3.0/" xsd:string -property_value: owl:versionInfo "2024-01-31" xsd:string +property_value: http://purl.org/dc/elements/1.1/description "Ontology of species-neutral phenotypes observed in pathogen-host interactions." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Pathogen Host Interactions Phenotype Ontology" xsd:string +property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/3.0/" xsd:string +property_value: owl:versionInfo "2024-04-04" xsd:string [Term] id: BFO:0000001 @@ -116,8 +121,8 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000020 ! characteristic +disjoint_from: BFO:0000020 ! characteristic disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant property_value: BFO:0000179 "ic" xsd:string @@ -146,6 +151,7 @@ def: "An occurrent that has temporal proper parts and for some time t, p s-depen def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent +relationship: part_of BFO:0000015 {all_only="true"} ! process property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string @@ -179,9 +185,10 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 +name: realizable name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity property_value: BFO:0000179 "realizable" xsd:string @@ -200,11 +207,12 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic relationship: part_of BFO:0000019 {all_only="true"} ! quality [Term] id: BFO:0000020 +name: characteristic name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} @@ -212,7 +220,8 @@ def: "b is a specifically dependent continuant = Def. b is a continuant & there comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant +relationship: has_part BFO:0000020 {all_only="true"} ! characteristic +relationship: part_of BFO:0000020 {all_only="true"} ! characteristic property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string @@ -230,13 +239,14 @@ property_value: IAO:0000116 "Specifically dependent continuant doesn't have a cl property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string [Term] id: BFO:0000023 name: role def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] -is_a: CHEBI:50906 ! role -equivalent_to: CHEBI:50906 ! role +is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000031 @@ -2255,6 +2265,7 @@ is_a: CHEBI:35107 ! azane is_a: CHEBI:37176 ! mononuclear parent hydride relationship: is_conjugate_acid_of CHEBI:29337 ! azanide relationship: is_conjugate_base_of CHEBI:28938 ! ammonium +relationship: RO:0000087 CHEBI:228364 ! has role NMR chemical shift reference compound relationship: RO:0000087 CHEBI:50910 ! has role neurotoxin relationship: RO:0000087 CHEBI:59740 ! has role nucleophilic reagent relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite @@ -5968,6 +5979,22 @@ is_a: CHEBI:27171 ! organic heterobicyclic compound is_a: CHEBI:38101 ! organonitrogen heterocyclic compound is_a: CHEBI:38180 ! polycyclic heteroarene +[Term] +id: CHEBI:228364 +name: NMR chemical shift reference compound +namespace: chebi_ontology +def: "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing." [] +subset: 3_STAR +synonym: "NMR chemical shift reference compounds" RELATED [ChEBI] +synonym: "NMR chemical shift standard" RELATED [ChEBI] +synonym: "NMR chemical shift standards" RELATED [ChEBI] +synonym: "NMR internal standard" RELATED [ChEBI] +synonym: "NMR internal standards" RELATED [ChEBI] +synonym: "NMR reference standard" RELATED [ChEBI] +synonym: "NMR reference standards" RELATED [ChEBI] +is_a: CHEBI:33232 ! application +is_a: CHEBI:51086 ! chemical role + [Term] id: CHEBI:22888 name: biphenyls @@ -6753,7 +6780,6 @@ namespace: chebi_ontology def: "A role played by the molecular entity or part thereof within a biological context." [] subset: 3_STAR synonym: "biological function" RELATED [ChEBI] -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -8097,6 +8123,7 @@ xref: Reaxys:1921286 {source="Reaxys"} xref: Wikipedia:Phosphoric_Acid is_a: CHEBI:59698 ! phosphoric acids relationship: is_conjugate_acid_of CHEBI:39745 ! dihydrogenphosphate +relationship: RO:0000087 CHEBI:228364 ! has role NMR chemical shift reference compound relationship: RO:0000087 CHEBI:33287 ! has role fertilizer relationship: RO:0000087 CHEBI:46787 ! has role solvent relationship: RO:0000087 CHEBI:77746 ! has role human metabolite @@ -13497,7 +13524,6 @@ name: application namespace: chebi_ontology def: "Intended use of the molecular entity or part thereof by humans." [] subset: 3_STAR -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -14910,10 +14936,17 @@ property_value: http://purl.obolibrary.org/obo/chebi/smiles "NC1NC(CC=N1)[C@@H]1 id: CHEBI:33710 name: alpha-amino-acid residue namespace: chebi_ontology +def: "An amino-acid residue derived from an alpha-amino acid." [] subset: 3_STAR synonym: "alpha-amino-acid residues" RELATED [ChEBI] +synonym: "an alpha-amino acid residue" RELATED [UniProt] is_a: CHEBI:33708 ! amino-acid residue relationship: is_substituent_group_from CHEBI:33704 ! alpha-amino acid +property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string +property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H2NOR" xsd:string +property_value: http://purl.obolibrary.org/obo/chebi/mass "56.043" xsd:string +property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "56.01364" xsd:string +property_value: http://purl.obolibrary.org/obo/chebi/smiles "*-NC([*])C(-*)=O" xsd:string [Term] id: CHEBI:33719 @@ -24463,7 +24496,7 @@ name: role namespace: chebi_ontology def: "A role is particular behaviour which a material entity may exhibit." [] subset: 3_STAR -is_a: BFO:0000023 ! role +is_a: PATO:0000001 ! quality [Term] id: CHEBI:50908 @@ -24617,7 +24650,6 @@ name: chemical role namespace: chebi_ontology def: "A role played by the molecular entity or part thereof within a chemical context." [] subset: 3_STAR -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -35840,7 +35872,11 @@ property_value: http://purl.obolibrary.org/obo/chebi/smiles "CC(C)[C@H]1OC(=O)C2 id: CL:0000000 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +def: "A material entity that has a plasma membrane and results from cellular division." [] +comment: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. +subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 @@ -35855,16 +35891,98 @@ is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: has_part GO:0005634 {gci_filler="PATO:0001407", gci_relation="bearer_of"} ! nucleus -relationship: has_part GO:0005634 {gci_filler="PATO:0001908", gci_relation="bearer_of"} ! nucleus -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: has_part GO:0005634 {gci_filler="PATO:0001407", gci_relation="bearer_of"} ! cell nucleus +relationship: has_part GO:0005634 {gci_filler="PATO:0001908", gci_relation="bearer_of"} ! cell nucleus +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl +[Term] +id: CL:0000151 +name: secretory cell +def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] +subset: cellxgene_subset +xref: BTO:0003659 +xref: FMA:86916 +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: capable_of GO:0032940 ! secretion by cell +relationship: capable_of GO:0032940 ! secretion by cell + +[Term] +id: CL:0000154 +name: protein secreting cell +is_a: CL:0000151 ! secretory cell +intersection_of: CL:0000151 ! secretory cell +intersection_of: capable_of GO:0009306 ! protein secretion +relationship: capable_of GO:0009306 ! protein secretion + +[Term] +id: CL:0000225 +name: anucleate cell +def: "A cell that lacks a nucleus." [FB:ma] +synonym: "non-nucleated cell" EXACT [] +xref: FMA:68647 +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001405 ! anucleate +disjoint_from: CL:0002242 ! nucleate cell +relationship: bearer_of PATO:0001405 ! anucleate + +[Term] +id: CL:0000226 +name: single nucleate cell +def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +is_a: CL:0002242 ! nucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001407 ! mononucleate +relationship: bearer_of PATO:0001407 ! mononucleate + +[Term] +id: CL:0000227 +name: binucleate cell +is_a: CL:0000228 ! multinucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001406 ! binucleate +relationship: bearer_of PATO:0001406 ! binucleate + +[Term] +id: CL:0000228 +name: multinucleate cell +def: "A cell with more than one nucleus." [FB:ma] +synonym: "syncitium" EXACT [] +synonym: "syncytial cell" EXACT [] +synonym: "syncytium" EXACT [] +xref: AEO:0000203 +xref: WBbt:0008074 +is_a: CL:0002242 ! nucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001908 ! multinucleate +relationship: bearer_of PATO:0001908 ! multinucleate + +[Term] +id: CL:0000255 +name: eukaryotic cell +subset: cellxgene_subset +xref: MESH:D005057 +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota + +[Term] +id: CL:0000521 +name: fungal cell +is_a: CL:0000255 ! eukaryotic cell +intersection_of: CL:0000000 ! cell +intersection_of: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi +relationship: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi + [Term] id: CL:0001061 name: abnormal cell def: "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models." [GOC:add, GOC:cg, GOC:wdd] comment: https://github.com/obophenotype/cell-ontology/issues/448 +subset: cellxgene_subset xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -35874,15 +35992,27 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001 property_value: http://purl.org/dc/terms/date "2017-01-30T18:53:32Z" xsd:dateTime [Term] -id: CL:0017505 -name: increased nucleus size -def: "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." [GOC:tfm] -is_a: GO:0005634 ! nucleus -intersection_of: GO:0005634 ! nucleus -intersection_of: bearer_of PATO:0000586 ! increased size -relationship: bearer_of PATO:0000586 ! increased size +id: CL:0002242 +name: nucleate cell +def: "A cell containing at least one nucleus." [GOC:tfm] +xref: FMA:67513 +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0002505 ! nucleated +relationship: bearer_of PATO:0002505 ! nucleated property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2009-12-23T10:53:24Z +creation_date: 2010-09-07T03:32:33Z + +[Term] +id: CL:0011115 +name: precursor cell +def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] +comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. +subset: cellxgene_subset +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: capable_of GO:0030154 ! cell differentiation +relationship: capable_of GO:0030154 ! cell differentiation [Term] id: GO:0000003 @@ -35898,7 +36028,7 @@ subset: goslim_pir subset: goslim_plant synonym: "reproductive physiological process" EXACT [] xref: Wikipedia:Reproduction -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl @@ -35939,35 +36069,8 @@ subset: goslim_pir synonym: "karyokinesis" RELATED [] is_a: GO:0048285 ! organelle fission intersection_of: GO:0048285 ! organelle fission -intersection_of: results_in_fission_of GO:0005634 ! nucleus -relationship: results_in_fission_of GO:0005634 ! nucleus - -[Term] -id: GO:0000740 -name: nuclear membrane fusion -namespace: biological_process -def: "The joining of 2 or more lipid bilayer membranes that surround the nucleus." [GOC:elh] -is_a: GO:0071763 ! nuclear membrane organization -is_a: GO:0090174 ! organelle membrane fusion -intersection_of: GO:0061025 ! membrane fusion -intersection_of: results_in_fusion_of GO:0031965 ! nuclear membrane -relationship: results_in_fusion_of GO:0031965 ! nuclear membrane - -[Term] -id: GO:0000741 -name: karyogamy -namespace: biological_process -alt_id: GO:0007335 -def: "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei." [GOC:elh] -synonym: "nuclear fusion" EXACT [] -synonym: "nuclear fusion during karyogamy" EXACT [] -xref: Wikipedia:Karyogamy -is_a: GO:0006997 ! nucleus organization -is_a: GO:0048284 ! organelle fusion -intersection_of: GO:0048284 ! organelle fusion -intersection_of: results_in_fusion_of GO:0005634 ! nucleus -relationship: part_of GO:0006997 ! nucleus organization -relationship: results_in_fusion_of GO:0005634 ! nucleus +intersection_of: results_in_fission_of GO:0005634 ! cell nucleus +relationship: results_in_fission_of GO:0005634 ! cell nucleus [Term] id: GO:0001677 @@ -35981,6 +36084,15 @@ intersection_of: results_in_assembly_of GO:0044207 ! translation initiation tern relationship: part_of GO:0006413 ! translational initiation relationship: results_in_assembly_of GO:0044207 ! translation initiation ternary complex +[Term] +id: GO:0001700 +name: embryonic development via the syncytial blastoderm +namespace: biological_process +def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster." [GOC:go_curators, GOC:mtg_sensu] +is_a: GO:0009792 ! embryo development ending in birth or egg hatching +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta + [Term] id: GO:0002252 name: immune effector process @@ -36002,7 +36114,7 @@ subset: goslim_generic subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase property_value: RO:0002161 NCBITaxon:4895 @@ -36083,12 +36195,14 @@ intersection_of: part_of GO:0000003 ! reproduction [Term] id: GO:0003674 +name: gene product or complex activity name: molecular_function namespace: molecular_function alt_id: GO:0005554 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +comment: This is the same as GO molecular function subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics @@ -36098,7 +36212,7 @@ subset: goslim_yeast synonym: "molecular function" EXACT [] is_a: BFO:0000015 ! process disjoint_from: GO:0005575 ! cellular_component -disjoint_from: GO:0008150 ! biological_process +disjoint_from: GO:0008150 ! biological process [Term] id: GO:0003676 @@ -36235,36 +36349,11 @@ subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote -subset: prokaryote_subset synonym: "carrier" RELATED [] xref: Reactome:R-HSA-168313 "Virion-associated M2 protein mediated ion infusion" xref: Reactome:R-HSA-178215 "SMAD7:SMURF1 complex is exported to the cytosol" is_a: GO:0003674 ! molecular_function -[Term] -id: GO:0005319 -name: lipid transporter activity -namespace: molecular_function -def: "Enables the directed movement of lipids into, out of or within a cell, or between cells." [GOC:ai] -synonym: "apolipoprotein" RELATED [] -synonym: "lipophorin" NARROW [] -xref: Reactome:R-HSA-1369028 "ABCAs mediate lipid efflux" -xref: Reactome:R-HSA-1369052 "ABCAs mediate lipid influx" -xref: Reactome:R-HSA-174786 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex" -xref: Reactome:R-HSA-5682285 "ABCA12 transports lipids from cytosol to extracellular region" -xref: Reactome:R-HSA-5682311 "Defective ABCA12 does not transport lipids from cytosol to extracellular region" -xref: Reactome:R-HSA-5683672 "Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body" -xref: Reactome:R-HSA-5683714 "ABCA3 transports PC, PG from ER membrane to lamellar body" -xref: Reactome:R-HSA-5688397 "Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body" -xref: Reactome:R-HSA-6801250 "TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane" -xref: Reactome:R-HSA-8848053 "ABCA5 transports CHOL from lysosomal lumen to cytosol" -xref: Reactome:R-HSA-8866329 "MTTP lipidates APOB-100, forming a pre-VLDL" -is_a: GO:0005215 ! transporter activity -intersection_of: GO:0005215 ! transporter activity -intersection_of: has_primary_input CHEBI:18059 ! lipid -relationship: has_primary_input CHEBI:18059 ! lipid -relationship: part_of GO:0006869 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! lipid transport - [Term] id: GO:0005488 name: binding @@ -36299,10 +36388,8 @@ id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 -def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao1337158144] def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. -comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics @@ -36314,7 +36401,7 @@ synonym: "cellular component" EXACT [] synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315] xref: NIF_Subcellular:sao1337158144 is_a: BFO:0000040 ! material entity -disjoint_from: GO:0008150 ! biological_process +disjoint_from: GO:0008150 ! biological process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17729" xsd:anyURI [Term] @@ -36332,8 +36419,8 @@ subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant +subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular is_a: GO:0110165 ! cellular anatomical entity @@ -36359,6 +36446,7 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ [Term] id: GO:0005634 +name: cell nucleus name: nucleus namespace: cellular_component def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] @@ -36379,8 +36467,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005635 @@ -36393,7 +36481,7 @@ subset: goslim_generic subset: goslim_plant xref: Wikipedia:Nuclear_envelope is_a: GO:0031967 ! organelle envelope -relationship: part_of GO:0005634 ! nucleus +relationship: part_of GO:0005634 ! cell nucleus relationship: part_of GO:0012505 ! endomembrane system [Term] @@ -36408,7 +36496,6 @@ subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset xref: Wikipedia:Cytoplasm is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005622 ! intracellular anatomical structure @@ -36474,7 +36561,6 @@ subset: goslim_mouse subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "bacterial inner membrane" NARROW [] synonym: "cell membrane" EXACT [] synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645] @@ -36563,22 +36649,6 @@ intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:61120 ! nucleobase-containing molecular entity relationship: has_primary_input_or_output CHEBI:61120 ! nucleobase-containing molecular entity -[Term] -id: GO:0006401 -name: RNA catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732] -subset: goslim_yeast -synonym: "RNA breakdown" EXACT [] -synonym: "RNA catabolism" EXACT [] -synonym: "RNA degradation" EXACT [] -is_a: GO:0009057 ! macromolecule catabolic process -is_a: GO:0016070 ! RNA metabolic process -is_a: GO:0034655 ! nucleobase-containing compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33697 ! ribonucleic acid -relationship: has_primary_input CHEBI:33697 ! ribonucleic acid - [Term] id: GO:0006403 name: RNA localization @@ -36603,7 +36673,7 @@ subset: goslim_drosophila subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "protein anabolism" EXACT [] synonym: "protein biosynthesis" EXACT [] synonym: "protein biosynthetic process" EXACT [] @@ -36676,9 +36746,7 @@ synonym: "regulation of protein anabolism" EXACT [] synonym: "regulation of protein biosynthesis" EXACT [] synonym: "regulation of protein formation" EXACT [] synonym: "regulation of protein synthesis" EXACT [] -is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010608 ! post-transcriptional regulation of gene expression -is_a: GO:0031326 ! regulation of cellular biosynthetic process is_a: GO:0034248 ! regulation of amide metabolic process is_a: GO:0051246 ! regulation of protein metabolic process intersection_of: GO:0065007 ! biological regulation @@ -36753,17 +36821,15 @@ subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "amino acid and derivative metabolism" RELATED [] synonym: "cellular amino acid and derivative metabolic process" RELATED [] synonym: "cellular amino acid metabolic process" EXACT [] synonym: "cellular amino acid metabolism" EXACT [] -is_a: GO:0019752 ! carboxylic acid metabolic process is_a: GO:0044238 ! primary metabolic process -is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process -intersection_of: has_primary_input_or_output CHEBI:37022 ! amino-acid anion -relationship: has_primary_input_or_output CHEBI:37022 ! amino-acid anion +intersection_of: has_primary_input_or_output CHEBI:35238 ! amino acid zwitterion +relationship: has_primary_input_or_output CHEBI:35238 ! amino acid zwitterion property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI [Term] @@ -36805,14 +36871,10 @@ subset: goslim_plant subset: goslim_pombe subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "lipid metabolism" EXACT [] xref: Wikipedia:Lipid_metabolism is_a: GO:0044238 ! primary metabolic process is_a: GO:0071704 ! organic substance metabolic process -intersection_of: GO:0008152 ! metabolic process -intersection_of: has_primary_input_or_output CHEBI:18059 ! lipid -relationship: has_primary_input_or_output CHEBI:18059 ! lipid [Term] id: GO:0006714 @@ -36912,7 +36974,6 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote -subset: prokaryote_subset synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI @@ -36964,20 +37025,6 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:33709 ! amino acid relationship: has_primary_input CHEBI:33709 ! amino acid -[Term] -id: GO:0006869 -name: lipid transport -namespace: biological_process -def: "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732] -subset: goslim_drosophila -subset: goslim_pir -subset: goslim_yeast -is_a: GO:0071702 ! organic substance transport -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:18059 ! lipid -relationship: has_primary_input CHEBI:18059 ! lipid -relationship: part_of GO:0010876 ! lipid localization - [Term] id: GO:0006886 name: intracellular protein transport @@ -36986,7 +37033,6 @@ alt_id: GO:0032779 def: "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah] subset: goslim_generic subset: goslim_prokaryote -subset: prokaryote_subset synonym: "copper-induced intracellular protein transport" RELATED [GOC:al] is_a: GO:0015031 ! protein transport is_a: GO:0046907 ! intracellular transport @@ -36995,24 +37041,6 @@ intersection_of: has_primary_input PR:000000001 ! protein intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure relationship: part_of GO:0008104 ! protein localization -[Term] -id: GO:0006887 -name: exocytosis -namespace: biological_process -alt_id: GO:0016194 -alt_id: GO:0016195 -def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] -subset: goslim_yeast -synonym: "nonselective vesicle exocytosis" RELATED [] -synonym: "vesicle exocytosis" EXACT [] -xref: Wikipedia:Exocytosis -is_a: GO:0016192 ! vesicle-mediated transport -is_a: GO:0032940 ! secretion by cell -intersection_of: GO:0006810 ! transport -intersection_of: process_has_causal_agent GO:0070382 ! exocytic vesicle -relationship: has_part GO:0099500 ! vesicle fusion to plasma membrane -relationship: process_has_causal_agent GO:0070382 ! exocytic vesicle - [Term] id: GO:0006897 name: endocytosis @@ -37031,7 +37059,6 @@ is_a: GO:0016192 ! vesicle-mediated transport is_a: GO:0098657 ! import into cell relationship: has_part GO:0006900 ! vesicle budding from membrane relationship: has_part GO:0010324 ! membrane invagination -relationship: has_target_end_location GO:0031410 ! cytoplasmic vesicle property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24907" xsd:anyURI property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25268" xsd:anyURI @@ -37055,18 +37082,6 @@ relationship: part_of GO:0016192 ! vesicle-mediated transport created_by: jl creation_date: 2013-12-19T15:26:17Z -[Term] -id: GO:0006906 -name: vesicle fusion -namespace: biological_process -def: "Fusion of the membrane of a transport vesicle with its target membrane." [GOC:jid] -is_a: GO:0016050 ! vesicle organization -is_a: GO:0090174 ! organelle membrane fusion -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0012506 ! vesicle membrane -relationship: part_of GO:0016192 ! vesicle-mediated transport -relationship: results_in_fusion_of GO:0012506 ! vesicle membrane - [Term] id: GO:0006914 name: autophagy @@ -37157,8 +37172,8 @@ synonym: "nuclear organization and biogenesis" RELATED [GOC:mah] synonym: "nucleus organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0005634 ! nucleus -relationship: results_in_organization_of GO:0005634 ! nucleus +intersection_of: results_in_organization_of GO:0005634 ! cell nucleus +relationship: results_in_organization_of GO:0005634 ! cell nucleus [Term] id: GO:0006998 @@ -37230,20 +37245,6 @@ intersection_of: GO:0046907 ! intracellular transport intersection_of: results_in_transport_to_from_or_in GO:0005773 ! vacuole relationship: results_in_transport_to_from_or_in GO:0005773 ! vacuole -[Term] -id: GO:0007039 -name: protein catabolic process in the vacuole -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases." [GOC:mah, GOC:vw] -synonym: "vacuolar protein breakdown" RELATED [] -synonym: "vacuolar protein catabolic process" RELATED [] -synonym: "vacuolar protein catabolism" RELATED [] -synonym: "vacuolar protein degradation" RELATED [] -is_a: GO:0030163 ! protein catabolic process -intersection_of: GO:0030163 ! protein catabolic process -intersection_of: occurs_in GO:0005773 ! vacuole -relationship: occurs_in GO:0005773 ! vacuole - [Term] id: GO:0007049 name: cell cycle @@ -37280,7 +37281,7 @@ is_a: GO:0046907 ! intracellular transport is_a: GO:0051647 ! nucleus localization is_a: GO:0051656 ! establishment of organelle localization intersection_of: GO:0046907 ! intracellular transport -intersection_of: has_primary_input GO:0005634 ! nucleus +intersection_of: has_primary_input GO:0005634 ! cell nucleus [Term] id: GO:0007127 @@ -37313,6 +37314,22 @@ xref: Wikipedia:Meiosis#Meiosis_II is_a: GO:0061983 ! meiosis II cell cycle process is_a: GO:0140013 ! meiotic nuclear division +[Term] +id: GO:0007275 +name: multicellular organism development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb] +comment: Note that this term was 'developmental process'. +subset: gocheck_do_not_annotate +subset: goslim_chembl +subset: goslim_plant +is_a: GO:0032501 ! multicellular organismal process +is_a: GO:0048856 ! anatomical structure development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_developmental_progression_of UBERON:0000468 ! multicellular organism +relationship: results_in_developmental_progression_of UBERON:0000468 ! multicellular organism +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21234" xsd:anyURI + [Term] id: GO:0008061 name: chitin binding @@ -37346,13 +37363,16 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ [Term] id: GO:0008150 +name: biological process name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [] +comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -37368,6 +37388,7 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process +relationship: has_part GO:0003674 ! molecular_function property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl created_by: jl @@ -37392,7 +37413,7 @@ synonym: "metabolism resulting in cell growth" NARROW [] synonym: "multicellular organism metabolic process" NARROW [] synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase disjoint_from: GO:0051179 ! localization created_by: jl @@ -37531,9 +37552,6 @@ synonym: "lipid synthesis" EXACT [] synonym: "lipogenesis" EXACT [GOC:sl] is_a: GO:0006629 ! lipid metabolic process is_a: GO:1901576 ! organic substance biosynthetic process -intersection_of: GO:0009058 ! biosynthetic process -intersection_of: has_primary_output CHEBI:18059 ! lipid -relationship: has_primary_output CHEBI:18059 ! lipid [Term] id: GO:0008641 @@ -37559,7 +37577,6 @@ synonym: "amino acid formation" EXACT [] synonym: "amino acid synthesis" EXACT [] synonym: "cellular amino acid biosynthetic process" EXACT [] xref: Wikipedia:Amino_acid_synthesis -is_a: GO:0006520 ! amino acid metabolic process is_a: GO:0046394 ! carboxylic acid biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process @@ -37587,28 +37604,6 @@ is_a: GO:0008152 ! metabolic process created_by: jl creation_date: 2012-10-17T15:52:35Z -[Term] -id: GO:0009057 -name: macromolecule catabolic process -namespace: biological_process -alt_id: GO:0043285 -alt_id: GO:0044266 -def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] -subset: goslim_pir -synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] -synonym: "cellular macromolecule catabolic process" RELATED [] -synonym: "cellular macromolecule catabolism" RELATED [] -synonym: "cellular macromolecule degradation" RELATED [] -synonym: "macromolecule breakdown" EXACT [] -synonym: "macromolecule catabolism" EXACT [] -synonym: "macromolecule degradation" EXACT [] -synonym: "multicellular organismal macromolecule catabolic process" NARROW [] -is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33694 ! biomacromolecule -relationship: has_primary_input CHEBI:33694 ! biomacromolecule - [Term] id: GO:0009058 name: biosynthetic process @@ -37643,28 +37638,13 @@ synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33694 ! biomacromolecule relationship: has_primary_output CHEBI:33694 ! biomacromolecule -property_value: IAO:0000233 "http://amigo.geneontology.org/amigo/term/GO:0070589" xsd:anyURI - -[Term] -id: GO:0009063 -name: amino acid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents." [GOC:ai] -synonym: "amino acid breakdown" EXACT [] -synonym: "amino acid catabolism" EXACT [] -synonym: "amino acid degradation" EXACT [] -synonym: "cellular amino acid catabolic process" EXACT [] -is_a: GO:0006520 ! amino acid metabolic process -is_a: GO:0046395 ! carboxylic acid catabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:37022 ! amino-acid anion -relationship: has_primary_input CHEBI:37022 ! amino-acid anion -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI [Term] id: GO:0009066 @@ -37762,20 +37742,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:32952 ! amine relationship: has_primary_output CHEBI:32952 ! amine -[Term] -id: GO:0009310 -name: amine catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl, ISBN:0198506732] -synonym: "amine breakdown" EXACT [] -synonym: "amine catabolism" EXACT [] -synonym: "amine degradation" EXACT [] -is_a: GO:0009308 ! amine metabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:32952 ! amine -relationship: has_primary_input CHEBI:32952 ! amine - [Term] id: GO:0009403 name: toxin biosynthetic process @@ -37849,6 +37815,43 @@ xref: Wikipedia:Morphogenesis is_a: GO:0032502 ! developmental process relationship: part_of GO:0048856 ! anatomical structure development +[Term] +id: GO:0009790 +name: embryo development +namespace: biological_process +alt_id: GO:0009795 +def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] +subset: gocheck_do_not_manually_annotate +subset: goslim_chembl +subset: goslim_plant +synonym: "embryogenesis" EXACT [] +synonym: "embryogenesis and morphogenesis" BROAD [] +synonym: "embryonal development" EXACT [] +xref: Wikipedia:Embryogenesis +is_a: GO:0007275 ! multicellular organism development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_development_of UBERON:0000922 ! embryo +relationship: results_in_development_of UBERON:0000922 ! embryo + +[Term] +id: GO:0009791 +name: post-embryonic development +namespace: biological_process +def: "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC:go_curators] +subset: goslim_plant +is_a: GO:0032501 ! multicellular organismal process +relationship: part_of GO:0007275 ! multicellular organism development + +[Term] +id: GO:0009792 +name: embryo development ending in birth or egg hatching +namespace: biological_process +def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] +synonym: "embryogenesis" BROAD [] +is_a: GO:0009790 ! embryo development +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa + [Term] id: GO:0009847 name: spore germination @@ -37954,56 +37957,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008152 ! metabolic process relationship: positively_regulates GO:0008152 ! metabolic process -[Term] -id: GO:0009894 -name: regulation of catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] -synonym: "regulation of breakdown" EXACT [] -synonym: "regulation of catabolism" EXACT [] -synonym: "regulation of degradation" EXACT [] -is_a: GO:0019222 ! regulation of metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0009056 ! catabolic process -relationship: regulates GO:0009056 ! catabolic process - -[Term] -id: GO:0009895 -name: negative regulation of catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] -synonym: "down regulation of catabolic process" EXACT [] -synonym: "down-regulation of catabolic process" EXACT [] -synonym: "downregulation of catabolic process" EXACT [] -synonym: "inhibition of catabolic process" NARROW [] -synonym: "negative regulation of breakdown" EXACT [] -synonym: "negative regulation of catabolism" EXACT [] -synonym: "negative regulation of degradation" EXACT [] -is_a: GO:0009892 ! negative regulation of metabolic process -is_a: GO:0009894 ! regulation of catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0009056 ! catabolic process -relationship: negatively_regulates GO:0009056 ! catabolic process - -[Term] -id: GO:0009896 -name: positive regulation of catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] -synonym: "activation of catabolic process" NARROW [] -synonym: "positive regulation of breakdown" EXACT [] -synonym: "positive regulation of catabolism" EXACT [] -synonym: "positive regulation of degradation" EXACT [] -synonym: "stimulation of catabolic process" NARROW [] -synonym: "up regulation of catabolic process" EXACT [] -synonym: "up-regulation of catabolic process" EXACT [] -synonym: "upregulation of catabolic process" EXACT [] -is_a: GO:0009893 ! positive regulation of metabolic process -is_a: GO:0009894 ! regulation of catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0009056 ! catabolic process -relationship: positively_regulates GO:0009056 ! catabolic process - [Term] id: GO:0009987 name: cellular process @@ -38019,7 +37972,7 @@ synonym: "cell growth and/or maintenance" NARROW [] synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase created_by: jl creation_date: 2012-12-11T16:56:55Z @@ -38053,11 +38006,12 @@ creation_date: 2013-12-02T13:58:34Z id: GO:0010467 name: gene expression namespace: biological_process -def: "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes." [GOC:txnOH-2018, PMID:25934543, PMID:31580950] +def: "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes." [GOC:txnOH-2018, PMID:25934543, PMID:31580950] subset: goslim_flybase_ribbon xref: Wikipedia:Gene_expression -is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0009059 ! macromolecule biosynthetic process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22557" xsd:anyURI +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25419" xsd:anyURI [Term] id: GO:0010468 @@ -38069,7 +38023,7 @@ synonym: "gene regulation" RELATED [GOC:cjm] synonym: "regulation of gene product expression" RELATED [] synonym: "regulation of protein expression" NARROW [] xref: Wikipedia:Regulation_of_gene_expression -is_a: GO:0060255 ! regulation of macromolecule metabolic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010467 ! gene expression relationship: regulates GO:0010467 ! gene expression @@ -38090,7 +38044,7 @@ id: GO:0010556 name: regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] -is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009059 ! macromolecule biosynthetic process @@ -38101,9 +38055,9 @@ id: GO:0010557 name: positive regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] -is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: positively_regulates GO:0009059 ! macromolecule biosynthetic process @@ -38113,9 +38067,9 @@ id: GO:0010558 name: negative regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] -is_a: GO:0009890 ! negative regulation of biosynthetic process is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: negatively_regulates GO:0009059 ! macromolecule biosynthetic process @@ -38174,17 +38128,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042181 ! ketone biosynthetic process relationship: regulates GO:0042181 ! ketone biosynthetic process -[Term] -id: GO:0010567 -name: regulation of ketone catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells." [GOC:dph, GOC:tb] -is_a: GO:0010565 ! regulation of cellular ketone metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0042182 ! ketone catabolic process -relationship: regulates GO:0042182 ! ketone catabolic process - [Term] id: GO:0010604 name: positive regulation of macromolecule metabolic process @@ -38221,7 +38164,7 @@ name: positive regulation of gene expression namespace: biological_process def: "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." [GOC:txnOH-2018] is_a: GO:0010468 ! regulation of gene expression -is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010467 ! gene expression relationship: positively_regulates GO:0010467 ! gene expression @@ -38235,7 +38178,7 @@ def: "Any process that decreases the frequency, rate or extent of gene expressio comment: This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. synonym: "gene silencing" RELATED [] is_a: GO:0010468 ! regulation of gene expression -is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010467 ! gene expression relationship: negatively_regulates GO:0010467 ! gene expression @@ -38268,15 +38211,26 @@ intersection_of: negatively_regulates GO:0006996 ! organelle organization relationship: negatively_regulates GO:0006996 ! organelle organization [Term] -id: GO:0010876 -name: lipid localization +id: GO:0010720 +name: positive regulation of cell development namespace: biological_process -def: "Any process in which a lipid is transported to, or maintained in, a specific location." [GOC:BHF, GOC:dph, GOC:tb] -synonym: "lipid localisation" EXACT [GOC:mah] -is_a: GO:0033036 ! macromolecule localization -intersection_of: GO:0033036 ! macromolecule localization -intersection_of: has_primary_input CHEBI:18059 ! lipid -relationship: has_primary_input CHEBI:18059 ! lipid +def: "Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048468 ! cell development +relationship: positively_regulates GO:0048468 ! cell development + +[Term] +id: GO:0010721 +name: negative regulation of cell development +namespace: biological_process +def: "Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048468 ! cell development +relationship: negatively_regulates GO:0048468 ! cell development [Term] id: GO:0010927 @@ -38353,17 +38307,6 @@ relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane relationship: part_of CL:0000000 ! cell -[Term] -id: GO:0012506 -name: vesicle membrane -namespace: cellular_component -def: "The lipid bilayer surrounding any membrane-bounded vesicle in the cell." [GOC:mah, GOC:vesicle] -xref: NIF_Subcellular:sao1153182838 -is_a: GO:0031090 ! organelle membrane -intersection_of: GO:0016020 ! membrane -intersection_of: part_of GO:0031982 ! vesicle -relationship: part_of GO:0031982 ! vesicle - [Term] id: GO:0015031 name: protein transport @@ -38504,9 +38447,6 @@ synonym: "multicellular organismal lipid catabolic process" NARROW [] xref: Wikipedia:Lipid_catabolism is_a: GO:0006629 ! lipid metabolic process is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:18059 ! lipid -relationship: has_primary_input CHEBI:18059 ! lipid [Term] id: GO:0016043 @@ -38540,9 +38480,6 @@ subset: goslim_yeast synonym: "vesicle organisation" EXACT [] synonym: "vesicle organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0031982 ! vesicle -relationship: results_in_organization_of GO:0031982 ! vesicle [Term] id: GO:0016053 @@ -38561,22 +38498,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:64709 ! organic acid relationship: has_primary_output CHEBI:64709 ! organic acid -[Term] -id: GO:0016054 -name: organic acid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] -synonym: "organic acid breakdown" EXACT [] -synonym: "organic acid catabolism" EXACT [] -synonym: "organic acid degradation" EXACT [] -is_a: GO:0006082 ! organic acid metabolic process -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:0044282 ! small molecule catabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:64709 ! organic acid -relationship: has_primary_input CHEBI:64709 ! organic acid - [Term] id: GO:0016070 name: RNA metabolic process @@ -38586,7 +38507,7 @@ subset: goslim_agr subset: goslim_candida subset: goslim_metagenomics subset: goslim_pir -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "RNA metabolism" EXACT [] is_a: GO:0090304 ! nucleic acid metabolic process intersection_of: GO:0008152 ! metabolic process @@ -38637,9 +38558,6 @@ synonym: "vesicle transport" EXACT [] synonym: "vesicular transport" EXACT [GOC:mah] is_a: GO:0006810 ! transport is_a: GO:0009987 ! cellular process -intersection_of: GO:0006810 ! transport -intersection_of: process_has_causal_agent GO:0031982 ! vesicle -relationship: process_has_causal_agent GO:0031982 ! vesicle property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25421" xsd:anyURI [Term] @@ -38702,7 +38620,6 @@ subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset xref: EC:2.-.-.- xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" @@ -38926,26 +38843,13 @@ synonym: "negative regulation of protein synthesis" EXACT [] synonym: "protein biosynthesis inhibitor activity" RELATED [] synonym: "protein biosynthetic process inhibitor activity" RELATED [] is_a: GO:0006417 ! regulation of translation -is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process is_a: GO:0010629 ! negative regulation of gene expression -is_a: GO:0031327 ! negative regulation of cellular biosynthetic process is_a: GO:0034249 ! negative regulation of amide metabolic process is_a: GO:0051248 ! negative regulation of protein metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006412 ! translation relationship: negatively_regulates GO:0006412 ! translation -[Term] -id: GO:0017157 -name: regulation of exocytosis -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of exocytosis." [GOC:go_curators] -is_a: GO:0060627 ! regulation of vesicle-mediated transport -is_a: GO:1903530 ! regulation of secretion by cell -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006887 ! exocytosis -relationship: regulates GO:0006887 ! exocytosis - [Term] id: GO:0018130 name: heterocycle biosynthetic process @@ -38982,17 +38886,6 @@ synonym: "host organism" EXACT [] xref: Wikipedia:Host_(biology) is_a: GO:0110165 ! cellular anatomical entity -[Term] -id: GO:0019216 -name: regulation of lipid metabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] -synonym: "regulation of lipid metabolism" EXACT [] -is_a: GO:0080090 ! regulation of primary metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006629 ! lipid metabolic process -relationship: regulates GO:0006629 ! lipid metabolic process - [Term] id: GO:0019219 name: regulation of nucleobase-containing compound metabolic process @@ -39050,22 +38943,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33655 ! aromatic compound relationship: has_primary_output CHEBI:33655 ! aromatic compound -[Term] -id: GO:0019439 -name: aromatic compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] -synonym: "aromatic compound breakdown" EXACT [] -synonym: "aromatic compound catabolism" EXACT [] -synonym: "aromatic compound degradation" EXACT [] -synonym: "aromatic hydrocarbon catabolic process" NARROW [] -synonym: "aromatic hydrocarbon catabolism" NARROW [] -is_a: GO:0006725 ! cellular aromatic compound metabolic process -is_a: GO:0044248 ! cellular catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33655 ! aromatic compound -relationship: has_primary_input CHEBI:33655 ! aromatic compound - [Term] id: GO:0019538 name: protein metabolic process @@ -39276,8 +39153,8 @@ alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: goslim_generic synonym: "single organism reproductive process" RELATED [] -is_a: GO:0008150 ! biological_process -intersection_of: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process +intersection_of: GO:0008150 ! biological process intersection_of: part_of GO:0000003 ! reproduction disjoint_from: GO:0044848 ! biological phase relationship: part_of GO:0000003 ! reproduction @@ -39326,61 +39203,22 @@ relationship: part_of GO:0022613 ! ribonucleoprotein complex biogenesis relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex [Term] -id: GO:0030100 -name: regulation of endocytosis +id: GO:0030154 +name: cell differentiation namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of endocytosis." [GOC:go_curators] -is_a: GO:0051128 ! regulation of cellular component organization -is_a: GO:0060627 ! regulation of vesicle-mediated transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006897 ! endocytosis -relationship: regulates GO:0006897 ! endocytosis - -[Term] -id: GO:0030133 -name: transport vesicle -namespace: cellular_component -def: "Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell." [GOC:mah, PMID:22160157] -comment: Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'. -synonym: "constitutive secretory pathway transport vesicle" EXACT [] -synonym: "Golgi to vacuole transport vesicle" NARROW [] -synonym: "Golgi-vacuole transport vesicle" NARROW [] -synonym: "secretory vesicle" RELATED [] -xref: NIF_Subcellular:sao885490876 -is_a: GO:0031410 ! cytoplasmic vesicle -relationship: part_of GO:0012505 ! endomembrane system - -[Term] -id: GO:0030163 -name: protein catabolic process -namespace: biological_process -alt_id: GO:0044254 -alt_id: GO:0044257 -def: "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:mah] -comment: This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children. -subset: goslim_candida +def: "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732] +subset: goslim_agr +subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic -subset: goslim_pombe -subset: prokaryote_subset -synonym: "cellular protein breakdown" EXACT [] -synonym: "cellular protein catabolic process" EXACT [] -synonym: "cellular protein catabolism" EXACT [] -synonym: "cellular protein degradation" EXACT [] -synonym: "multicellular organismal protein catabolic process" NARROW [] -synonym: "pheromone catabolic process" RELATED [] -synonym: "pheromone catabolism" RELATED [] -synonym: "protein breakdown" EXACT [] -synonym: "protein catabolism" EXACT [] -synonym: "protein degradation" EXACT [] -xref: Wikipedia:Protein_catabolism -is_a: GO:0009057 ! macromolecule catabolic process -is_a: GO:0019538 ! protein metabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input PR:000000001 ! protein -relationship: has_primary_input PR:000000001 ! protein -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI +subset: goslim_mouse +subset: goslim_plant +xref: Wikipedia:Cellular_differentiation +is_a: GO:0048869 ! cellular developmental process +intersection_of: GO:0048869 ! cellular developmental process +intersection_of: results_in_acquisition_of_features_of CL:0000000 ! cell +relationship: results_in_acquisition_of_features_of CL:0000000 ! cell +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24390" xsd:anyURI [Term] id: GO:0030246 @@ -39483,16 +39321,6 @@ synonym: "symbiont invasive hypha formation within host" EXACT [] is_a: GO:0030447 ! filamentous growth property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/19013" xsd:anyURI -[Term] -id: GO:0030659 -name: cytoplasmic vesicle membrane -namespace: cellular_component -def: "The lipid bilayer surrounding a cytoplasmic vesicle." [GOC:mah] -is_a: GO:0012506 ! vesicle membrane -intersection_of: GO:0016020 ! membrane -intersection_of: part_of GO:0031410 ! cytoplasmic vesicle -relationship: part_of GO:0031410 ! cytoplasmic vesicle - [Term] id: GO:0031090 name: organelle membrane @@ -39611,59 +39439,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0044249 ! cellular biosynthetic process relationship: positively_regulates GO:0044249 ! cellular biosynthetic process -[Term] -id: GO:0031329 -name: regulation of cellular catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -synonym: "regulation of cellular breakdown" EXACT [] -synonym: "regulation of cellular catabolism" EXACT [] -synonym: "regulation of cellular degradation" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0044248 ! cellular catabolic process -relationship: regulates GO:0044248 ! cellular catabolic process - -[Term] -id: GO:0031330 -name: negative regulation of cellular catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -synonym: "down regulation of cellular catabolic process" EXACT [] -synonym: "down-regulation of cellular catabolic process" EXACT [] -synonym: "downregulation of cellular catabolic process" EXACT [] -synonym: "inhibition of cellular catabolic process" NARROW [] -synonym: "negative regulation of cellular breakdown" EXACT [] -synonym: "negative regulation of cellular catabolism" EXACT [] -synonym: "negative regulation of cellular degradation" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0044248 ! cellular catabolic process -relationship: negatively_regulates GO:0044248 ! cellular catabolic process - -[Term] -id: GO:0031331 -name: positive regulation of cellular catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -synonym: "activation of cellular catabolic process" NARROW [] -synonym: "positive regulation of cellular breakdown" EXACT [] -synonym: "positive regulation of cellular catabolism" EXACT [] -synonym: "positive regulation of cellular degradation" EXACT [] -synonym: "stimulation of cellular catabolic process" NARROW [] -synonym: "up regulation of cellular catabolic process" EXACT [] -synonym: "up-regulation of cellular catabolic process" EXACT [] -synonym: "upregulation of cellular catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0044248 ! cellular catabolic process -relationship: positively_regulates GO:0044248 ! cellular catabolic process - [Term] id: GO:0031333 name: negative regulation of protein-containing complex assembly @@ -39698,71 +39473,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0065003 ! protein-containing complex assembly relationship: positively_regulates GO:0065003 ! protein-containing complex assembly -[Term] -id: GO:0031338 -name: regulation of vesicle fusion -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of vesicle fusion." [GOC:mah] -is_a: GO:0033043 ! regulation of organelle organization -is_a: GO:0060627 ! regulation of vesicle-mediated transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006906 ! vesicle fusion -relationship: regulates GO:0006906 ! vesicle fusion - -[Term] -id: GO:0031339 -name: negative regulation of vesicle fusion -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion." [GOC:mah] -synonym: "down regulation of vesicle fusion" EXACT [] -synonym: "down-regulation of vesicle fusion" EXACT [] -synonym: "downregulation of vesicle fusion" EXACT [] -synonym: "inhibition of vesicle fusion" NARROW [] -is_a: GO:0010639 ! negative regulation of organelle organization -is_a: GO:0031338 ! regulation of vesicle fusion -is_a: GO:0051051 ! negative regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006906 ! vesicle fusion -relationship: negatively_regulates GO:0006906 ! vesicle fusion - -[Term] -id: GO:0031340 -name: positive regulation of vesicle fusion -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of vesicle fusion." [GOC:mah] -synonym: "activation of vesicle fusion" NARROW [] -synonym: "stimulation of vesicle fusion" NARROW [] -synonym: "up regulation of vesicle fusion" EXACT [] -synonym: "up-regulation of vesicle fusion" EXACT [] -synonym: "upregulation of vesicle fusion" EXACT [] -is_a: GO:0010638 ! positive regulation of organelle organization -is_a: GO:0031338 ! regulation of vesicle fusion -is_a: GO:0051050 ! positive regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006906 ! vesicle fusion -relationship: positively_regulates GO:0006906 ! vesicle fusion - -[Term] -id: GO:0031410 -name: cytoplasmic vesicle -namespace: cellular_component -alt_id: GO:0016023 -def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_generic -subset: goslim_mouse -subset: goslim_yeast -synonym: "cytoplasmic membrane bounded vesicle" RELATED [] -synonym: "cytoplasmic membrane-enclosed vesicle" RELATED [] -synonym: "cytoplasmic, membrane-bounded vesicle" RELATED [] -xref: NIF_Subcellular:sao180601769 -is_a: GO:0097708 ! intracellular vesicle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0005737 ! cytoplasm - [Term] id: GO:0031503 name: protein-containing complex localization @@ -39790,7 +39500,7 @@ def: "Either of the lipid bilayers that surround the nucleus and form the nuclea xref: NIF_Subcellular:sao1687101204 is_a: GO:0031090 ! organelle membrane intersection_of: GO:0016020 ! membrane -intersection_of: part_of GO:0005634 ! nucleus +intersection_of: part_of GO:0005634 ! cell nucleus relationship: part_of GO:0005635 ! nuclear envelope [Term] @@ -39811,19 +39521,6 @@ def: "A multilayered structure surrounding all or part of a cell; encompasses on is_a: GO:0110165 ! cellular anatomical entity relationship: part_of CL:0000000 ! cell -[Term] -id: GO:0031982 -name: vesicle -namespace: cellular_component -alt_id: GO:0031988 -def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] -subset: goslim_pir -synonym: "membrane-bounded vesicle" RELATED [] -synonym: "membrane-enclosed vesicle" RELATED [] -xref: NIF_Subcellular:sao221389602 -xref: Wikipedia:Vesicle_(biology) -is_a: GO:0043227 ! membrane-bounded organelle - [Term] id: GO:0032179 name: germ tube @@ -39877,105 +39574,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0015931 ! nucleobase-containing compound transport relationship: positively_regulates GO:0015931 ! nucleobase-containing compound transport -[Term] -id: GO:0032365 -name: intracellular lipid transport -namespace: biological_process -def: "The directed movement of lipids within cells." [GOC:mah] -is_a: GO:0006869 ! lipid transport -is_a: GO:0046907 ! intracellular transport -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:18059 ! lipid -intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure - -[Term] -id: GO:0032368 -name: regulation of lipid transport -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] -is_a: GO:0051049 ! regulation of transport -is_a: GO:1905952 ! regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006869 ! lipid transport -relationship: regulates GO:0006869 ! lipid transport - -[Term] -id: GO:0032369 -name: negative regulation of lipid transport -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] -synonym: "down regulation of lipid transport" EXACT [] -synonym: "down-regulation of lipid transport" EXACT [] -synonym: "downregulation of lipid transport" EXACT [] -synonym: "inhibition of lipid transport" NARROW [] -is_a: GO:0032368 ! regulation of lipid transport -is_a: GO:0051051 ! negative regulation of transport -is_a: GO:1905953 ! negative regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006869 ! lipid transport -relationship: negatively_regulates GO:0006869 ! lipid transport - -[Term] -id: GO:0032370 -name: positive regulation of lipid transport -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] -synonym: "activation of lipid transport" NARROW [] -synonym: "stimulation of lipid transport" NARROW [] -synonym: "up regulation of lipid transport" EXACT [] -synonym: "up-regulation of lipid transport" EXACT [] -synonym: "upregulation of lipid transport" EXACT [] -is_a: GO:0032368 ! regulation of lipid transport -is_a: GO:0051050 ! positive regulation of transport -is_a: GO:1905954 ! positive regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006869 ! lipid transport -relationship: positively_regulates GO:0006869 ! lipid transport - -[Term] -id: GO:0032377 -name: regulation of intracellular lipid transport -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells." [GOC:mah] -is_a: GO:0032368 ! regulation of lipid transport -is_a: GO:0032386 ! regulation of intracellular transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0032365 ! intracellular lipid transport -relationship: regulates GO:0032365 ! intracellular lipid transport - -[Term] -id: GO:0032378 -name: negative regulation of intracellular lipid transport -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells." [GOC:mah] -synonym: "down regulation of intracellular lipid transport" EXACT [] -synonym: "down-regulation of intracellular lipid transport" EXACT [] -synonym: "downregulation of intracellular lipid transport" EXACT [] -synonym: "inhibition of intracellular lipid transport" NARROW [] -is_a: GO:0032369 ! negative regulation of lipid transport -is_a: GO:0032377 ! regulation of intracellular lipid transport -is_a: GO:0032387 ! negative regulation of intracellular transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0032365 ! intracellular lipid transport -relationship: negatively_regulates GO:0032365 ! intracellular lipid transport - -[Term] -id: GO:0032379 -name: positive regulation of intracellular lipid transport -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells." [GOC:mah] -synonym: "activation of intracellular lipid transport" NARROW [] -synonym: "stimulation of intracellular lipid transport" NARROW [] -synonym: "up regulation of intracellular lipid transport" EXACT [] -synonym: "up-regulation of intracellular lipid transport" EXACT [] -synonym: "upregulation of intracellular lipid transport" EXACT [] -is_a: GO:0032370 ! positive regulation of lipid transport -is_a: GO:0032377 ! regulation of intracellular lipid transport -is_a: GO:0032388 ! positive regulation of intracellular transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0032365 ! intracellular lipid transport -relationship: positively_regulates GO:0032365 ! intracellular lipid transport - [Term] id: GO:0032386 name: regulation of intracellular transport @@ -40021,50 +39619,23 @@ intersection_of: positively_regulates GO:0046907 ! intracellular transport relationship: positively_regulates GO:0046907 ! intracellular transport [Term] -id: GO:0032409 -name: regulation of transporter activity -namespace: biological_process -def: "Any process that modulates the activity of a transporter." [GOC:mah] -subset: term_scheduled_for_obsoletion -is_a: GO:0065009 ! regulation of molecular function -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0005215 ! transporter activity -relationship: regulates GO:0005215 ! transporter activity - -[Term] -id: GO:0032410 -name: negative regulation of transporter activity -namespace: biological_process -def: "Any process that stops or reduces the activity of a transporter." [GOC:mah] -subset: term_scheduled_for_obsoletion -synonym: "down regulation of transporter activity" EXACT [] -synonym: "down-regulation of transporter activity" EXACT [] -synonym: "downregulation of transporter activity" EXACT [] -synonym: "inhibition of transporter activity" NARROW [] -is_a: GO:0032409 ! regulation of transporter activity -is_a: GO:0044092 ! negative regulation of molecular function -is_a: GO:0051051 ! negative regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0005215 ! transporter activity -relationship: negatively_regulates GO:0005215 ! transporter activity - -[Term] -id: GO:0032411 -name: positive regulation of transporter activity +id: GO:0032501 +name: multicellular organismal process namespace: biological_process -def: "Any process that activates or increases the activity of a transporter." [GOC:mah] -subset: term_scheduled_for_obsoletion -synonym: "activation of transporter activity" NARROW [] -synonym: "stimulation of transporter activity" NARROW [] -synonym: "up regulation of transporter activity" EXACT [] -synonym: "up-regulation of transporter activity" EXACT [] -synonym: "upregulation of transporter activity" EXACT [] -is_a: GO:0032409 ! regulation of transporter activity -is_a: GO:0044093 ! positive regulation of molecular function -is_a: GO:0051050 ! positive regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0005215 ! transporter activity -relationship: positively_regulates GO:0005215 ! transporter activity +alt_id: GO:0044707 +alt_id: GO:0050874 +def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "organismal physiological process" EXACT [] +synonym: "single-multicellular organism process" RELATED [] +is_a: GO:0008150 ! biological process +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 +created_by: jl +creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 @@ -40077,7 +39648,7 @@ subset: goslim_flybase_ribbon subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase created_by: jl creation_date: 2012-12-19T12:21:31Z @@ -40115,20 +39686,10 @@ synonym: "RNA synthesis" EXACT [] is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0016070 ! RNA metabolic process is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process -intersection_of: GO:0009058 ! biosynthetic process +intersection_of: GO:0009059 ! macromolecule biosynthetic process intersection_of: has_primary_output CHEBI:33697 ! ribonucleic acid relationship: has_primary_output CHEBI:33697 ! ribonucleic acid -[Term] -id: GO:0032871 -name: regulation of karyogamy -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion." [GOC:mah] -is_a: GO:1903353 ! regulation of nucleus organization -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0000741 ! karyogamy -relationship: regulates GO:0000741 ! karyogamy - [Term] id: GO:0032879 name: regulation of localization @@ -40363,52 +39924,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009308 ! amine metabolic process relationship: positively_regulates GO:0009308 ! amine metabolic process -[Term] -id: GO:0033241 -name: regulation of amine catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah] -synonym: "regulation of amine breakdown" EXACT [] -synonym: "regulation of amine catabolism" EXACT [] -synonym: "regulation of amine degradation" EXACT [] -synonym: "regulation of cellular amine catabolic process" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0033238 ! regulation of amine metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0009310 ! amine catabolic process -relationship: regulates GO:0009310 ! amine catabolic process - -[Term] -id: GO:0033242 -name: negative regulation of amine catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah] -synonym: "negative regulation of amine breakdown" EXACT [] -synonym: "negative regulation of amine catabolism" EXACT [] -synonym: "negative regulation of amine degradation" EXACT [] -synonym: "negative regulation of cellular amine catabolic process" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0033239 ! negative regulation of amine metabolic process -is_a: GO:0033241 ! regulation of amine catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0009310 ! amine catabolic process -relationship: negatively_regulates GO:0009310 ! amine catabolic process - -[Term] -id: GO:0033243 -name: positive regulation of amine catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah] -synonym: "positive regulation of amine breakdown" EXACT [] -synonym: "positive regulation of amine catabolism" EXACT [] -synonym: "positive regulation of amine degradation" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0033240 ! positive regulation of amine metabolic process -is_a: GO:0033241 ! regulation of amine catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0009310 ! amine catabolic process -relationship: positively_regulates GO:0009310 ! amine catabolic process - [Term] id: GO:0033365 name: protein localization to organelle @@ -40436,7 +39951,7 @@ id: GO:0033673 name: negative regulation of kinase activity namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate synonym: "down regulation of kinase activity" EXACT [] synonym: "down-regulation of kinase activity" EXACT [] synonym: "downregulation of kinase activity" EXACT [] @@ -40454,7 +39969,7 @@ id: GO:0033674 name: positive regulation of kinase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate synonym: "kinase activator" NARROW [] synonym: "stimulation of kinase activity" NARROW [] synonym: "up regulation of kinase activity" EXACT [] @@ -40517,53 +40032,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0043603 ! amide metabolic process relationship: positively_regulates GO:0043603 ! amide metabolic process -[Term] -id: GO:0034251 -name: regulation of amide catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah] -synonym: "regulation of amide breakdown" EXACT [] -synonym: "regulation of amide catabolism" EXACT [] -synonym: "regulation of amide degradation" EXACT [] -synonym: "regulation of cellular amide catabolic process" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0034248 ! regulation of amide metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0043605 ! amide catabolic process -relationship: regulates GO:0043605 ! amide catabolic process - -[Term] -id: GO:0034252 -name: negative regulation of amide catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah] -synonym: "negative regulation of amide breakdown" EXACT [] -synonym: "negative regulation of amide catabolism" EXACT [] -synonym: "negative regulation of amide degradation" RELATED [] -synonym: "negative regulation of cellular amide catabolic process" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0034249 ! negative regulation of amide metabolic process -is_a: GO:0034251 ! regulation of amide catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0043605 ! amide catabolic process -relationship: negatively_regulates GO:0043605 ! amide catabolic process - -[Term] -id: GO:0034253 -name: positive regulation of amide catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah] -synonym: "positive regulation of amide breakdown" EXACT [] -synonym: "positive regulation of amide catabolism" EXACT [] -synonym: "positive regulation of amide degradation" RELATED [] -synonym: "positive regulation of cellular amide catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0034250 ! positive regulation of amide metabolic process -is_a: GO:0034251 ! regulation of amide catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0043605 ! amide catabolic process -relationship: positively_regulates GO:0043605 ! amide catabolic process - [Term] id: GO:0034293 name: sexual sporulation @@ -40620,8 +40088,8 @@ synonym: "protein localization in nucleus" EXACT [GOC:mah] synonym: "protein targeting to nucleus" RELATED [] is_a: GO:0033365 ! protein localization to organelle intersection_of: GO:0008104 ! protein localization -intersection_of: has_target_end_location GO:0005634 ! nucleus -relationship: has_target_end_location GO:0005634 ! nucleus +intersection_of: has_target_end_location GO:0005634 ! cell nucleus +relationship: has_target_end_location GO:0005634 ! cell nucleus creation_date: 2012-11-07T15:45:54Z [Term] @@ -40629,10 +40097,12 @@ id: GO:0034641 name: cellular nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_chembl synonym: "cellular nitrogen compound metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044237 ! cellular metabolic process +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [Term] id: GO:0034654 @@ -40653,23 +40123,15 @@ intersection_of: has_primary_output CHEBI:61120 ! nucleobase-containing molecula relationship: has_primary_output CHEBI:61120 ! nucleobase-containing molecular entity [Term] -id: GO:0034655 -name: nucleobase-containing compound catabolic process +id: GO:0035190 +name: syncytial nuclear migration namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] -subset: goslim_chembl -synonym: "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" EXACT [] -synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process" RELATED [GOC:dph, GOC:tb] -synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" EXACT [] -synonym: "nucleobase, nucleoside, nucleotide and nucleic acid degradation" EXACT [] -is_a: GO:0006139 ! nucleobase-containing compound metabolic process -is_a: GO:0019439 ! aromatic compound catabolic process -is_a: GO:0044270 ! cellular nitrogen compound catabolic process -is_a: GO:0046700 ! heterocycle catabolic process -is_a: GO:1901361 ! organic cyclic compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:61120 ! nucleobase-containing molecular entity -relationship: has_primary_input CHEBI:61120 ! nucleobase-containing molecular entity +def: "The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex." [GOC:bf, ISBN:0879694238, PMID:8314839] +is_a: GO:0007097 ! nuclear migration +intersection_of: GO:0007097 ! nuclear migration +intersection_of: occurs_in CL:0000228 ! multinucleate cell +relationship: occurs_in CL:0000228 ! multinucleate cell +relationship: part_of GO:0001700 ! embryonic development via the syncytial blastoderm [Term] id: GO:0035592 @@ -40730,9 +40192,26 @@ subset: goslim_pir subset: goslim_plant synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase +[Term] +id: GO:0040019 +name: positive regulation of embryonic development +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of embryonic development." [GOC:go_curators] +synonym: "activation of embryonic development" NARROW [] +synonym: "stimulation of embryonic development" NARROW [] +synonym: "up regulation of embryonic development" EXACT [] +synonym: "up-regulation of embryonic development" EXACT [] +synonym: "upregulation of embryonic development" EXACT [] +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009790 ! embryo development +relationship: positively_regulates GO:0009790 ! embryo development + [Term] id: GO:0040020 name: regulation of meiotic nuclear division @@ -40758,76 +40237,6 @@ intersection_of: regulates GO:0008283 ! cell population proliferation relationship: regulates GO:0008283 ! cell population proliferation property_value: RO:0002161 NCBITaxon:4751 -[Term] -id: GO:0042176 -name: regulation of protein catabolic process -namespace: biological_process -alt_id: GO:1903362 -alt_id: GO:2000598 -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators, GOC:jl] -synonym: "regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "regulation of cellular protein catabolic process" EXACT [] -synonym: "regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "regulation of cyclin breakdown" NARROW [GOC:obol] -synonym: "regulation of cyclin catabolic process" NARROW [] -synonym: "regulation of cyclin catabolism" NARROW [GOC:obol] -synonym: "regulation of cyclin degradation" NARROW [GOC:obol] -synonym: "regulation of degradation of cyclin" NARROW [GOC:obol] -synonym: "regulation of protein breakdown" EXACT [] -synonym: "regulation of protein catabolism" EXACT [] -synonym: "regulation of protein degradation" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0051246 ! regulation of protein metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0030163 ! protein catabolic process -relationship: regulates GO:0030163 ! protein catabolic process -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI -created_by: kmv -creation_date: 2014-08-21T15:05:45Z - -[Term] -id: GO:0042177 -name: negative regulation of protein catabolic process -namespace: biological_process -alt_id: GO:1903363 -alt_id: GO:2000599 -def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process." [GO_REF:0000058, GOC:kmv, GOC:obol, GOC:TermGenie, PMID:24785082] -synonym: "down regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "down regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "down regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "down regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "down regulation of protein catabolic process" EXACT [] -synonym: "down-regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "down-regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "down-regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "down-regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "down-regulation of protein catabolic process" EXACT [] -synonym: "downregulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "downregulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "downregulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "downregulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "downregulation of protein catabolic process" EXACT [] -synonym: "inhibition of cellular protein breakdown" NARROW [GOC:TermGenie] -synonym: "inhibition of cellular protein catabolic process" NARROW [GOC:TermGenie] -synonym: "inhibition of cellular protein catabolism" NARROW [GOC:TermGenie] -synonym: "inhibition of cellular protein degradation" NARROW [GOC:TermGenie] -synonym: "inhibition of protein catabolic process" NARROW [] -synonym: "negative regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "negative regulation of cellular protein catabolic process" EXACT [] -synonym: "negative regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "negative regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "negative regulation of protein breakdown" EXACT [] -synonym: "negative regulation of protein catabolism" EXACT [] -synonym: "negative regulation of protein degradation" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0042176 ! regulation of protein catabolic process -is_a: GO:0051248 ! negative regulation of protein metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0030163 ! protein catabolic process -relationship: negatively_regulates GO:0030163 ! protein catabolic process -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI - [Term] id: GO:0042180 name: cellular ketone metabolic process @@ -40859,22 +40268,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:17087 ! ketone relationship: has_primary_output CHEBI:17087 ! ketone -[Term] -id: GO:0042182 -name: ketone catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:go_curators] -synonym: "ketone breakdown" EXACT [] -synonym: "ketone catabolism" EXACT [] -synonym: "ketone degradation" EXACT [] -is_a: GO:0042180 ! cellular ketone metabolic process -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:0044282 ! small molecule catabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:17087 ! ketone -relationship: has_primary_input CHEBI:17087 ! ketone - [Term] id: GO:0042325 name: regulation of phosphorylation @@ -40949,7 +40342,7 @@ name: extracellular structure organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "extracellular structure organisation" EXACT [] synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization @@ -40963,8 +40356,8 @@ name: positive regulation of catalytic activity namespace: biological_process alt_id: GO:0048554 def: "Any process that activates or increases the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] +subset: gocheck_do_not_annotate subset: goslim_chembl -subset: term_scheduled_for_obsoletion synonym: "activation of enzyme activity" NARROW [] synonym: "activation of metalloenzyme activity" NARROW [] synonym: "positive regulation of enzyme activity" EXACT [GOC:tb] @@ -40989,7 +40382,7 @@ name: negative regulation of catalytic activity namespace: biological_process alt_id: GO:0048553 def: "Any process that stops or reduces the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate synonym: "down regulation of enzyme activity" EXACT [] synonym: "down regulation of metalloenzyme activity" NARROW [] synonym: "down-regulation of enzyme activity" EXACT [] @@ -41042,21 +40435,6 @@ intersection_of: has_primary_input_or_output CHEBI:33694 ! biomacromolecule relationship: has_primary_input_or_output CHEBI:33694 ! biomacromolecule property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0043171 -name: peptide catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [GOC:jl] -synonym: "peptide breakdown" EXACT [] -synonym: "peptide catabolism" EXACT [] -synonym: "peptide degradation" EXACT [] -is_a: GO:0006518 ! peptide metabolic process -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:16670 ! peptide -relationship: has_primary_input CHEBI:16670 ! peptide - [Term] id: GO:0043207 name: response to external biotic stimulus @@ -41074,7 +40452,6 @@ subset: goslim_chembl subset: goslim_generic subset: goslim_pir subset: goslim_prokaryote -subset: prokaryote_subset xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle is_a: GO:0110165 ! cellular anatomical entity @@ -41258,7 +40635,7 @@ namespace: biological_process def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl] subset: goslim_chembl subset: goslim_pir -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process [Term] id: GO:0043476 @@ -41283,7 +40660,7 @@ id: GO:0043549 name: regulation of kinase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:bf] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate is_a: GO:0042325 ! regulation of phosphorylation is_a: GO:0051338 ! regulation of transferase activity intersection_of: GO:0065007 ! biological regulation @@ -41314,18 +40691,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:32988 ! amide relationship: has_primary_output CHEBI:32988 ! amide -[Term] -id: GO:0043605 -name: amide catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [GOC:curators] -synonym: "cellular amide catabolic process" EXACT [] -is_a: GO:0009056 ! catabolic process -is_a: GO:0043603 ! amide metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_output CHEBI:32988 ! amide -relationship: has_primary_output CHEBI:32988 ! amide - [Term] id: GO:0043933 name: protein-containing complex organization @@ -41452,15 +40817,15 @@ namespace: biological_process def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane." [GOC:jl] is_a: GO:0044085 ! cellular component biogenesis intersection_of: GO:0044085 ! cellular component biogenesis -intersection_of: has_output GO:0016020 ! membrane -relationship: has_output GO:0016020 ! membrane +intersection_of: has_primary_output GO:0016020 ! membrane +relationship: has_primary_output GO:0016020 ! membrane [Term] id: GO:0044092 name: negative regulation of molecular function namespace: biological_process def: "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003674 ! molecular_function @@ -41473,7 +40838,7 @@ id: GO:0044093 name: positive regulation of molecular function namespace: biological_process def: "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003674 ! molecular_function @@ -41581,17 +40946,6 @@ synonym: "cellular lipid metabolism" EXACT [] is_a: GO:0006629 ! lipid metabolic process is_a: GO:0044237 ! cellular metabolic process -[Term] -id: GO:0044270 -name: cellular nitrogen compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] -synonym: "nitrogen compound breakdown" BROAD [] -synonym: "nitrogen compound catabolism" BROAD [] -synonym: "nitrogen compound degradation" BROAD [] -is_a: GO:0034641 ! cellular nitrogen compound metabolic process -is_a: GO:0044248 ! cellular catabolic process - [Term] id: GO:0044271 name: cellular nitrogen compound biosynthetic process @@ -41618,18 +40972,6 @@ is_a: GO:0008152 ! metabolic process created_by: jl creation_date: 2010-01-26T12:05:20Z -[Term] -id: GO:0044282 -name: small molecule catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:vw] -comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. -synonym: "small molecule catabolism" EXACT [] -is_a: GO:0009056 ! catabolic process -is_a: GO:0044281 ! small molecule metabolic process -created_by: jl -creation_date: 2010-01-26T12:06:10Z - [Term] id: GO:0044283 name: small molecule biosynthetic process @@ -41637,7 +40979,6 @@ namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. subset: goslim_prokaryote -subset: prokaryote_subset synonym: "small molecule biosynthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0044281 ! small molecule metabolic process @@ -41724,7 +41065,7 @@ synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI property_value: RO:0002161 NCBITaxon:4895 @@ -41757,7 +41098,7 @@ namespace: biological_process def: "A distinct period or stage in a biological process or cycle." [GOC:jl] comment: Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase. subset: gocheck_do_not_manually_annotate -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0050896 ! response to stimulus disjoint_from: GO:0051179 ! localization disjoint_from: GO:0071840 ! cellular component organization or biogenesis @@ -41777,20 +41118,6 @@ is_a: GO:0005488 ! binding created_by: jl creation_date: 2014-12-16T11:38:58Z -[Term] -id: GO:0045026 -name: plasma membrane fusion -namespace: biological_process -alt_id: GO:0006947 -def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] -synonym: "cell fusion" BROAD [] -synonym: "cell-cell fusion" BROAD [] -is_a: GO:0007009 ! plasma membrane organization -is_a: GO:0061025 ! membrane fusion -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0005886 ! plasma membrane -relationship: results_in_fusion_of GO:0005886 ! plasma membrane - [Term] id: GO:0045087 name: innate immune response @@ -41827,6 +41154,50 @@ synonym: "external encapsulating structure organisation" EXACT [] synonym: "external encapsulating structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization +[Term] +id: GO:0045595 +name: regulation of cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features." [GOC:go_curators] +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030154 ! cell differentiation +relationship: regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045596 +name: negative regulation of cell differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation." [GOC:go_curators] +synonym: "down regulation of cell differentiation" EXACT [] +synonym: "down-regulation of cell differentiation" EXACT [] +synonym: "downregulation of cell differentiation" EXACT [] +synonym: "inhibition of cell differentiation" NARROW [] +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051093 ! negative regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030154 ! cell differentiation +relationship: negatively_regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045597 +name: positive regulation of cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell differentiation." [GOC:go_curators] +synonym: "activation of cell differentiation" NARROW [] +synonym: "stimulation of cell differentiation" NARROW [] +synonym: "up regulation of cell differentiation" EXACT [] +synonym: "up-regulation of cell differentiation" EXACT [] +synonym: "upregulation of cell differentiation" EXACT [] +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030154 ! cell differentiation +relationship: positively_regulates GO:0030154 ! cell differentiation + [Term] id: GO:0045727 name: positive regulation of translation @@ -41844,9 +41215,7 @@ synonym: "up regulation of protein biosynthetic process" EXACT [] synonym: "up-regulation of protein biosynthetic process" EXACT [] synonym: "upregulation of protein biosynthetic process" EXACT [] is_a: GO:0006417 ! regulation of translation -is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process is_a: GO:0010628 ! positive regulation of gene expression -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0034250 ! positive regulation of amide metabolic process is_a: GO:0051247 ! positive regulation of protein metabolic process intersection_of: GO:0065007 ! biological regulation @@ -41863,54 +41232,6 @@ synonym: "oxidative burst" EXACT [] xref: Wikipedia:Respiratory_burst is_a: GO:0008152 ! metabolic process -[Term] -id: GO:0045732 -name: positive regulation of protein catabolic process -namespace: biological_process -alt_id: GO:1903364 -alt_id: GO:2000600 -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators] -synonym: "activation of cellular protein breakdown" NARROW [GOC:TermGenie] -synonym: "activation of cellular protein catabolic process" NARROW [GOC:TermGenie] -synonym: "activation of cellular protein catabolism" NARROW [GOC:TermGenie] -synonym: "activation of cellular protein degradation" NARROW [GOC:TermGenie] -synonym: "activation of protein catabolic process" NARROW [] -synonym: "positive regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "positive regulation of cellular protein catabolic process" EXACT [] -synonym: "positive regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "positive regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "positive regulation of cyclin breakdown" NARROW [GOC:obol] -synonym: "positive regulation of cyclin catabolic process" NARROW [] -synonym: "positive regulation of cyclin catabolism" NARROW [GOC:obol] -synonym: "positive regulation of cyclin degradation" NARROW [GOC:obol] -synonym: "positive regulation of degradation of cyclin" NARROW [GOC:obol] -synonym: "positive regulation of protein breakdown" EXACT [] -synonym: "positive regulation of protein catabolism" EXACT [] -synonym: "positive regulation of protein degradation" EXACT [] -synonym: "stimulation of protein catabolic process" NARROW [] -synonym: "up regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "up regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "up regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "up regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "up regulation of protein catabolic process" EXACT [] -synonym: "up-regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "up-regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "up-regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "up-regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "up-regulation of protein catabolic process" EXACT [] -synonym: "upregulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "upregulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "upregulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "upregulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "upregulation of protein catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0042176 ! regulation of protein catabolic process -is_a: GO:0051247 ! positive regulation of protein metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0030163 ! protein catabolic process -relationship: positively_regulates GO:0030163 ! protein catabolic process -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI - [Term] id: GO:0045763 name: negative regulation of cellular amino acid metabolic process @@ -41922,9 +41243,7 @@ synonym: "downregulation of amino acid metabolic process" EXACT [] synonym: "inhibition of amino acid metabolic process" NARROW [] synonym: "negative regulation of amino acid metabolism" EXACT [] is_a: GO:0006521 ! regulation of cellular amino acid metabolic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0033239 ! negative regulation of amine metabolic process -is_a: GO:0062014 ! negative regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006520 ! amino acid metabolic process relationship: negatively_regulates GO:0006520 ! amino acid metabolic process @@ -41942,9 +41261,7 @@ synonym: "up regulation of amino acid metabolic process" EXACT [] synonym: "up-regulation of amino acid metabolic process" EXACT [] synonym: "upregulation of amino acid metabolic process" EXACT [] is_a: GO:0006521 ! regulation of cellular amino acid metabolic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0033240 ! positive regulation of amine metabolic process -is_a: GO:0062013 ! positive regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006520 ! amino acid metabolic process relationship: positively_regulates GO:0006520 ! amino acid metabolic process @@ -41984,72 +41301,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007049 ! cell cycle relationship: positively_regulates GO:0007049 ! cell cycle -[Term] -id: GO:0045806 -name: negative regulation of endocytosis -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis." [GOC:go_curators] -synonym: "down regulation of endocytosis" EXACT [] -synonym: "down-regulation of endocytosis" EXACT [] -synonym: "downregulation of endocytosis" EXACT [] -synonym: "inhibition of endocytosis" NARROW [] -is_a: GO:0030100 ! regulation of endocytosis -is_a: GO:0051051 ! negative regulation of transport -is_a: GO:0051129 ! negative regulation of cellular component organization -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006897 ! endocytosis -relationship: negatively_regulates GO:0006897 ! endocytosis - -[Term] -id: GO:0045807 -name: positive regulation of endocytosis -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of endocytosis." [GOC:go_curators] -synonym: "activation of endocytosis" NARROW [] -synonym: "stimulation of endocytosis" NARROW [] -synonym: "up regulation of endocytosis" EXACT [] -synonym: "up-regulation of endocytosis" EXACT [] -synonym: "upregulation of endocytosis" EXACT [] -is_a: GO:0030100 ! regulation of endocytosis -is_a: GO:0051050 ! positive regulation of transport -is_a: GO:0051130 ! positive regulation of cellular component organization -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006897 ! endocytosis -relationship: positively_regulates GO:0006897 ! endocytosis - -[Term] -id: GO:0045833 -name: negative regulation of lipid metabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] -synonym: "down regulation of lipid metabolic process" EXACT [] -synonym: "down-regulation of lipid metabolic process" EXACT [] -synonym: "downregulation of lipid metabolic process" EXACT [] -synonym: "inhibition of lipid metabolic process" NARROW [] -synonym: "negative regulation of lipid metabolism" EXACT [] -is_a: GO:0009892 ! negative regulation of metabolic process -is_a: GO:0019216 ! regulation of lipid metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006629 ! lipid metabolic process -relationship: negatively_regulates GO:0006629 ! lipid metabolic process - -[Term] -id: GO:0045834 -name: positive regulation of lipid metabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] -synonym: "activation of lipid metabolic process" NARROW [] -synonym: "positive regulation of lipid metabolism" EXACT [] -synonym: "stimulation of lipid metabolic process" NARROW [] -synonym: "up regulation of lipid metabolic process" EXACT [] -synonym: "up-regulation of lipid metabolic process" EXACT [] -synonym: "upregulation of lipid metabolic process" EXACT [] -is_a: GO:0009893 ! positive regulation of metabolic process -is_a: GO:0019216 ! regulation of lipid metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006629 ! lipid metabolic process -relationship: positively_regulates GO:0006629 ! lipid metabolic process - [Term] id: GO:0045835 name: negative regulation of meiotic nuclear division @@ -42151,37 +41402,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006415 ! translational termination relationship: positively_regulates GO:0006415 ! translational termination -[Term] -id: GO:0045920 -name: negative regulation of exocytosis -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis." [GOC:go_curators] -synonym: "down regulation of exocytosis" EXACT [] -synonym: "down-regulation of exocytosis" EXACT [] -synonym: "downregulation of exocytosis" EXACT [] -synonym: "inhibition of exocytosis" NARROW [] -is_a: GO:0017157 ! regulation of exocytosis -is_a: GO:1903531 ! negative regulation of secretion by cell -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006887 ! exocytosis -relationship: negatively_regulates GO:0006887 ! exocytosis - -[Term] -id: GO:0045921 -name: positive regulation of exocytosis -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of exocytosis." [GOC:go_curators] -synonym: "activation of exocytosis" NARROW [] -synonym: "stimulation of exocytosis" NARROW [] -synonym: "up regulation of exocytosis" EXACT [] -synonym: "up-regulation of exocytosis" EXACT [] -synonym: "upregulation of exocytosis" EXACT [] -is_a: GO:0017157 ! regulation of exocytosis -is_a: GO:1903532 ! positive regulation of secretion by cell -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006887 ! exocytosis -relationship: positively_regulates GO:0006887 ! exocytosis - [Term] id: GO:0045934 name: negative regulation of nucleobase-containing compound metabolic process @@ -42283,6 +41503,32 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006413 ! translational initiation relationship: positively_regulates GO:0006413 ! translational initiation +[Term] +id: GO:0045992 +name: negative regulation of embryonic development +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development." [GOC:go_curators] +synonym: "down regulation of embryonic development" EXACT [] +synonym: "down-regulation of embryonic development" EXACT [] +synonym: "downregulation of embryonic development" EXACT [] +synonym: "inhibition of embryonic development" NARROW [] +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009790 ! embryo development +relationship: negatively_regulates GO:0009790 ! embryo development + +[Term] +id: GO:0045995 +name: regulation of embryonic development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of embryonic development." [GOC:go_curators] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009790 ! embryo development +relationship: regulates GO:0009790 ! embryo development + [Term] id: GO:0046112 name: nucleobase biosynthetic process @@ -42300,22 +41546,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:18282 ! nucleobase relationship: has_primary_output CHEBI:18282 ! nucleobase -[Term] -id: GO:0046113 -name: nucleobase catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid." [GOC:ai] -synonym: "nucleobase breakdown" EXACT [] -synonym: "nucleobase catabolism" EXACT [] -synonym: "nucleobase degradation" EXACT [] -is_a: GO:0009112 ! nucleobase metabolic process -is_a: GO:0046700 ! heterocycle catabolic process -is_a: GO:1901361 ! organic cyclic compound catabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:18282 ! nucleobase -relationship: has_primary_input CHEBI:18282 ! nucleobase - [Term] id: GO:0046165 name: alcohol biosynthetic process @@ -42357,20 +41587,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:29067 ! carboxylic acid anion relationship: has_primary_output CHEBI:29067 ! carboxylic acid anion -[Term] -id: GO:0046395 -name: carboxylic acid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." [ISBN:0198506732] -synonym: "carboxylic acid breakdown" EXACT [] -synonym: "carboxylic acid catabolism" EXACT [] -synonym: "carboxylic acid degradation" EXACT [] -is_a: GO:0016054 ! organic acid catabolic process -is_a: GO:0019752 ! carboxylic acid metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:29067 ! carboxylic acid anion -relationship: has_primary_input CHEBI:29067 ! carboxylic acid anion - [Term] id: GO:0046483 name: heterocycle metabolic process @@ -42383,58 +41599,6 @@ intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:5686 ! heterocyclic compound relationship: has_primary_input_or_output CHEBI:5686 ! heterocyclic compound -[Term] -id: GO:0046700 -name: heterocycle catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [GOC:ai] -synonym: "heterocycle breakdown" EXACT [] -synonym: "heterocycle catabolism" EXACT [] -synonym: "heterocycle degradation" EXACT [] -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:0046483 ! heterocycle metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:5686 ! heterocyclic compound -relationship: has_primary_input CHEBI:5686 ! heterocyclic compound - -[Term] -id: GO:0046889 -name: positive regulation of lipid biosynthetic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] -synonym: "activation of lipid biosynthetic process" NARROW [] -synonym: "positive regulation of lipid anabolism" EXACT [] -synonym: "positive regulation of lipid biosynthesis" EXACT [] -synonym: "positive regulation of lipid formation" EXACT [] -synonym: "positive regulation of lipid synthesis" EXACT [] -synonym: "positive regulation of lipogenesis" EXACT [GOC:sl] -synonym: "stimulation of lipid biosynthetic process" NARROW [] -synonym: "up regulation of lipid biosynthetic process" EXACT [] -synonym: "up-regulation of lipid biosynthetic process" EXACT [] -synonym: "upregulation of lipid biosynthetic process" EXACT [] -is_a: GO:0009891 ! positive regulation of biosynthetic process -is_a: GO:0045834 ! positive regulation of lipid metabolic process -is_a: GO:0046890 ! regulation of lipid biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0008610 ! lipid biosynthetic process -relationship: positively_regulates GO:0008610 ! lipid biosynthetic process - -[Term] -id: GO:0046890 -name: regulation of lipid biosynthetic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] -synonym: "regulation of lipid anabolism" EXACT [] -synonym: "regulation of lipid biosynthesis" EXACT [] -synonym: "regulation of lipid formation" EXACT [] -synonym: "regulation of lipid synthesis" EXACT [] -synonym: "regulation of lipogenesis" EXACT [GOC:sl] -is_a: GO:0009889 ! regulation of biosynthetic process -is_a: GO:0019216 ! regulation of lipid metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0008610 ! lipid biosynthetic process -relationship: regulates GO:0008610 ! lipid biosynthetic process - [Term] id: GO:0046903 name: secretion @@ -42494,18 +41658,6 @@ intersection_of: GO:0012501 ! programmed cell death intersection_of: has_part GO:0016236 ! macroautophagy relationship: has_part GO:0016236 ! macroautophagy -[Term] -id: GO:0048284 -name: organelle fusion -namespace: biological_process -def: "The creation of a single organelle from two or more organelles." [GOC:jid] -subset: goslim_pir -subset: goslim_yeast -is_a: GO:0006996 ! organelle organization -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0043226 ! organelle -relationship: results_in_fusion_of GO:0043226 ! organelle - [Term] id: GO:0048285 name: organelle fission @@ -42519,15 +41671,30 @@ intersection_of: results_in_fission_of GO:0043226 ! organelle relationship: results_in_fission_of GO:0043226 ! organelle [Term] -id: GO:0048288 -name: nuclear membrane fusion involved in karyogamy +id: GO:0048468 +name: cell development +namespace: biological_process +def: "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place." [GOC:go_curators] +subset: goslim_candida +synonym: "terminal differentiation" RELATED [GOC:dph, GOC:tb] +is_a: GO:0048856 ! anatomical structure development +is_a: GO:0048869 ! cellular developmental process +intersection_of: GO:0008150 ! biological process +intersection_of: results_in_development_of CL:0000000 ! cell +relationship: part_of GO:0030154 ! cell differentiation +relationship: results_in_development_of CL:0000000 ! cell +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24390" xsd:anyURI + +[Term] +id: GO:0048513 +name: animal organ development namespace: biological_process -def: "The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei." [GOC:jid] -synonym: "nuclear membrane fusion during karyogamy" RELATED [GOC:dph, GOC:tb] -is_a: GO:0000740 ! nuclear membrane fusion -intersection_of: GO:0000740 ! nuclear membrane fusion -intersection_of: part_of GO:0000741 ! karyogamy -relationship: part_of GO:0000741 ! karyogamy +def: "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dph, GOC:jid] +synonym: "development of an organ" EXACT [] +synonym: "organogenesis" EXACT [] +xref: Wikipedia:Organogenesis +is_a: GO:0048856 ! anatomical structure development +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25943" xsd:anyURI [Term] id: GO:0048518 @@ -42544,8 +41711,8 @@ synonym: "up-regulation of biological process" EXACT [] synonym: "upregulation of biological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0008150 ! biological_process -relationship: positively_regulates GO:0008150 ! biological_process +intersection_of: positively_regulates GO:0008150 ! biological process +relationship: positively_regulates GO:0008150 ! biological process [Term] id: GO:0048519 @@ -42561,8 +41728,8 @@ synonym: "inhibition of biological process" NARROW [] synonym: "negative regulation of physiological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0008150 ! biological_process -relationship: negatively_regulates GO:0008150 ! biological_process +intersection_of: negatively_regulates GO:0008150 ! biological process +relationship: negatively_regulates GO:0008150 ! biological process [Term] id: GO:0048522 @@ -42601,6 +41768,49 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009987 ! cellular process relationship: negatively_regulates GO:0009987 ! cellular process +[Term] +id: GO:0048580 +name: regulation of post-embryonic development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." [GOC:jid] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009791 ! post-embryonic development +relationship: regulates GO:0009791 ! post-embryonic development + +[Term] +id: GO:0048581 +name: negative regulation of post-embryonic development +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." [GOC:jid] +synonym: "down regulation of post-embryonic development" EXACT [] +synonym: "down-regulation of post-embryonic development" EXACT [] +synonym: "downregulation of post-embryonic development" EXACT [] +synonym: "inhibition of post-embryonic development" NARROW [] +is_a: GO:0048580 ! regulation of post-embryonic development +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009791 ! post-embryonic development +relationship: negatively_regulates GO:0009791 ! post-embryonic development + +[Term] +id: GO:0048582 +name: positive regulation of post-embryonic development +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." [GOC:jid] +synonym: "activation of post-embryonic development" NARROW [] +synonym: "stimulation of post-embryonic development" NARROW [] +synonym: "up regulation of post-embryonic development" EXACT [] +synonym: "up-regulation of post-embryonic development" EXACT [] +synonym: "upregulation of post-embryonic development" EXACT [] +is_a: GO:0048580 ! regulation of post-embryonic development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009791 ! post-embryonic development +relationship: positively_regulates GO:0009791 ! post-embryonic development + [Term] id: GO:0048589 name: developmental growth @@ -42633,6 +41843,9 @@ subset: goslim_generic subset: goslim_plant synonym: "development of an anatomical structure" EXACT [] is_a: GO:0032502 ! developmental process +intersection_of: GO:0032502 ! developmental process +intersection_of: results_in_development_of UBERON:0000061 ! anatomical structure +relationship: results_in_development_of UBERON:0000061 ! anatomical structure property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [Term] @@ -42720,8 +41933,8 @@ subset: goslim_pir synonym: "regulation of physiological process" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0008150 ! biological_process -relationship: regulates GO:0008150 ! biological_process +intersection_of: regulates GO:0008150 ! biological process +relationship: regulates GO:0008150 ! biological process [Term] id: GO:0050790 @@ -42729,8 +41942,8 @@ name: regulation of catalytic activity namespace: biological_process alt_id: GO:0048552 def: "Any process that modulates the activity of an enzyme." [GOC:ai, GOC:ebc, GOC:vw] +subset: gocheck_do_not_annotate subset: goslim_chembl -subset: term_scheduled_for_obsoletion synonym: "regulation of enzyme activity" EXACT [] synonym: "regulation of metalloenzyme activity" NARROW [] is_a: GO:0065009 ! regulation of molecular function @@ -42738,6 +41951,16 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003824 ! catalytic activity relationship: regulates GO:0003824 ! catalytic activity +[Term] +id: GO:0050793 +name: regulation of developmental process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:go_curators] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032502 ! developmental process +relationship: regulates GO:0032502 ! developmental process + [Term] id: GO:0050794 name: regulation of cellular process @@ -42765,60 +41988,7 @@ subset: goslim_mouse subset: goslim_pir subset: goslim_prokaryote synonym: "physiological response to stimulus" EXACT [] -is_a: GO:0008150 ! biological_process - -[Term] -id: GO:0050994 -name: regulation of lipid catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids." [GOC:ai] -synonym: "regulation of lipid breakdown" EXACT [] -synonym: "regulation of lipid catabolism" EXACT [] -synonym: "regulation of lipid degradation" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0019216 ! regulation of lipid metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0016042 ! lipid catabolic process -relationship: regulates GO:0016042 ! lipid catabolic process - -[Term] -id: GO:0050995 -name: negative regulation of lipid catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids." [GOC:ai] -synonym: "down regulation of lipid catabolic process" EXACT [] -synonym: "down-regulation of lipid catabolic process" EXACT [] -synonym: "downregulation of lipid catabolic process" EXACT [] -synonym: "inhibition of lipid catabolic process" NARROW [] -synonym: "negative regulation of lipid breakdown" EXACT [] -synonym: "negative regulation of lipid catabolism" EXACT [] -synonym: "negative regulation of lipid degradation" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0045833 ! negative regulation of lipid metabolic process -is_a: GO:0050994 ! regulation of lipid catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0016042 ! lipid catabolic process -relationship: negatively_regulates GO:0016042 ! lipid catabolic process - -[Term] -id: GO:0050996 -name: positive regulation of lipid catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids." [GOC:ai] -synonym: "activation of lipid catabolic process" NARROW [] -synonym: "positive regulation of lipid breakdown" EXACT [] -synonym: "positive regulation of lipid catabolism" EXACT [] -synonym: "positive regulation of lipid degradation" EXACT [] -synonym: "stimulation of lipid catabolic process" NARROW [] -synonym: "up regulation of lipid catabolic process" EXACT [] -synonym: "up-regulation of lipid catabolic process" EXACT [] -synonym: "upregulation of lipid catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0045834 ! positive regulation of lipid metabolic process -is_a: GO:0050994 ! regulation of lipid catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0016042 ! lipid catabolic process -relationship: positively_regulates GO:0016042 ! lipid catabolic process +is_a: GO:0008150 ! biological process [Term] id: GO:0051046 @@ -42903,27 +42073,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006810 ! transport relationship: negatively_regulates GO:0006810 ! transport -[Term] -id: GO:0051055 -name: negative regulation of lipid biosynthetic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] -synonym: "down regulation of lipid biosynthetic process" EXACT [] -synonym: "down-regulation of lipid biosynthetic process" EXACT [] -synonym: "downregulation of lipid biosynthetic process" EXACT [] -synonym: "inhibition of lipid biosynthetic process" NARROW [] -synonym: "negative regulation of lipid anabolism" EXACT [] -synonym: "negative regulation of lipid biosynthesis" EXACT [] -synonym: "negative regulation of lipid formation" EXACT [] -synonym: "negative regulation of lipid synthesis" EXACT [] -synonym: "negative regulation of lipogenesis" EXACT [GOC:sl] -is_a: GO:0009890 ! negative regulation of biosynthetic process -is_a: GO:0045833 ! negative regulation of lipid metabolic process -is_a: GO:0046890 ! regulation of lipid biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0008610 ! lipid biosynthetic process -relationship: negatively_regulates GO:0008610 ! lipid biosynthetic process - [Term] id: GO:0051078 name: meiotic nuclear membrane disassembly @@ -42953,6 +42102,37 @@ intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0031965 ! nuclear membrane relationship: results_in_disassembly_of GO:0031965 ! nuclear membrane +[Term] +id: GO:0051093 +name: negative regulation of developmental process +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] +synonym: "down regulation of developmental process" EXACT [] +synonym: "down-regulation of developmental process" EXACT [] +synonym: "downregulation of developmental process" EXACT [] +synonym: "inhibition of developmental process" NARROW [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032502 ! developmental process +relationship: negatively_regulates GO:0032502 ! developmental process + +[Term] +id: GO:0051094 +name: positive regulation of developmental process +namespace: biological_process +def: "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] +synonym: "activation of developmental process" NARROW [] +synonym: "stimulation of developmental process" NARROW [] +synonym: "up regulation of developmental process" EXACT [] +synonym: "up-regulation of developmental process" EXACT [] +synonym: "upregulation of developmental process" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032502 ! developmental process +relationship: positively_regulates GO:0032502 ! developmental process + [Term] id: GO:0051128 name: regulation of cellular component organization @@ -43013,8 +42193,8 @@ xref: Wikipedia:Nuclear_transport is_a: GO:0046907 ! intracellular transport intersection_of: GO:0006810 ! transport intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure -intersection_of: results_in_transport_to_from_or_in GO:0005634 ! nucleus -relationship: results_in_transport_to_from_or_in GO:0005634 ! nucleus +intersection_of: results_in_transport_to_from_or_in GO:0005634 ! cell nucleus +relationship: results_in_transport_to_from_or_in GO:0005634 ! cell nucleus [Term] id: GO:0051171 @@ -43089,7 +42269,7 @@ synonym: "establishment and maintenance of substrate location" NARROW [] synonym: "localisation" EXACT [GOC:mah] synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process created_by: jl creation_date: 2013-12-18T13:51:04Z @@ -43162,6 +42342,47 @@ synonym: "RNA recruitment" EXACT [] is_a: GO:0051234 ! establishment of localization relationship: part_of GO:0006403 ! RNA localization +[Term] +id: GO:0051239 +name: regulation of multicellular organismal process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai, GOC:dph, GOC:tb] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032501 ! multicellular organismal process +relationship: regulates GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0051240 +name: positive regulation of multicellular organismal process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] +synonym: "activation of multicellular organismal process" NARROW [] +synonym: "stimulation of multicellular organismal process" NARROW [] +synonym: "up regulation of multicellular organismal process" EXACT [] +synonym: "up-regulation of multicellular organismal process" EXACT [] +synonym: "upregulation of multicellular organismal process" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032501 ! multicellular organismal process +relationship: positively_regulates GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0051241 +name: negative regulation of multicellular organismal process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] +synonym: "down regulation of multicellular organismal process" EXACT [] +synonym: "down-regulation of multicellular organismal process" EXACT [] +synonym: "downregulation of multicellular organismal process" EXACT [] +synonym: "inhibition of multicellular organismal process" NARROW [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032501 ! multicellular organismal process +relationship: negatively_regulates GO:0032501 ! multicellular organismal process + [Term] id: GO:0051246 name: regulation of protein metabolic process @@ -43294,9 +42515,9 @@ is_a: GO:0022414 ! reproductive process intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140013 ! meiotic nuclear division relationship: has_part GO:0140013 ! meiotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0019953 ! sexual reproduction +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24599" xsd:anyURI [Term] @@ -43329,8 +42550,8 @@ name: regulation of transferase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. +subset: gocheck_do_not_annotate subset: gocheck_do_not_manually_annotate -subset: term_scheduled_for_obsoletion synonym: "transferase regulator" EXACT [] is_a: GO:0050790 ! regulation of catalytic activity intersection_of: GO:0065007 ! biological regulation @@ -43343,8 +42564,8 @@ name: positive regulation of transferase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. +subset: gocheck_do_not_annotate subset: gocheck_do_not_manually_annotate -subset: term_scheduled_for_obsoletion synonym: "activation of transferase activity" NARROW [] synonym: "stimulation of transferase activity" NARROW [] synonym: "transferase activator" EXACT [] @@ -43363,8 +42584,8 @@ name: negative regulation of transferase activity namespace: biological_process def: "Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. +subset: gocheck_do_not_annotate subset: gocheck_do_not_manually_annotate -subset: term_scheduled_for_obsoletion synonym: "down regulation of transferase activity" EXACT [] synonym: "down-regulation of transferase activity" EXACT [] synonym: "downregulation of transferase activity" EXACT [] @@ -43430,21 +42651,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051321 ! meiotic cell cycle relationship: negatively_regulates GO:0051321 ! meiotic cell cycle -[Term] -id: GO:0051469 -name: vesicle fusion with vacuole -namespace: biological_process -alt_id: GO:0042146 -def: "The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole." [GOC:ai] -synonym: "heterotypic vacuole fusion (non-autophagic)" RELATED [] -synonym: "heterotypic vacuole fusion, non-autophagic" RELATED [] -is_a: GO:0006906 ! vesicle fusion -is_a: GO:0097576 ! vacuole fusion -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0005773 ! vacuole -intersection_of: results_in_fusion_of GO:0031982 ! vesicle -relationship: results_in_fusion_of GO:0031982 ! vesicle - [Term] id: GO:0051640 name: organelle localization @@ -43457,8 +42663,8 @@ is_a: GO:0051179 ! localization intersection_of: GO:0051179 ! localization intersection_of: has_primary_input GO:0043226 ! organelle relationship: has_primary_input GO:0043226 ! organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI [Term] @@ -43491,21 +42697,8 @@ synonym: "localization of nucleus" EXACT [] synonym: "nucleus localisation" EXACT [GOC:mah] is_a: GO:0051640 ! organelle localization intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0005634 ! nucleus -relationship: has_primary_input GO:0005634 ! nucleus - -[Term] -id: GO:0051648 -name: vesicle localization -namespace: biological_process -def: "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location." [GOC:ai] -synonym: "cytoplasmic vesicle localization" EXACT [] -synonym: "establishment and maintenance of vesicle localization" EXACT [] -synonym: "vesicle localisation" EXACT [GOC:mah] -is_a: GO:0051640 ! organelle localization -intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0031982 ! vesicle -relationship: has_primary_input GO:0031982 ! vesicle +intersection_of: has_primary_input GO:0005634 ! cell nucleus +relationship: has_primary_input GO:0005634 ! cell nucleus [Term] id: GO:0051649 @@ -43520,22 +42713,10 @@ synonym: "positioning within cell" NARROW [] is_a: GO:0051234 ! establishment of localization intersection_of: GO:0051234 ! establishment of localization intersection_of: occurs_in CL:0000000 ! cell -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms relationship: occurs_in CL:0000000 ! cell -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms relationship: part_of GO:0051641 ! cellular localization - -[Term] -id: GO:0051650 -name: establishment of vesicle localization -namespace: biological_process -def: "The directed movement of a vesicle to a specific location." [GOC:ai] -synonym: "establishment of vesicle localisation" EXACT [GOC:mah] -is_a: GO:0051648 ! vesicle localization -is_a: GO:0051649 ! establishment of localization in cell -is_a: GO:0051656 ! establishment of organelle localization -intersection_of: GO:0051234 ! establishment of localization -intersection_of: has_primary_input GO:0031982 ! vesicle +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0051656 @@ -43602,7 +42783,7 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ id: GO:0051704 name: multi-organism process def: "A biological process which involves another organism of the same or different species." [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] @@ -43792,8 +42973,8 @@ def: "The cellular chemical reactions and pathways involving a nucleobase-contai subset: goslim_drosophila subset: goslim_generic subset: goslim_pombe +subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] synonym: "nucleobase, nucleoside and nucleotide metabolism" EXACT [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process @@ -43809,6 +42990,16 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0043170 ! macromolecule metabolic process relationship: regulates GO:0043170 ! macromolecule metabolic process +[Term] +id: GO:0060284 +name: regulation of cell development +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:dph, GOC:tb] +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048468 ! cell development +relationship: regulates GO:0048468 ! cell development + [Term] id: GO:0060341 name: regulation of cellular localization @@ -43834,19 +43025,6 @@ relationship: part_of GO:0009653 ! anatomical structure morphogenesis created_by: dph creation_date: 2009-04-28T08:42:53Z -[Term] -id: GO:0060627 -name: regulation of vesicle-mediated transport -namespace: biological_process -def: "Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell." [GOC:dph, GOC:tb] -is_a: GO:0050794 ! regulation of cellular process -is_a: GO:0051049 ! regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0016192 ! vesicle-mediated transport -relationship: regulates GO:0016192 ! vesicle-mediated transport -created_by: dph -creation_date: 2009-05-18T02:29:43Z - [Term] id: GO:0061024 name: membrane organization @@ -43860,7 +43038,6 @@ subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote -subset: prokaryote_subset synonym: "cellular membrane organisation" EXACT [] synonym: "cellular membrane organization" EXACT [] synonym: "membrane organisation" EXACT [GOC:mah] @@ -43873,24 +43050,6 @@ relationship: results_in_organization_of GO:0016020 ! membrane created_by: jl creation_date: 2010-02-08T02:43:11Z -[Term] -id: GO:0061025 -name: membrane fusion -namespace: biological_process -alt_id: GO:0006944 -alt_id: GO:0044801 -def: "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] -subset: goslim_yeast -synonym: "cellular membrane fusion" EXACT [] -synonym: "single-organism membrane fusion" RELATED [] -xref: Wikipedia:Lipid_bilayer_fusion -is_a: GO:0061024 ! membrane organization -intersection_of: GO:0061024 ! membrane organization -intersection_of: results_in_fusion_of GO:0016020 ! membrane -relationship: results_in_fusion_of GO:0016020 ! membrane -created_by: jl -creation_date: 2010-02-08T02:48:06Z - [Term] id: GO:0061650 name: ubiquitin-like protein conjugating enzyme activity @@ -44057,7 +43216,7 @@ subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_pombe -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "cellular macromolecule complex assembly" RELATED [] synonym: "cellular protein complex assembly" EXACT [] synonym: "cellular protein-containing complex assembly" RELATED [] @@ -44081,7 +43240,7 @@ def: "Any process that modulates a measurable attribute of any biological proces subset: gocheck_do_not_annotate subset: goslim_pir synonym: "regulation" BROAD [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process [Term] id: GO:0065009 @@ -44091,7 +43250,6 @@ def: "Any process that modulates the frequency, rate or extent of a molecular fu subset: gocheck_do_not_annotate subset: goslim_pir subset: goslim_plant -subset: term_scheduled_for_obsoletion synonym: "regulation of a molecular function" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation @@ -44131,18 +43289,6 @@ synonym: "necrosis" BROAD [GOC:mah] property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24680" xsd:anyURI is_obsolete: true -[Term] -id: GO:0070382 -name: exocytic vesicle -namespace: cellular_component -def: "A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis." [GOC:kad, GOC:mah] -synonym: "exocytic constitutive secretory pathway transport vesicle" EXACT [] -synonym: "exocytotic vesicle" EXACT [GOC:kad] -is_a: GO:0030133 ! transport vesicle -is_a: GO:0099503 ! secretory vesicle -intersection_of: GO:0030133 ! transport vesicle -intersection_of: capable_of GO:0099500 ! vesicle fusion to plasma membrane - [Term] id: GO:0070727 name: cellular macromolecule localization @@ -44328,7 +43474,6 @@ creation_date: 2010-09-10T01:39:16Z id: GO:0071944 name: cell periphery namespace: cellular_component -def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon is_a: GO:0110165 ! cellular anatomical entity @@ -44364,7 +43509,7 @@ id: GO:0072657 name: protein localization to membrane namespace: biological_process def: "A process in which a protein is transported to, or maintained in, a specific location in a membrane." [GOC:mah] -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "protein localisation in membrane" EXACT [GOC:mah] synonym: "protein localization in membrane" EXACT [] is_a: GO:0008104 ! protein localization @@ -44538,19 +43683,6 @@ intersection_of: has_target_end_location GO:0016020 ! membrane created_by: tb creation_date: 2009-12-08T03:18:51Z -[Term] -id: GO:0090174 -name: organelle membrane fusion -namespace: biological_process -def: "The joining of two lipid bilayers to form a single organelle membrane." [GOC:ascb_2009, GOC:dph, GOC:tb] -is_a: GO:0048284 ! organelle fusion -is_a: GO:0061025 ! membrane fusion -intersection_of: GO:0061025 ! membrane fusion -intersection_of: results_in_fusion_of GO:0031090 ! organelle membrane -relationship: results_in_fusion_of GO:0031090 ! organelle membrane -created_by: tb -creation_date: 2009-12-11T11:44:58Z - [Term] id: GO:0090304 name: nucleic acid metabolic process @@ -44561,6 +43693,7 @@ is_a: GO:0043170 ! macromolecule metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33696 ! nucleic acid relationship: has_primary_input_or_output CHEBI:33696 ! nucleic acid +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26133" xsd:anyURI created_by: tb creation_date: 2010-04-07T10:18:47Z @@ -44613,8 +43746,8 @@ def: "A macromolecular localization process in which RNA is transported to and m synonym: "RNA localisation to nucleus" EXACT [GOC:mah] is_a: GO:0006403 ! RNA localization intersection_of: GO:0006403 ! RNA localization -intersection_of: has_target_end_location GO:0005634 ! nucleus -relationship: has_target_end_location GO:0005634 ! nucleus +intersection_of: has_target_end_location GO:0005634 ! cell nucleus +relationship: has_target_end_location GO:0005634 ! cell nucleus created_by: tb creation_date: 2016-07-19T17:00:49Z @@ -44664,31 +43797,6 @@ is_a: GO:0005488 ! binding created_by: pr creation_date: 2012-08-02T13:03:39Z -[Term] -id: GO:0097576 -name: vacuole fusion -namespace: biological_process -def: "Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole." [GOC:pr, GOC:vw, Wikipedia:Vacuole] -is_a: GO:0007033 ! vacuole organization -is_a: GO:0048284 ! organelle fusion -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0005773 ! vacuole -relationship: results_in_fusion_of GO:0005773 ! vacuole -created_by: pr -creation_date: 2014-02-28T09:49:31Z - -[Term] -id: GO:0097708 -name: intracellular vesicle -namespace: cellular_component -def: "Any vesicle that is part of the intracellular region." [GOC:vesicles] -is_a: GO:0031982 ! vesicle -is_a: GO:0043231 ! intracellular membrane-bounded organelle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr -creation_date: 2016-03-29T17:39:45Z - [Term] id: GO:0098542 name: defense response to other organism @@ -44779,43 +43887,6 @@ intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -[Term] -id: GO:0098876 -name: vesicle-mediated transport to the plasma membrane -namespace: biological_process -def: "The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis." [GOC:dos] -is_a: GO:0016192 ! vesicle-mediated transport -is_a: GO:0051668 ! localization within membrane -intersection_of: GO:0006810 ! transport -intersection_of: has_target_end_location GO:0005886 ! plasma membrane -intersection_of: process_has_causal_agent GO:0031982 ! vesicle -relationship: ends_with GO:0006887 ! exocytosis -relationship: has_target_end_location GO:0005886 ! plasma membrane - -[Term] -id: GO:0099500 -name: vesicle fusion to plasma membrane -namespace: biological_process -def: "Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space." [GOC:aruk, GOC:bc, ISBN:0071120009, PMID:18618940] -is_a: GO:0006906 ! vesicle fusion -is_a: GO:0140029 ! exocytic process -intersection_of: GO:0061025 ! membrane fusion -intersection_of: part_of GO:0006887 ! exocytosis -intersection_of: results_in_fusion_of GO:0012506 ! vesicle membrane -intersection_of: results_in_fusion_of GO:0098590 ! plasma membrane region -relationship: results_in_fusion_of GO:0098590 ! plasma membrane region - -[Term] -id: GO:0099503 -name: secretory vesicle -namespace: cellular_component -def: "A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space." [GOC:dos] -subset: goslim_drosophila -is_a: GO:0031410 ! cytoplasmic vesicle -intersection_of: GO:0031982 ! vesicle -intersection_of: capable_of GO:0099500 ! vesicle fusion to plasma membrane -relationship: capable_of GO:0099500 ! vesicle fusion to plasma membrane - [Term] id: GO:0099568 name: cytoplasmic region @@ -44858,8 +43929,8 @@ namespace: biological_process def: "The process in which a nuclear membrane is synthesized, aggregates, and bonds together." [GOC:vw] is_a: GO:0044091 ! membrane biogenesis intersection_of: GO:0044085 ! cellular component biogenesis -intersection_of: has_output GO:0031965 ! nuclear membrane -relationship: has_output GO:0031965 ! nuclear membrane +intersection_of: has_primary_output GO:0031965 ! nuclear membrane +relationship: has_primary_output GO:0031965 ! nuclear membrane relationship: part_of GO:0071763 ! nuclear membrane organization [Term] @@ -44896,50 +43967,6 @@ is_a: GO:0044001 ! migration in host created_by: hjd creation_date: 2020-05-01T14:09:35Z -[Term] -id: GO:0110112 -name: regulation of lipid transporter activity -namespace: biological_process -def: "Any process that modulates the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: term_scheduled_for_obsoletion -is_a: GO:0032368 ! regulation of lipid transport -is_a: GO:0032409 ! regulation of transporter activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0005319 ! lipid transporter activity -relationship: regulates GO:0005319 ! lipid transporter activity -created_by: kmv -creation_date: 2018-07-06T18:53:55Z - -[Term] -id: GO:0110113 -name: positive regulation of lipid transporter activity -namespace: biological_process -def: "Any process that increases the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: term_scheduled_for_obsoletion -is_a: GO:0032370 ! positive regulation of lipid transport -is_a: GO:0032411 ! positive regulation of transporter activity -is_a: GO:0110112 ! regulation of lipid transporter activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0005319 ! lipid transporter activity -relationship: positively_regulates GO:0005319 ! lipid transporter activity -created_by: kmv -creation_date: 2018-07-06T19:14:13Z - -[Term] -id: GO:0110114 -name: negative regulation of lipid transporter activity -namespace: biological_process -def: "Any process that decreases the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: term_scheduled_for_obsoletion -is_a: GO:0032369 ! negative regulation of lipid transport -is_a: GO:0032410 ! negative regulation of transporter activity -is_a: GO:0110112 ! regulation of lipid transporter activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0005319 ! lipid transporter activity -relationship: negatively_regulates GO:0005319 ! lipid transporter activity -created_by: kmv -creation_date: 2018-07-06T19:21:44Z - [Term] id: GO:0110165 name: cellular anatomical entity @@ -44948,6 +43975,7 @@ def: "A part of a cellular organism that is either an immaterial entity or a mat subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0005575 ! cellular_component +is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI created_by: kmv @@ -44996,19 +44024,6 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ created_by: pg creation_date: 2017-03-23T09:40:00Z -[Term] -id: GO:0140029 -name: exocytic process -namespace: biological_process -def: "The cellular processes that contribute to exocytosis." [Wikipedia:Exocytosis] -subset: gocheck_do_not_annotate -is_a: GO:0009987 ! cellular process -intersection_of: GO:0009987 ! cellular process -intersection_of: part_of GO:0006887 ! exocytosis -relationship: part_of GO:0006887 ! exocytosis -created_by: pg -creation_date: 2017-05-15T13:20:45Z - [Term] id: GO:0140096 name: catalytic activity, acting on a protein @@ -45016,11 +44031,10 @@ namespace: molecular_function def: "Catalytic activity that acts to modify a protein." [GOC:molecular_function_refactoring, GOC:pdt] subset: goslim_generic subset: goslim_prokaryote -subset: prokaryote_subset is_a: GO:0003824 ! catalytic activity intersection_of: GO:0003824 ! catalytic activity -intersection_of: has_input PR:000000001 ! protein -relationship: has_input PR:000000001 ! protein +intersection_of: has_primary_input PR:000000001 ! protein +relationship: has_primary_input PR:000000001 ! protein property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI created_by: pg creation_date: 2017-09-14T10:32:59Z @@ -45031,11 +44045,11 @@ name: catalytic activity, acting on RNA namespace: molecular_function def: "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis." [GOC:molecular_function_refactoring, GOC:pdt] subset: goslim_generic -subset: prokaryote_subset +subset: goslim_prokaryote is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid intersection_of: GO:0003824 ! catalytic activity -intersection_of: has_input CHEBI:33697 ! ribonucleic acid -relationship: has_input CHEBI:33697 ! ribonucleic acid +intersection_of: has_primary_input CHEBI:33697 ! ribonucleic acid +relationship: has_primary_input CHEBI:33697 ! ribonucleic acid property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21612" xsd:anyURI created_by: pg @@ -45051,24 +44065,6 @@ is_a: GO:0005515 ! protein binding created_by: pg creation_date: 2018-10-01T10:03:21Z -[Term] -id: GO:0140318 -name: protein transporter activity -namespace: molecular_function -def: "Directly binding to a specific protein and delivering it to a specific cellular location." [PMID:18706423] -comment: Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation. -synonym: "protein carrier activity" RELATED [] -synonym: "protein transport chaperone" RELATED [] -xref: Reactome:R-HSA-9662747 "iRHOM2 transports ADAM17 from ER to the Golgi-network" -xref: Reactome:R-HSA-9662818 "iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane" -is_a: GO:0005215 ! transporter activity -intersection_of: GO:0005215 ! transporter activity -intersection_of: has_primary_input PR:000000001 ! protein -relationship: has_primary_input PR:000000001 ! protein -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17073" xsd:anyURI -created_by: pg -creation_date: 2019-04-01T10:41:38Z - [Term] id: GO:0140352 name: export from cell @@ -45085,37 +44081,6 @@ relationship: has_target_start_location GO:0005622 ! intracellular anatomical st created_by: pg creation_date: 2019-05-22T11:20:45Z -[Term] -id: GO:0140353 -name: lipid export from cell -namespace: biological_process -def: "The directed movement of a lipid from a cell, into the extracellular region." [GOC:pg] -synonym: "lipid efflux" BROAD [] -is_a: GO:0006869 ! lipid transport -is_a: GO:0140352 ! export from cell -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:18059 ! lipid -intersection_of: has_target_end_location GO:0005576 ! extracellular region -intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg -creation_date: 2019-05-22T11:33:07Z - -[Term] -id: GO:0140354 -name: lipid import into cell -namespace: biological_process -def: "The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis." [GOC:pg] -synonym: "lipid uptake" BROAD [] -is_a: GO:0006869 ! lipid transport -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:18059 ! lipid -intersection_of: has_target_end_location GO:0005622 ! intracellular anatomical structure -intersection_of: has_target_start_location GO:0005576 ! extracellular region -relationship: has_target_end_location GO:0005622 ! intracellular anatomical structure -relationship: has_target_start_location GO:0005576 ! extracellular region -created_by: pg -creation_date: 2019-05-22T11:38:15Z - [Term] id: GO:0140513 name: nuclear protein-containing complex @@ -45125,8 +44090,8 @@ subset: gocheck_do_not_annotate synonym: "nuclear complex" EXACT [] is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex -intersection_of: part_of GO:0005634 ! nucleus -relationship: part_of GO:0005634 ! nucleus +intersection_of: part_of GO:0005634 ! cell nucleus +relationship: part_of GO:0005634 ! cell nucleus created_by: pg creation_date: 2020-09-09T05:12:38Z @@ -45160,8 +44125,8 @@ namespace: molecular_function def: "Catalytic activity that acts to modify a nucleic acid." [GOC:pg] is_a: GO:0003824 ! catalytic activity intersection_of: GO:0003824 ! catalytic activity -intersection_of: has_input CHEBI:33696 ! nucleic acid -relationship: has_input CHEBI:33696 ! nucleic acid +intersection_of: has_primary_input CHEBI:33696 ! nucleic acid +relationship: has_primary_input CHEBI:33696 ! nucleic acid property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21402" xsd:anyURI created_by: pg creation_date: 2021-05-11T06:31:07Z @@ -45212,6 +44177,7 @@ synonym: "L-amino acid anabolism" EXACT [] synonym: "L-amino acid biosynthesis" EXACT [] synonym: "L-amino acid formation" EXACT [] synonym: "L-amino acid synthesis" EXACT [] +is_a: GO:0008652 ! amino acid biosynthetic process is_a: GO:0170033 ! L-amino acid metabolic process is_a: GO:1901607 ! alpha-amino acid biosynthetic process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23268" xsd:anyURI @@ -45241,6 +44207,8 @@ namespace: biological_process def: "The chemical reactions and pathways involving any amino acid that is incorporated into protein naturally by ribosomal translation of mRNA, and that has a specific codon for translation from mRNA to protein." [GOC:ew] synonym: "proteinogenic amino acid metabolism" EXACT [] is_a: GO:0006520 ! amino acid metabolic process +is_a: GO:0019752 ! carboxylic acid metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23268" xsd:anyURI created_by: ew creation_date: 2023-12-18T17:31:08Z @@ -45395,22 +44363,6 @@ relationship: has_primary_input_or_output CHEBI:33832 ! organic cyclic compound created_by: bf creation_date: 2012-09-14T09:03:51Z -[Term] -id: GO:1901361 -name: organic cyclic compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound." [GOC:TermGenie] -synonym: "organic cyclic compound breakdown" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound catabolism" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound degradation" EXACT [GOC:TermGenie] -is_a: GO:1901360 ! organic cyclic compound metabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33832 ! organic cyclic compound -relationship: has_primary_input CHEBI:33832 ! organic cyclic compound -created_by: bf -creation_date: 2012-09-14T09:05:04Z - [Term] id: GO:1901362 name: organic cyclic compound biosynthetic process @@ -45458,22 +44410,6 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ created_by: pr creation_date: 2012-11-04T15:17:52Z -[Term] -id: GO:1901565 -name: organonitrogen compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound." [GOC:pr, GOC:TermGenie] -synonym: "organonitrogen compound breakdown" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound catabolism" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound degradation" EXACT [GOC:TermGenie] -is_a: GO:1901564 ! organonitrogen compound metabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:35352 ! organonitrogen compound -relationship: has_primary_input CHEBI:35352 ! organonitrogen compound -created_by: pr -creation_date: 2012-11-04T15:17:56Z - [Term] id: GO:1901566 name: organonitrogen compound biosynthetic process @@ -45505,9 +44441,6 @@ synonym: "organic substance catabolism" EXACT [] synonym: "organic substance degradation" EXACT [] is_a: GO:0009056 ! catabolic process is_a: GO:0071704 ! organic substance metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:50860 ! organic molecular entity -relationship: has_primary_input CHEBI:50860 ! organic molecular entity created_by: pr creation_date: 2012-11-05T11:04:36Z @@ -45540,28 +44473,14 @@ namespace: biological_process def: "The chemical reactions and pathways involving an alpha-amino acid." [GOC:TermGenie] synonym: "alpha-amino acid metabolism" EXACT [GOC:TermGenie] is_a: GO:0006520 ! amino acid metabolic process +is_a: GO:0019752 ! carboxylic acid metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:78608 ! alpha-amino acid zwitterion relationship: has_primary_input_or_output CHEBI:78608 ! alpha-amino acid zwitterion created_by: tb creation_date: 2012-11-08T17:39:50Z -[Term] -id: GO:1901606 -name: alpha-amino acid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid." [GOC:TermGenie] -synonym: "alpha-amino acid breakdown" EXACT [GOC:TermGenie] -synonym: "alpha-amino acid catabolism" EXACT [GOC:TermGenie] -synonym: "alpha-amino acid degradation" EXACT [GOC:TermGenie] -is_a: GO:1901575 ! organic substance catabolic process -is_a: GO:1901605 ! alpha-amino acid metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:78608 ! alpha-amino acid zwitterion -relationship: has_primary_input CHEBI:78608 ! alpha-amino acid zwitterion -created_by: tb -creation_date: 2012-11-08T17:39:54Z - [Term] id: GO:1901607 name: alpha-amino acid biosynthetic process @@ -45571,7 +44490,8 @@ synonym: "alpha-amino acid anabolism" EXACT [GOC:TermGenie] synonym: "alpha-amino acid biosynthesis" EXACT [GOC:TermGenie] synonym: "alpha-amino acid formation" EXACT [GOC:TermGenie] synonym: "alpha-amino acid synthesis" EXACT [GOC:TermGenie] -is_a: GO:0008652 ! amino acid biosynthetic process +is_a: GO:0046394 ! carboxylic acid biosynthetic process +is_a: GO:1901566 ! organonitrogen compound biosynthetic process is_a: GO:1901605 ! alpha-amino acid metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:78608 ! alpha-amino acid zwitterion @@ -45651,38 +44571,6 @@ relationship: positively_regulates GO:0070925 ! organelle assembly created_by: pr creation_date: 2013-05-14T09:43:36Z -[Term] -id: GO:1902369 -name: negative regulation of RNA catabolic process -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process." [GOC:bf, GOC:TermGenie, PMID:16640457] -synonym: "down regulation of RNA breakdown" EXACT [GOC:TermGenie] -synonym: "down regulation of RNA catabolic process" EXACT [GOC:TermGenie] -synonym: "down regulation of RNA catabolism" EXACT [GOC:TermGenie] -synonym: "down regulation of RNA degradation" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA breakdown" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA catabolic process" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA catabolism" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA degradation" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA breakdown" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA catabolic process" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA catabolism" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA degradation" EXACT [GOC:TermGenie] -synonym: "inhibition of RNA breakdown" NARROW [GOC:TermGenie] -synonym: "inhibition of RNA catabolic process" NARROW [GOC:TermGenie] -synonym: "inhibition of RNA catabolism" NARROW [GOC:TermGenie] -synonym: "inhibition of RNA degradation" NARROW [GOC:TermGenie] -synonym: "negative regulation of RNA breakdown" EXACT [GOC:TermGenie] -synonym: "negative regulation of RNA catabolism" EXACT [GOC:TermGenie] -synonym: "negative regulation of RNA degradation" EXACT [GOC:TermGenie] -is_a: GO:0031330 ! negative regulation of cellular catabolic process -is_a: GO:0051253 ! negative regulation of RNA metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006401 ! RNA catabolic process -relationship: negatively_regulates GO:0006401 ! RNA catabolic process -created_by: bf -creation_date: 2013-08-22T14:59:39Z - [Term] id: GO:1902494 name: catalytic complex @@ -45752,7 +44640,6 @@ synonym: "negative regulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA formation" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA synthesis" EXACT [GOC:TermGenie] is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process -is_a: GO:0031327 ! negative regulation of cellular biosynthetic process is_a: GO:0051253 ! negative regulation of RNA metabolic process is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0065007 ! biological regulation @@ -45791,7 +44678,6 @@ synonym: "upregulation of RNA biosynthetic process" EXACT [GOC:TermGenie] synonym: "upregulation of RNA formation" EXACT [GOC:TermGenie] synonym: "upregulation of RNA synthesis" EXACT [GOC:TermGenie] is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0051254 ! positive regulation of RNA metabolic process is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0065007 ! biological regulation @@ -46076,19 +44962,6 @@ relationship: positively_regulates GO:0032940 ! secretion by cell created_by: pm creation_date: 2014-10-08T13:25:17Z -[Term] -id: GO:1903561 -name: extracellular vesicle -namespace: cellular_component -def: "Any vesicle that is part of the extracellular region." [GO_REF:0000064, GOC:pm, GOC:TermGenie, PMID:24769233] -synonym: "microparticle" RELATED [GOC:vesicles] -is_a: GO:0031982 ! vesicle -is_a: GO:0065010 ! extracellular membrane-bounded organelle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl -creation_date: 2014-10-22T14:26:11Z - [Term] id: GO:1903729 name: regulation of plasma membrane organization @@ -46149,96 +45022,6 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ created_by: jl creation_date: 2015-01-20T14:32:33Z -[Term] -id: GO:1904350 -name: regulation of protein catabolic process in the vacuole -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:25635054] -synonym: "regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -is_a: GO:0042176 ! regulation of protein catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0007039 ! protein catabolic process in the vacuole -relationship: regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl -creation_date: 2015-06-12T09:10:36Z - -[Term] -id: GO:1904351 -name: negative regulation of protein catabolic process in the vacuole -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:25635054] -synonym: "down regulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "down regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "down regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "down regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "down regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "down-regulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "down-regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "down-regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "down-regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "down-regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "downregulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "downregulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "downregulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "downregulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "downregulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "inhibition of protein catabolic process in the vacuole" NARROW [GOC:TermGenie] -synonym: "inhibition of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "inhibition of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "inhibition of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "inhibition of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "negative regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "negative regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "negative regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "negative regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -is_a: GO:0042177 ! negative regulation of protein catabolic process -is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0007039 ! protein catabolic process in the vacuole -relationship: negatively_regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl -creation_date: 2015-06-12T09:10:42Z - -[Term] -id: GO:1904352 -name: positive regulation of protein catabolic process in the vacuole -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:25635054] -synonym: "activation of protein catabolic process in the vacuole" NARROW [GOC:TermGenie] -synonym: "activation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "activation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "activation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "activation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "positive regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "positive regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "positive regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "positive regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "up regulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "up regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "up regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "up regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "up regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "up-regulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "up-regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "up-regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "up-regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "up-regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "upregulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "upregulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "upregulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "upregulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "upregulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -is_a: GO:0045732 ! positive regulation of protein catabolic process -is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0007039 ! protein catabolic process in the vacuole -relationship: positively_regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl -creation_date: 2015-06-12T09:10:49Z - [Term] id: GO:1904375 name: regulation of protein localization to cell periphery @@ -46421,52 +45204,6 @@ relationship: part_of GO:0016236 ! macroautophagy created_by: bf creation_date: 2016-03-08T14:18:10Z -[Term] -id: GO:1905153 -name: regulation of membrane invagination -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of membrane invagination." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353] -is_a: GO:0051128 ! regulation of cellular component organization -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0010324 ! membrane invagination -relationship: regulates GO:0010324 ! membrane invagination -created_by: bf -creation_date: 2016-04-18T15:43:54Z - -[Term] -id: GO:1905154 -name: negative regulation of membrane invagination -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353] -synonym: "down regulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "down-regulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "downregulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "inhibition of membrane invagination" NARROW [GOC:TermGenie] -is_a: GO:0051129 ! negative regulation of cellular component organization -is_a: GO:1905153 ! regulation of membrane invagination -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0010324 ! membrane invagination -relationship: negatively_regulates GO:0010324 ! membrane invagination -created_by: bf -creation_date: 2016-04-18T15:44:04Z - -[Term] -id: GO:1905155 -name: positive regulation of membrane invagination -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of membrane invagination." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie] -synonym: "activation of membrane invagination" NARROW [GOC:TermGenie] -synonym: "up regulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "up-regulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "upregulation of membrane invagination" EXACT [GOC:TermGenie] -is_a: GO:0051130 ! positive regulation of cellular component organization -is_a: GO:1905153 ! regulation of membrane invagination -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0010324 ! membrane invagination -relationship: positively_regulates GO:0010324 ! membrane invagination -created_by: bf -creation_date: 2016-04-18T15:44:12Z - [Term] id: GO:1905475 name: regulation of protein localization to membrane @@ -46544,68 +45281,11 @@ synonym: "cell nucleus disassembly" EXACT [GOC:TermGenie] is_a: GO:0006997 ! nucleus organization is_a: GO:1903008 ! organelle disassembly intersection_of: GO:0022411 ! cellular component disassembly -intersection_of: results_in_disassembly_of GO:0005634 ! nucleus -relationship: results_in_disassembly_of GO:0005634 ! nucleus +intersection_of: results_in_disassembly_of GO:0005634 ! cell nucleus +relationship: results_in_disassembly_of GO:0005634 ! cell nucleus created_by: pr creation_date: 2016-11-14T13:38:57Z -[Term] -id: GO:1905952 -name: regulation of lipid localization -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] -synonym: "regulation of lipid localisation" EXACT [GOC:TermGenie] -is_a: GO:0032879 ! regulation of localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0010876 ! lipid localization -relationship: regulates GO:0010876 ! lipid localization -created_by: rz -creation_date: 2017-02-21T12:12:22Z - -[Term] -id: GO:1905953 -name: negative regulation of lipid localization -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] -synonym: "down regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "down regulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "down-regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "down-regulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "downregulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "downregulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "inhibition of lipid localisation" NARROW [GOC:TermGenie] -synonym: "inhibition of lipid localization" NARROW [GOC:TermGenie] -synonym: "negative regulation of lipid localisation" EXACT [GOC:TermGenie] -is_a: GO:0048519 ! negative regulation of biological process -is_a: GO:1905952 ! regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0010876 ! lipid localization -relationship: negatively_regulates GO:0010876 ! lipid localization -created_by: rz -creation_date: 2017-02-21T12:12:41Z - -[Term] -id: GO:1905954 -name: positive regulation of lipid localization -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] -synonym: "activation of lipid localisation" NARROW [GOC:TermGenie] -synonym: "activation of lipid localization" NARROW [GOC:TermGenie] -synonym: "positive regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "up regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "up regulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "up-regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "up-regulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "upregulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "upregulation of lipid localization" EXACT [GOC:TermGenie] -is_a: GO:0048518 ! positive regulation of biological process -is_a: GO:1905952 ! regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0010876 ! lipid localization -relationship: positively_regulates GO:0010876 ! lipid localization -created_by: rz -creation_date: 2017-02-21T12:12:49Z - [Term] id: GO:1990234 name: transferase complex @@ -46618,19 +45298,6 @@ relationship: capable_of GO:0016740 ! transferase activity created_by: bhm creation_date: 2013-11-12T13:20:12Z -[Term] -id: GO:1990351 -name: transporter complex -namespace: cellular_component -def: "A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells." [GOC:bhm, PMID:15449578] -comment: An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay). -is_a: GO:0032991 ! protein-containing complex -intersection_of: GO:0032991 ! protein-containing complex -intersection_of: capable_of GO:0005215 ! transporter activity -relationship: capable_of GO:0005215 ! transporter activity -created_by: bhm -creation_date: 2014-03-26T14:23:27Z - [Term] id: GO:1990778 name: protein localization to cell periphery @@ -46678,6 +45345,19 @@ relationship: has_part CHEBI:33697 ! ribonucleic acid created_by: pr creation_date: 2015-11-19T12:26:37Z +[Term] +id: GO:2000026 +name: regulation of multicellular organismal development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of multicellular organismal development." [GOC:obol] +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007275 ! multicellular organism development +relationship: regulates GO:0007275 ! multicellular organism development +created_by: tb +creation_date: 2010-08-05T11:25:59Z + [Term] id: GO:2000241 name: regulation of reproductive process @@ -46726,8 +45406,9 @@ synonym: "regulation of cellular amino acid anabolism" EXACT [GOC:obol] synonym: "regulation of cellular amino acid biosynthesis" EXACT [GOC:obol] synonym: "regulation of cellular amino acid formation" EXACT [GOC:obol] synonym: "regulation of cellular amino acid synthesis" EXACT [GOC:obol] -is_a: GO:0006521 ! regulation of cellular amino acid metabolic process is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0051171 ! regulation of nitrogen compound metabolic process +is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008652 ! amino acid biosynthetic process relationship: regulates GO:0008652 ! amino acid biosynthetic process @@ -46745,7 +45426,8 @@ synonym: "negative regulation of amino acid formation" EXACT [GOC:obol] synonym: "negative regulation of amino acid synthesis" EXACT [GOC:obol] synonym: "negative regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol] is_a: GO:0031327 ! negative regulation of cellular biosynthetic process -is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process +is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process +is_a: GO:0062014 ! negative regulation of small molecule metabolic process is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008652 ! amino acid biosynthetic process @@ -46764,7 +45446,8 @@ synonym: "positive regulation of amino acid formation" EXACT [GOC:obol] synonym: "positive regulation of amino acid synthesis" EXACT [GOC:obol] synonym: "positive regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol] is_a: GO:0031328 ! positive regulation of cellular biosynthetic process -is_a: GO:0045764 ! positive regulation of amino acid metabolic process +is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process +is_a: GO:0062013 ! positive regulation of small molecule metabolic process is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008652 ! amino acid biosynthetic process @@ -46782,7 +45465,6 @@ synonym: "regulation of RNA biosynthesis" EXACT [GOC:obol] synonym: "regulation of RNA formation" EXACT [GOC:obol] synonym: "regulation of RNA synthesis" EXACT [GOC:obol] is_a: GO:0010556 ! regulation of macromolecule biosynthetic process -is_a: GO:0031326 ! regulation of cellular biosynthetic process is_a: GO:0051252 ! regulation of RNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032774 ! RNA biosynthetic process @@ -46867,7 +45549,7 @@ property_value: IAO:0000117 "Lindsay Cowell" xsd:string id: IDO:0000626 name: appearance of disorder def: "A process by which a disorder comes into existence." [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process relationship: results_in_formation_of OGMS:0000045 ! disorder property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000117 "Alexander Diehl" xsd:string @@ -46879,8 +45561,18 @@ name: root namespace: ncbi_taxonomy synonym: "all" RELATED synonym [] xref: GC_ID:1 +xref: PMID:30365038 +xref: PMID:32761142 is_a: OBI:0100026 +[Term] +id: NCBITaxon:1206794 +name: Ecdysozoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33317 ! Protostomia +property_value: has_rank NCBITaxon:clade + [Term] id: NCBITaxon:131567 name: cellular organisms @@ -46889,6 +45581,133 @@ synonym: "biota" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:1 ! root +[Term] +id: NCBITaxon:147537 +name: Saccharomycotina +namespace: ncbi_taxonomy +synonym: "true yeasts" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:716545 ! saccharomyceta +property_value: has_rank NCBITaxon:subphylum + +[Term] +id: NCBITaxon:147554 +name: Schizosaccharomycetes +namespace: ncbi_taxonomy +synonym: "Archiascomycota" RELATED in_part [] +xref: GC_ID:1 +is_a: NCBITaxon:451866 ! Taphrinomycotina +property_value: has_rank NCBITaxon:class + +[Term] +id: NCBITaxon:197562 +name: Pancrustacea +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:10874751 +xref: PMID:11557979 +is_a: NCBITaxon:197563 ! Mandibulata +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:197563 +name: Mandibulata +namespace: ncbi_taxonomy +synonym: "mandibulates" EXACT OMO:0003003 [] +xref: GC_ID:1 +xref: PMID:11557979 +xref: PMID:9727836 +is_a: NCBITaxon:6656 ! Arthropoda +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:2 +name: Bacteria +namespace: ncbi_taxonomy +synonym: "bacteria" RELATED blast_name [] +synonym: "eubacteria" EXACT genbank_common_name [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11542017 +xref: PMID:11542087 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:270744 +xref: PMID:32628106 +xref: PMID:36748408 +xref: PMID:7520741 +xref: PMID:8123559 +xref: PMID:8186100 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom + +[Term] +id: NCBITaxon:2157 +name: Archaea +namespace: ncbi_taxonomy +synonym: "archaea" RELATED blast_name [] +synonym: "Archaebacteria" RELATED synonym [] +synonym: "Mendosicutes" RELATED synonym [] +synonym: "Metabacteria" RELATED synonym [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11541975 +xref: PMID:11542064 +xref: PMID:11542149 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:25527841 +xref: PMID:270744 +xref: PMID:32628106 +xref: PMID:36748408 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom + [Term] id: NCBITaxon:2759 name: Eukaryota @@ -46898,7 +45717,7 @@ synonym: "Eucaryotae" RELATED synonym [] synonym: "eucaryotes" EXACT genbank_common_name [] synonym: "Eukarya" RELATED synonym [] synonym: "Eukaryotae" RELATED synonym [] -synonym: "eukaryotes" EXACT common_name [] +synonym: "eukaryotes" EXACT OMO:0003003 [] synonym: "eukaryotes" RELATED blast_name [] xref: GC_ID:1 xref: PMID:23020233 @@ -46916,6 +45735,63 @@ xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:clade +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT OMO:0003003 [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:33317 +name: Protostomia +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:34346 +name: Schizosaccharomycetales +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:147554 ! Schizosaccharomycetes +property_value: has_rank NCBITaxon:order + +[Term] +id: NCBITaxon:451864 +name: Dikarya +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:15689432 +xref: PMID:16151185 +xref: PMID:17010206 +xref: PMID:17051209 +xref: PMID:17572334 +is_a: NCBITaxon:4751 ! Fungi +property_value: has_rank NCBITaxon:subkingdom + +[Term] +id: NCBITaxon:451866 +name: Taphrinomycotina +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:4890 ! Ascomycota +property_value: has_rank NCBITaxon:subphylum + [Term] id: NCBITaxon:4751 name: Fungi @@ -46928,6 +45804,162 @@ xref: PMID:12684019 is_a: NCBITaxon:33154 ! Opisthokonta property_value: has_rank NCBITaxon:kingdom +[Term] +id: NCBITaxon:4890 +name: Ascomycota +namespace: ncbi_taxonomy +synonym: "ascomycete fungi" RELATED blast_name [] +synonym: "ascomycetes" EXACT genbank_common_name [] +synonym: "sac fungi" EXACT OMO:0003003 [] +xref: GC_ID:1 +xref: PMID:17572334 +is_a: NCBITaxon:451864 ! Dikarya +property_value: has_rank NCBITaxon:phylum + +[Term] +id: NCBITaxon:4891 +name: Saccharomycetes +namespace: ncbi_taxonomy +synonym: "Hemiascomycetes" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:147537 ! Saccharomycotina +property_value: has_rank NCBITaxon:class + +[Term] +id: NCBITaxon:4892 +name: Saccharomycetales +namespace: ncbi_taxonomy +synonym: "budding yeasts" RELATED blast_name [] +synonym: "Endomycetales" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:4891 ! Saccharomycetes +property_value: has_rank NCBITaxon:order + +[Term] +id: NCBITaxon:4893 +name: Saccharomycetaceae +namespace: ncbi_taxonomy +alt_id: NCBITaxon:221665 +alt_id: NCBITaxon:44280 +xref: GC_ID:1 +is_a: NCBITaxon:4892 ! Saccharomycetales +property_value: has_rank NCBITaxon:family + +[Term] +id: NCBITaxon:4894 +name: Schizosaccharomycetaceae +namespace: ncbi_taxonomy +synonym: "fission yeasts" EXACT genbank_common_name [] +synonym: "Schizosaccharomycetoideae" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:34346 ! Schizosaccharomycetales +property_value: has_rank NCBITaxon:family + +[Term] +id: NCBITaxon:4895 +name: Schizosaccharomyces +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:4894 ! Schizosaccharomycetaceae +property_value: has_rank NCBITaxon:genus + +[Term] +id: NCBITaxon:4896 +name: Schizosaccharomyces pombe +namespace: ncbi_taxonomy +alt_id: NCBITaxon:45042 +synonym: "fission yeast" EXACT genbank_common_name [] +synonym: "Schizosaccharomyces malidevorans" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:4895 ! Schizosaccharomyces +property_value: has_rank NCBITaxon:species + +[Term] +id: NCBITaxon:4930 +name: Saccharomyces +namespace: ncbi_taxonomy +alt_id: NCBITaxon:36915 +synonym: "Pachytichospora" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:4893 ! Saccharomycetaceae +property_value: has_rank NCBITaxon:genus + +[Term] +id: NCBITaxon:4932 +name: Saccharomyces cerevisiae +namespace: ncbi_taxonomy +alt_id: NCBITaxon:41870 +synonym: "baker's yeast" EXACT OMO:0003003 [] +synonym: "brewer's yeast" EXACT genbank_common_name [] +synonym: "Candida robusta" RELATED synonym [] +synonym: "Mycoderma cerevisiae" RELATED synonym [] +synonym: "Saccharomyces capensis" RELATED synonym [] +synonym: "Saccharomyces cerevisiae 'var. diastaticus'" EXACT equivalent_name [] +synonym: "Saccharomyces diastaticus" RELATED synonym [] +synonym: "Saccharomyces italicus" RELATED synonym [] +synonym: "Saccharomyces oviformis" RELATED synonym [] +synonym: "Saccharomyces uvarum var. melibiosus" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:4930 ! Saccharomyces +property_value: has_rank NCBITaxon:species + +[Term] +id: NCBITaxon:50557 +name: Insecta +namespace: ncbi_taxonomy +synonym: "insects" RELATED blast_name [] +synonym: "true insects" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:6960 ! Hexapoda +property_value: has_rank NCBITaxon:class + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:6656 +name: Arthropoda +namespace: ncbi_taxonomy +synonym: "arthropods" EXACT genbank_common_name [] +synonym: "arthropods" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:88770 ! Panarthropoda +property_value: has_rank NCBITaxon:phylum + +[Term] +id: NCBITaxon:6960 +name: Hexapoda +namespace: ncbi_taxonomy +synonym: "Atelocerata" RELATED in_part [] +synonym: "hexapods" RELATED blast_name [] +synonym: "insects" EXACT genbank_common_name [] +synonym: "Tracheata" RELATED in_part [] +synonym: "Uniramia" RELATED in_part [] +xref: GC_ID:1 +is_a: NCBITaxon:197562 ! Pancrustacea +property_value: has_rank NCBITaxon:subphylum + +[Term] +id: NCBITaxon:716545 +name: saccharomyceta +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:4890 ! Ascomycota +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:88770 +name: Panarthropoda +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:1206794 ! Ecdysozoa +property_value: has_rank NCBITaxon:clade + [Term] id: OGMS:0000045 name: disorder @@ -46941,7 +45973,7 @@ name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic [Term] id: PATO:0000033 @@ -47650,6 +46682,23 @@ subset: mpath_slim subset: value_slim is_a: PATO:0002505 ! nucleated +[Term] +id: PATO:0001992 +name: cellularity +namespace: quality +def: "An organismal quality inhering in a bearer by virtue of the bearer's consisting cells." [PATOC:GVG] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0001995 ! organismal quality + +[Term] +id: PATO:0001993 +name: multicellular +namespace: quality +def: "A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell." [PATOC:GVG] +subset: value_slim +is_a: PATO:0001992 ! cellularity + [Term] id: PATO:0001995 name: organismal quality @@ -58312,7 +57361,7 @@ namespace: single_species_phenotype def: "A single species cell morphology phenotype in which fungal hyphae form an increased number of branches." [] synonym: "increased branching of hyphae" EXACT [] synonym: "increased hyphal branching" EXACT [] -is_a: PHIPO:0001205 ! abnormal filament morphology +is_a: PHIPO:0001427 ! abnormal hyphal branching created_by: alaynecuzick creation_date: 2020-03-04T14:33:49Z @@ -60751,6 +59800,258 @@ is_a: PHIPO:0001308 ! normal growth on chemical created_by: alaynecuzick creation_date: 2024-01-30T14:16:53Z +[Term] +id: PHIPO:0001411 +name: resistance to dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001412 +name: sensitive to dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001413 +name: normal growth on dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001414 +name: resistance to thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001415 +name: sensitive to thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001416 +name: normal growth on thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001417 +name: resistance to penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001418 +name: sensitive to penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001419 +name: normal growth on penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001420 +name: resistance to flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001421 +name: sensitive to flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001422 +name: normal growth on flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001423 +name: resistance to imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001424 +name: sensitive to imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001425 +name: normal growth on imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001426 +name: normal growth on fludioxonil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-28T09:44:54Z + +[Term] +id: PHIPO:0001427 +name: abnormal hyphal branching +namespace: single_species_phenotype +def: "A single species cell morphology phenotype in which fungal hyphae branching is abnormal." [] +is_a: PHIPO:0001205 ! abnormal filament morphology +created_by: alaynecuzick +creation_date: 2024-03-04T15:00:58Z + +[Term] +id: PHIPO:0001428 +name: normal growth on brefeldin A +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-12T15:12:17Z + +[Term] +id: PHIPO:0001429 +name: normal growth on fluconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-12T15:14:22Z + +[Term] +id: PHIPO:0001430 +name: resistance to ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001431 +name: sensitive to ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001432 +name: normal growth on ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001433 +name: resistance to cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001434 +name: sensitive to cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001435 +name: normal growth on cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001436 +name: normal growth on caspofungin +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + +[Term] +id: PHIPO:0001437 +name: normal growth on terbinafine +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + +[Term] +id: PHIPO:0001438 +name: normal growth on bifonazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + [Term] id: PR:000000001 name: protein @@ -60784,8 +60085,8 @@ synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: CHEBI:36080 ! protein is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000050567 @@ -60813,6 +60114,7 @@ namespace: uberon def: "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." [span:ProcessualEntity] subset: common_anatomy subset: upper_level +xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 @@ -60833,7 +60135,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 +xref: FBbt:00007001 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -60848,11 +60150,61 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage +relationship: RO:0002496 UBERON:0000106 {gci_filler="NCBITaxon:33208", gci_relation="RO:0002162"} ! existence starts during or after zygote stage +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0000066 +name: fully formed stage +namespace: uberon +def: "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "adult stage" BROAD [] +synonym: "fully formed animal stage" EXACT [] +synonym: "juvenile-adult stage" EXACT [] +xref: BilaDO:0000004 +xref: BTO:0001043 +xref: EFO:0001272 +xref: FBdv:00005369 +xref: WBls:0000041 +xref: XtroDO:0000084 +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000092 ! post-embryonic stage +relationship: preceded_by UBERON:0000111 ! organogenesis stage +relationship: precedes UBERON:0000071 ! death stage +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/566" xsd:anyURI + +[Term] +id: UBERON:0000068 +name: embryo stage +namespace: uberon +def: "A life cycle stage that starts with fertilization and ends with the fully formed embryo." [http://orcid.org/0000-0002-6601-2165] +synonym: "embryogenesis" RELATED [] +synonym: "embryonic stage" EXACT [] +xref: BilaDO:0000002 +xref: EV:0300001 +xref: FBdv:00005289 +xref: FMA:72652 +xref: HsapDv:0000002 +xref: MmusDv:0000002 +xref: OGES:000000 +xref: OGES:000022 +xref: SCTID:296280003 +xref: WBls:0000003 +xref: WBls:0000092 +xref: WBls:0000102 +xref: XAO:1000012 +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +disjoint_from: UBERON:0000092 ! post-embryonic stage +relationship: precedes UBERON:0000066 ! fully formed stage +relationship: precedes UBERON:0000092 ! post-embryonic stage +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development + [Term] id: UBERON:0000071 name: death stage @@ -60864,12 +60216,34 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle +relationship: RO:0002229 UBERON:0000104 ! ends life cycle property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +[Term] +id: UBERON:0000092 +name: post-embryonic stage +namespace: uberon +def: "Stage succeeding embryo, including mature structure." [https://orcid.org/0000-0002-6601-2165] +synonym: "post-hatching stage" NARROW [] +synonym: "postembryonic" RELATED [] +synonym: "postembryonic stage" EXACT [] +xref: BilaDO:0000003 +xref: OGES:000010 +xref: OGES:000014 +xref: OGES:000024 +xref: WBls:0000022 +xref: WBls:0000093 +xref: WBls:0000103 +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +relationship: preceded_by UBERON:0000068 ! embryo stage +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI +property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string + [Term] id: UBERON:0000104 name: life cycle @@ -60890,6 +60264,7 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage +relationship: starts_with UBERON:0000106 {gci_filler="NCBITaxon:33208", gci_relation="RO:0002162"} ! zygote stage property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 @@ -60928,6 +60303,59 @@ property_value: RO:0002175 NCBITaxon:4751 property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +[Term] +id: UBERON:0000106 +name: zygote stage +namespace: uberon +def: "A stage at which the organism is a single cell produced by means of sexual reproduction." [Wikipedia:Zygote] +subset: efo_slim +synonym: "1-cell stage" EXACT [] +synonym: "fertilized egg stage" EXACT [BTO:0000854] +synonym: "fertilized egg stage" RELATED [] +synonym: "one cell stage" EXACT [] +synonym: "one-cell stage" RELATED [VHOG:0000745] +synonym: "zygote" RELATED [VHOG:0000745] +synonym: "zygotum" RELATED OMO:0003011 [Wikipedia:Zygote] +xref: BilaDO:0000005 +xref: BILS:0000106 +xref: EFO:0001322 +xref: EHDAA:27 +xref: FBdv:00005288 +xref: IDOMAL:0000302 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration", https://w3id.org/sssom/author_id="https://orcid.org/0000-0003-4423-4370", https://w3id.org/sssom/mapping_provider="https://github.com/biopragmatics/biomappings"} +xref: NCIT:C12601 +xref: PdumDv:0000100 +xref: VHOG:0000745 +xref: Wikipedia:Zygote +xref: XAO:1000001 +xref: ZFS:0000001 +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 +property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} + +[Term] +id: UBERON:0000111 +name: organogenesis stage +namespace: uberon +def: "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism." [Wikipedia:Organogenesis] +synonym: "segmentation stage" RELATED [] +xref: BilaDO:0000010 +xref: BILS:0000111 +xref: HsapDv:0000015 +xref: MmusDv:0000018 +xref: OGES:000005 +xref: OGES:000032 +xref: Wikipedia:Organogenesis +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI + [Term] id: UBERON:0000465 name: material anatomical entity @@ -60940,7 +60368,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 +xref: FBbt:00007016 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -60952,6 +60380,107 @@ property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0000468 +name: multicellular organism +namespace: uberon +def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, http://orcid.org/0000-0001-9114-8737, Wikipedia:Multi-cellular_organism] +subset: common_anatomy +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "body" RELATED [AEO:0000103, BIRNLEX:18, FMA:256135, NCIT:C13041] +synonym: "Koerper" RELATED [BTO:0001489] +synonym: "multi-cellular organism" EXACT [CARO:0000012] +synonym: "organism" BROAD [FBbt:00000001, VHOG:0000671, WBbt:0007833] +synonym: "whole body" RELATED [BTO:0001489] +synonym: "whole organism" RELATED [FBbt:00000001] +xref: AAO:0010026 +xref: AEO:0000191 +xref: BILA:0000012 +xref: BIRNLEX:18 +xref: BSA:0000038 +xref: BTO:0000042 +xref: CARO:0000012 +xref: EFO:0002906 +xref: EHDAA2:0003103 +xref: EHDAA2:0003191 +xref: EHDAA:1 +xref: EMAPA:25765 +xref: EV:0100016 +xref: FBbt:00000001 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FMA:256135 +xref: galen:Organism +xref: HAO:0000012 +xref: NCIT:C13041 +xref: ncithesaurus:Whole_Organism +xref: SCTID:243928005 +xref: TADS:0000001 +xref: TAO:0001094 +xref: TGMA:0001832 +xref: VHOG:0000671 +xref: WBbt:0007833 +xref: Wikipedia:Multi-cellular_organism +xref: XAO:0003004 +xref: ZFA:0001094 +is_a: UBERON:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: UBPROP:0000007 "organismal" xsd:string + +[Term] +id: UBERON:0000922 +name: embryo +namespace: uberon +def: "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, Wikipedia:Embryo] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "developing organism" RELATED [BILA:0000056] +synonym: "developmental tissue" RELATED [] +synonym: "embryonic organism" EXACT [BILA:0000056] +xref: AAO:0011035 +xref: AEO:0000169 +xref: BILA:0000056 +xref: BSA:0000039 +xref: BTO:0000379 +xref: CALOHA:TS-0229 +xref: EFO:0001367 +xref: EHDAA2:0000002 +xref: EHDAA2_RETIRED:0003236 +xref: EHDAA:38 +xref: EMAPA:16039 +xref: FBbt:00000052 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FMA:69068 +xref: GAID:963 +xref: http://neurolex.org/wiki/Category\:Embryonic_organism +xref: IDOMAL:0000646 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration", https://w3id.org/sssom/author_id="https://orcid.org/0000-0003-4423-4370", https://w3id.org/sssom/mapping_provider="https://github.com/biopragmatics/biomappings"} +xref: MAT:0000226 +xref: MESH:D004622 +xref: MIAA:0000019 +xref: NCIT:C28147 +xref: OGEM:000001 +xref: SCTID:57991002 +xref: UMLS:C0013935 {source="ncithesaurus:Embryo"} +xref: VHOG:0001766 +xref: Wikipedia:Embryo +xref: XAO:0000113 +xref: ZFA:0000103 +is_a: UBERON:0000468 ! multicellular organism +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI +property_value: UBPROP:0000007 "embryonic" xsd:string +property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} + [Term] id: UBERON:0001062 name: anatomical entity @@ -60961,11 +60490,12 @@ subset: common_anatomy subset: upper_level xref: AAO:0010841 xref: AEO:0000000 +xref: BFO:0000004 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 +xref: FBbt:10000000 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -60981,6 +60511,42 @@ property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0009953 +name: post-embryonic organism +namespace: uberon +def: "A multicellular organism that existence_starts_with a post-embryonic stage." [OBOL:automatic] +synonym: "post-hatching organism" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "post-natal organism" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "postnatal mouse" NARROW [MA:0002405] +synonym: "postnatal organism" EXACT [] +synonym: "TS28 mouse" NARROW [MA:0002405] +xref: MA:0002405 +is_a: UBERON:0000468 ! multicellular organism +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: RO:0002489 UBERON:0000092 ! existence starts with post-embryonic stage +relationship: RO:0002489 UBERON:0000092 ! existence starts with post-embryonic stage +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/667" xsd:anyURI + +[Term] +id: UBERON:0010000 +name: multicellular anatomical structure +namespace: uberon +def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] +subset: common_anatomy +subset: upper_level +synonym: "multicellular structure" EXACT [FBbt:00100313] +xref: CARO:0010000 +xref: FBbt:00100313 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular +relationship: has_part CL:0000000 ! cell +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 + [Typedef] id: BFO:0000054 name: realized in @@ -61010,6 +60576,14 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + [Typedef] id: IDO:0000660 name: results_in @@ -61063,7 +60637,7 @@ property_value: IAO:0000116 "A quality inheres in its bearer at all times for wh property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! inheres in -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 @@ -61088,6 +60662,16 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role @@ -61123,7 +60707,6 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z @@ -61132,7 +60715,6 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z @@ -61143,55 +60725,67 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: has_component ! has component -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z +[Typedef] +id: RO:0002081 +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after @@ -61201,6 +60795,38 @@ property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +range: OBI:0100026 +holds_over_chain: capable_of RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002222 name: temporally related to @@ -61214,6 +60840,31 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part_of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: part_of ! part_of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + [Typedef] id: RO:0002263 name: acts upstream of @@ -61231,7 +60882,6 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process @@ -61291,6 +60941,13 @@ inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string + [Typedef] id: RO:0002329 name: part of structure that is capable of @@ -61298,7 +60955,7 @@ def: "this relation holds between c and p when c is part of some c', and c' is c property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002331 @@ -61308,7 +60965,6 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI -property_value: seeAlso Involved:in holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -61321,8 +60977,8 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 @@ -61333,6 +60989,16 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 ! process range: BFO:0000002 ! continuant +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to + [Typedef] id: RO:0002354 name: formed as result of @@ -61415,14 +61081,13 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string @@ -61430,8 +61095,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI holds_over_chain: RO:0002327 occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002434 @@ -61535,6 +61200,72 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002488 ! existence starts during + +[Typedef] +id: RO:0002490 +name: existence overlaps +def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002487 ! relation between physical entity and a process or stage + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: part_of RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part_of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: part_of RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part_of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process @@ -61623,8 +61354,8 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string -domain: BFO:0000020 ! specifically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic +range: BFO:0000020 ! characteristic [Typedef] id: RO:0002584 @@ -61633,7 +61364,7 @@ def: "s 'has part structure that is capable of' p if and only if there exists so property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -61684,7 +61415,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -61693,7 +61424,6 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -61717,7 +61447,6 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -61731,7 +61460,6 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_negative_effect is_a: RO:0002263 ! acts upstream of @@ -61772,7 +61500,6 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: causally_upstream_of ! causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 -created_by: pg creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -61782,7 +61509,6 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p is_a: regulates ! regulates is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 -created_by: pg creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -61848,14 +61574,14 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string +range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 @@ -61874,14 +61600,13 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -61964,44 +61689,6 @@ is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - [Typedef] id: decreased_in_magnitude_relative_to name: obsolete decreased_in_magnitude_relative_to @@ -62062,20 +61749,6 @@ property_value: RO:0002575 RO:0002211 is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: regulates ! regulates -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with - [Typedef] id: ends_during name: ends during @@ -62086,7 +61759,6 @@ xref: RO:0002093 id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 @@ -62098,28 +61770,6 @@ is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes - -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - [Typedef] id: happens_during name: happens during @@ -62132,7 +61782,6 @@ is_a: ends_during ! ends during id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 @@ -62175,7 +61824,7 @@ property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_negative_regulatory_component_activity @@ -62186,7 +61835,6 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z @@ -62203,6 +61851,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -62214,7 +61863,6 @@ name: has_part namespace: external namespace: quality namespace: sequence -namespace: uberon def: "a core relation that holds between a whole and its part" [] def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1] comment: Example: operon has_part gene. @@ -62241,7 +61889,6 @@ name: has participant namespace: external def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string @@ -62250,6 +61897,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: has_part has_participant @@ -62257,7 +61905,7 @@ holds_over_chain: has_part has_participant id: has_primary_input name: has primary input namespace: external -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -62280,7 +61928,7 @@ creation_date: 2018-12-13T11:26:17Z id: has_primary_output name: has primary output namespace: external -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -62288,18 +61936,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -range: BFO:0000019 ! quality -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -62308,7 +61944,6 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: regulated_by ! regulated by is_a: RO:0002017 ! has component activity -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z @@ -62387,7 +62022,6 @@ is_a: immediately_precedes ! immediately precedes id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string @@ -62411,29 +62045,6 @@ property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: capable_of in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: increased_in_magnitude_relative_to name: obsolete increased_in_magnitude_relative_to @@ -62446,18 +62057,6 @@ is_transitive: true is_obsolete: true replaced_by: RO:0015007 -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - [Typedef] id: negatively_regulated_by name: negatively regulated by @@ -62514,44 +62113,28 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process +inverse_of: BFO:0000067 ! contains process transitive_over: part_of ! part_of -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon - [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -62573,7 +62156,6 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term @@ -62609,7 +62191,6 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 property_value: IAO:0000111 "participates in" xsd:string @@ -62665,11 +62246,9 @@ is_a: regulates_characteristic ! regulates characteristic id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string @@ -62686,7 +62265,6 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 @@ -62710,7 +62288,6 @@ is_a: RO:0002410 ! causally related to id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 @@ -62723,7 +62300,6 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco @@ -62786,6 +62362,22 @@ range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic is_a: RO:0002410 ! causally related to +[Typedef] +id: results_in_acquisition_of_features_of +name: results in acquisition of features of +namespace: external +def: "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002315 +property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string +range: UBERON:0000061 ! anatomical structure +is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure +is_a: results_in_developmental_progression_of ! results in developmental progression of + [Typedef] id: results_in_assembly_of name: results in assembly of @@ -62807,6 +62399,22 @@ is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z +[Typedef] +id: results_in_development_of +name: results in development of +namespace: external +def: "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002296 +property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI +is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure +is_a: results_in_developmental_progression_of ! results in developmental progression of + [Typedef] id: results_in_developmental_progression_of name: results in developmental progression of @@ -62817,7 +62425,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions -domain: GO:0008150 ! biological_process +domain: GO:0008150 ! biological process +range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -62839,6 +62448,7 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -62855,18 +62465,6 @@ is_a: IDO:0000660 ! results_in is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of -[Typedef] -id: results_in_fusion_of -name: results in fusion of -namespace: external -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0012008 -is_a: results_in_organization_of ! results in organization of -created_by: pg -creation_date: 2021-02-26T07:28:29Z - [Typedef] id: results_in_organization_of name: results in organization of @@ -62885,26 +62483,10 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 diff --git a/phipo-full.owl b/phipo-full.owl index 228314c..f6312f4 100644 --- a/phipo-full.owl +++ b/phipo-full.owl @@ -1,6 +1,7 @@ - + alaynecuzick 2018-07-09T13:43:00Z Ontology of species-neutral phenotypes observed in pathogen-host interactions. Pathogen Host Interactions Phenotype Ontology https://creativecommons.org/licenses/by/3.0/ - 2024-01-31 + 2024-04-04 @@ -220,6 +221,22 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + @@ -300,6 +317,24 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + + + @@ -452,6 +487,14 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + @@ -572,22 +615,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - @@ -596,9 +623,9 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + @@ -618,6 +645,14 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + @@ -736,6 +771,22 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + @@ -744,6 +795,14 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + @@ -760,14 +819,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -779,14 +831,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -804,14 +849,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + @@ -841,14 +879,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - + @@ -890,13 +921,17 @@ We also have the outstanding issue of how to aim different definitions to differ - + + created by + - + + creation date + @@ -906,12 +941,24 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + @@ -1008,7 +1055,9 @@ We also have the outstanding issue of how to aim different definitions to differ - + + id + @@ -1020,9 +1069,9 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + @@ -1044,12 +1093,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -1068,12 +1111,36 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + + + + + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + @@ -1778,7 +1828,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -1866,7 +1915,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0002131 external - uberon overlaps @@ -1900,10 +1948,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -1914,6 +1958,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -1922,10 +1967,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - @@ -1934,25 +1975,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -1971,7 +2000,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0002180 external - uberon has_component has_component @@ -2101,7 +2129,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -2125,7 +2152,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of @@ -2172,12 +2198,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -2197,7 +2218,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. started by RO:0002224 external - uberon starts_with starts_with @@ -2217,12 +2237,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of ends with Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -2241,7 +2256,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. finished by RO:0002230 external - uberon ends_with ends_with @@ -2353,6 +2367,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_output has output has output + https://wiki.geneontology.org/Has_output @@ -2387,7 +2402,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. affects acts upstream of or within - https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2398,6 +2412,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -2413,6 +2428,29 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + every flower development (GO:0009908) results in development of some flower (PO:0009046) + + p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + + http://www.geneontology.org/GO.doc.development.shtml + RO:0002296 + external + results_in_development_of + + + + results_in_development_of + results in development of + results in development of + + + + @@ -2435,6 +2473,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. results_in_formation_of results in formation of results in formation of + results in formation of anatomical entity @@ -2513,6 +2552,29 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + + GOC:mtg_berkeley_2013 + RO:0002315 + external + results_in_acquisition_of_features_of + + + + results_in_acquisition_of_features_of + results in acquisition of features of + results in acquisition of features of + + + + @@ -2582,11 +2644,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -2635,7 +2692,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. actively involved in enables part of involved in - https://wiki.geneontology.org/Involved_in @@ -2649,6 +2705,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -2792,13 +2849,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of has input - RO:0002352 - uberon - input_of - input_of - input of input of @@ -2813,7 +2865,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0002353 external - uberon output_of @@ -3148,13 +3199,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - @@ -3331,6 +3375,102 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + + existence starts during + + + + + + + + + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + + existence starts with + + + + + + + + + x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence overlaps + + + + + + + + + + + + + + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during + + + + + + + + + x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends with + + + + + + + + + + + + + + + + + + + + + + + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts during or after + + + + @@ -3347,12 +3487,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -3733,7 +3873,6 @@ For example, A and B may be gene products and binding of B by A positively regul RO:0003000 external - uberon produces produces @@ -3754,7 +3893,6 @@ For example, A and B may be gene products and binding of B by A positively regul RO:0003001 external - uberon produced_by produced_by @@ -3800,7 +3938,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -3828,7 +3966,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -3866,7 +4004,6 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -3905,7 +4042,6 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -3926,7 +4062,6 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -3971,32 +4106,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - pg - 2021-02-26T07:28:29Z - RO:0012008 - external - results_in_fusion_of - - - - results_in_fusion_of - results in fusion of - results in fusion of - - - - p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg 2022-09-26T06:07:17Z indirectly causally upstream of @@ -4010,7 +4125,6 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg 2022-09-26T06:08:01Z indirectly regulates @@ -4109,7 +4223,6 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z 2021-11-08T12:00:00Z utilizes device utilizes material @@ -4634,6 +4747,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + process Process a process of cell-division, \ a beating of the heart @@ -4736,6 +4855,7 @@ For example, A and B may be gene products and binding of B by A positively regul (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + realizable realizable entity @@ -4790,6 +4910,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + sdc SpecificallyDependentContinuant @@ -4812,7 +4938,10 @@ For example, A and B may be gene products and binding of B by A positively regul (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + characteristic specifically dependent continuant + https://github.com/OBOFoundry/COB/issues/65 + https://github.com/oborel/obo-relations/pull/284 @@ -4851,8 +4980,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role @@ -11666,6 +11794,36 @@ For example, A and B may be gene products and binding of B by A positively regul cytosine + + + + CAS:71-30-7 + ChemIDplus + + + + + CAS:71-30-7 + KEGG COMPOUND + + + + + CAS:71-30-7 + NIST Chemistry WebBook + + + + + Gmelin:82472 + Gmelin + + + + + PMID:14253484 + Europe PMC + @@ -11745,36 +11903,6 @@ For example, A and B may be gene products and binding of B by A positively regul Beilstein:2637 Beilstein - - - - CAS:71-30-7 - ChemIDplus - - - - - CAS:71-30-7 - KEGG COMPOUND - - - - - CAS:71-30-7 - NIST Chemistry WebBook - - - - - Gmelin:82472 - Gmelin - - - - - PMID:14253484 - Europe PMC - @@ -11863,6 +11991,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -26830,6 +26964,69 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Any compound that produces a peak used to reference an NMR spectrum during data pre-processing. + chebi_ontology + NMR chemical shift reference compounds + NMR chemical shift standard + NMR chemical shift standards + NMR internal standard + NMR internal standards + NMR reference standard + NMR reference standards + CHEBI:228364 + + NMR chemical shift reference compound + + + + + NMR chemical shift reference compounds + ChEBI + + + + + NMR chemical shift standard + ChEBI + + + + + NMR chemical shift standards + ChEBI + + + + + NMR internal standard + ChEBI + + + + + NMR internal standards + ChEBI + + + + + NMR reference standard + ChEBI + + + + + NMR reference standards + ChEBI + + + + @@ -29071,7 +29268,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A role played by the molecular entity or part thereof within a biological context. chebi_ontology @@ -32860,6 +33056,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -52822,7 +53024,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Intended use of the molecular entity or part thereof by humans. chebi_ontology @@ -57210,8 +57411,15 @@ For example, A and B may be gene products and binding of B by A positively regul + An amino-acid residue derived from an alpha-amino acid. + 0 + C2H2NOR + 56.043 + 56.01364 + *-NC([*])C(-*)=O chebi_ontology alpha-amino-acid residues + an alpha-amino acid residue CHEBI:33710 alpha-amino-acid residue @@ -57222,6 +57430,12 @@ For example, A and B may be gene products and binding of B by A positively regul alpha-amino-acid residues ChEBI + + + + an alpha-amino acid residue + UniProt + @@ -90142,7 +90356,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A role is particular behaviour which a material entity may exhibit. chebi_ontology CHEBI:50906 @@ -90647,7 +90861,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A role played by the molecular entity or part thereof within a chemical context. chebi_ontology @@ -95418,13 +95631,6 @@ For example, A and B may be gene products and binding of B by A positively regul hygromycin B(3+) - - - - (1R,2S,3R,5S,6R)-3-azaniumyl-2,6-dihydroxy-5-(methylazaniumyl)cyclohexyl O-6-azaniumyl-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1->2-3)-beta-D-talopyranoside - IUPAC - - @@ -95437,6 +95643,13 @@ For example, A and B may be gene products and binding of B by A positively regul hygromycin B trication ChEBI + + + + (1R,2S,3R,5S,6R)-3-azaniumyl-2,6-dihydroxy-5-(methylazaniumyl)cyclohexyl O-6-azaniumyl-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1->2-3)-beta-D-talopyranoside + IUPAC + + @@ -95532,24 +95745,6 @@ For example, A and B may be gene products and binding of B by A positively regul 3',5'-cyclic AMP(1-) - - - - adenosine 3',5'-cyclic monophosphate - ChEBI - - - - - adenosine 3',5'-cyclic monophosphate anion - ChEBI - - - - - adenosine 3',5'-cyclic monophosphate(1-) - ChEBI - @@ -95587,6 +95782,24 @@ For example, A and B may be gene products and binding of B by A positively regul 3',5'-cyclic AMP anion ChEBI + + + + adenosine 3',5'-cyclic monophosphate + ChEBI + + + + + adenosine 3',5'-cyclic monophosphate anion + ChEBI + + + + + adenosine 3',5'-cyclic monophosphate(1-) + ChEBI + @@ -129893,6 +130106,7 @@ For example, A and B may be gene products and binding of B by A positively regul A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity that has a plasma membrane and results from cellular division. CALOHA:TS-2035 FBbt:00007002 @@ -129903,8 +130117,11 @@ For example, A and B may be gene products and binding of B by A positively regul VHOG:0001533 WBbt:0004017 XAO:0003012 + + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell cell @@ -129917,6 +130134,257 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + A cell that specializes in controlled release of one or more substances. + BTO:0003659 + FMA:86916 + + secretory cell + + + + + A cell that specializes in controlled release of one or more substances. + GOC:tfm + ISBN:0721662544 + + + + + + + + + + + + + + + + + + + + + + + + + + protein secreting cell + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell that lacks a nucleus. + FMA:68647 + non-nucleated cell + anucleate cell + + + + + A cell that lacks a nucleus. + FB:ma + + + + + + + + + + + + + + + + + + + + + + + + + + A cell with a single nucleus. + single nucleate cell + + + + + A cell with a single nucleus. + FB:ma + GOC:tfm + + + + + + + + + + + + + + + + + + + + + + + + + + binucleate cell + + + + + + + + + + + + + + + + + + + + + + + + + + A cell with more than one nucleus. + AEO:0000203 + WBbt:0008074 + syncitium + syncytial cell + syncytium + multinucleate cell + + + + + A cell with more than one nucleus. + FB:ma + + + + + + + + + + + + + + + + + + + + + + + + + + MESH:D005057 + + eukaryotic cell + + + + + + + + + + + + + + + + + + + + + + + + + + fungal cell + + + + @@ -129954,6 +130422,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2017-01-30T18:53:32Z https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 + https://github.com/obophenotype/cell-ontology/issues/448 abnormal cell @@ -129968,41 +130437,77 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - + - + - + - A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. + A cell containing at least one nucleus. - 2009-12-23T10:53:24Z - increased nucleus size + 2010-09-07T03:32:33Z + FMA:67513 + nucleate cell - + - A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. + A cell containing at least one nucleus. GOC:tfm + + + + + + + + + + + + + + + + + + + + + + A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. + precursor cell + + + + + A cell that, by division or terminal differentiation, can give rise to other cell types. + GOC:dos + + + + @@ -130155,126 +130660,75 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The joining of 2 or more lipid bilayer membranes that surround the nucleus. - biological_process - GO:0000740 - nuclear membrane fusion - - - - - The joining of 2 or more lipid bilayer membranes that surround the nucleus. - GOC:elh - - - - - + - + - + - - + + - - + - + - - + + - The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. - GO:0007335 - Wikipedia:Karyogamy - nuclear fusion - nuclear fusion during karyogamy + Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + translation initiation ternary complex assembly biological_process - GO:0000741 - karyogamy + GO:0001677 + formation of translation initiation ternary complex - + - The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. - GOC:elh + Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + GOC:hjd - + - - - - - - - - - - - - - + + - - + + - - + + - Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - translation initiation ternary complex assembly + The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster. biological_process - GO:0001677 - formation of translation initiation ternary complex + GO:0001700 + embryonic development via the syncytial blastoderm - + - Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - GOC:hjd + The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster. + GOC:go_curators + GOC:mtg_sensu @@ -130579,6 +131033,8 @@ For example, A and B may be gene products and binding of B by A positively regul Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -130903,7 +131359,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. transporter activity @@ -130929,131 +131384,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Enables the directed movement of lipids into, out of or within a cell, or between cells. - Reactome:R-HSA-1369028 - Reactome:R-HSA-1369052 - Reactome:R-HSA-174786 - Reactome:R-HSA-5682285 - Reactome:R-HSA-5682311 - Reactome:R-HSA-5683672 - Reactome:R-HSA-5683714 - Reactome:R-HSA-5688397 - Reactome:R-HSA-6801250 - Reactome:R-HSA-8848053 - Reactome:R-HSA-8866329 - lipophorin - molecular_function - apolipoprotein - GO:0005319 - lipid transporter activity - - - - - - - - - - GO_REF:0000090 - - - - - Enables the directed movement of lipids into, out of or within a cell, or between cells. - GOC:ai - - - - - Reactome:R-HSA-1369028 - ABCAs mediate lipid efflux - - - - - Reactome:R-HSA-1369052 - ABCAs mediate lipid influx - - - - - Reactome:R-HSA-174786 - ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex - - - - - Reactome:R-HSA-5682285 - ABCA12 transports lipids from cytosol to extracellular region - - - - - Reactome:R-HSA-5682311 - Defective ABCA12 does not transport lipids from cytosol to extracellular region - - - - - Reactome:R-HSA-5683672 - Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body - - - - - Reactome:R-HSA-5683714 - ABCA3 transports PC, PG from ER membrane to lamellar body - - - - - Reactome:R-HSA-5688397 - Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body - - - - - Reactome:R-HSA-6801250 - TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane - - - - - Reactome:R-HSA-8848053 - ABCA5 transports CHOL from lysosomal lumen to cytosol - - - - - Reactome:R-HSA-8866329 - MTTP lipidates APOB-100, forming a pre-VLDL - - - - @@ -131112,7 +131442,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 GO:0008372 @@ -131129,16 +131458,8 @@ For example, A and B may be gene products and binding of B by A positively regul Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. - Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component - - - - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - GOC:pdt - NIF_Subcellular:sao1337158144 - @@ -131172,8 +131493,8 @@ For example, A and B may be gene products and binding of B by A positively regul + - Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. extracellular region @@ -131274,6 +131595,7 @@ For example, A and B may be gene products and binding of B by A positively regul + cell nucleus nucleus @@ -131351,7 +131673,6 @@ For example, A and B may be gene products and binding of B by A positively regul - cytoplasm @@ -131497,7 +131818,6 @@ For example, A and B may be gene products and binding of B by A positively regul - plasma membrane @@ -131705,47 +132025,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. - RNA breakdown - RNA catabolism - RNA degradation - biological_process - GO:0006401 - - RNA catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. - ISBN:0198506732 - - - - @@ -131843,7 +132122,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + translation @@ -131965,9 +132244,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -132177,18 +132454,17 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + - + The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. @@ -132207,7 +132483,6 @@ For example, A and B may be gene products and binding of B by A positively regul - amino acid metabolic process @@ -132280,25 +132555,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. Wikipedia:Lipid_metabolism lipid metabolism @@ -132316,7 +132574,6 @@ For example, A and B may be gene products and binding of B by A positively regul - lipid metabolic process @@ -132566,7 +132823,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport @@ -132722,50 +132978,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. - biological_process - GO:0006869 - - - - lipid transport - - - - - The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. - ISBN:0198506732 - - - - @@ -132799,7 +133011,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0006886 - intracellular protein transport @@ -132817,56 +133028,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. - GO:0016194 - GO:0016195 - Wikipedia:Exocytosis - vesicle exocytosis - biological_process - nonselective vesicle exocytosis - GO:0006887 - - exocytosis - - - - - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. - GOC:mah - ISBN:0716731363 - PMID:22323285 - - - - @@ -132884,12 +133045,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/go-ontology/issues/24907 https://github.com/geneontology/go-ontology/issues/25268 @@ -132961,48 +133116,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Fusion of the membrane of a transport vesicle with its target membrane. - biological_process - GO:0006906 - vesicle fusion - - - - - Fusion of the membrane of a transport vesicle with its target membrane. - GOC:jid - - - - @@ -133484,46 +133597,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases. - biological_process - vacuolar protein breakdown - vacuolar protein catabolic process - vacuolar protein catabolism - vacuolar protein degradation - GO:0007039 - protein catabolic process in the vacuole - - - - - The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases. - GOC:mah - GOC:vw - - - - @@ -133674,6 +133747,50 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + https://github.com/geneontology/go-ontology/issues/21234 + biological_process + GO:0007275 + + + + Note that this term was 'developmental process'. + multicellular organism development + + + + + The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:dph + GOC:ems + GOC:isa_complete + GOC:tb + + + + @@ -133770,7 +133887,14 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. https://github.com/geneontology/go-ontology/issues/24968 @@ -133793,8 +133917,10 @@ For example, A and B may be gene products and binding of B by A positively regul + A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological process biological_process @@ -134181,25 +134307,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. lipid anabolism lipid biosynthesis @@ -134264,7 +134373,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -134325,59 +134433,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - GO:0043285 - GO:0044266 - biopolymer catabolic process - macromolecule breakdown - macromolecule catabolism - macromolecule degradation - multicellular organismal macromolecule catabolic process - biological_process - cellular macromolecule catabolic process - cellular macromolecule catabolism - cellular macromolecule degradation - GO:0009057 - - macromolecule catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - GOC:mah - - - - - biopolymer catabolic process - GOC:mtg_chebi_dec09 - - - - @@ -134426,6 +134481,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -134434,7 +134490,8 @@ For example, A and B may be gene products and binding of B by A positively regul The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - http://amigo.geneontology.org/amigo/term/GO:0070589 + https://github.com/geneontology/go-ontology/issues/15249 + https://github.com/geneontology/go-ontology/issues/25418 GO:0043284 biopolymer biosynthetic process macromolecule anabolism @@ -134461,48 +134518,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. - https://github.com/geneontology/go-ontology/issues/17904 - amino acid breakdown - amino acid catabolism - amino acid degradation - cellular amino acid catabolic process - biological_process - GO:0009063 - amino acid catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. - GOC:ai - - - - @@ -134729,46 +134744,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. - amine breakdown - amine catabolism - amine degradation - biological_process - GO:0009310 - amine catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. - GOC:jl - ISBN:0198506732 - - - - @@ -134914,6 +134889,109 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + GO:0009795 + embryogenesis and morphogenesis + Wikipedia:Embryogenesis + embryogenesis + embryonal development + biological_process + GO:0009790 + + + + embryo development + + + + + The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + GOC:go_curators + GOC:isa_complete + GOC:mtg_sensu + + + + + + + + + + + + + + + The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. + biological_process + GO:0009791 + + post-embryonic development + + + + + The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. + embryogenesis + biological_process + GO:0009792 + embryo development ending in birth or egg hatching + + + + + The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. + GOC:go_curators + GOC:isa_complete + GOC:mtg_sensu + + + + @@ -135155,131 +135233,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. - regulation of breakdown - regulation of catabolism - regulation of degradation - biological_process - GO:0009894 - regulation of catabolic process - - - - - Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. - down regulation of catabolic process - down-regulation of catabolic process - downregulation of catabolic process - negative regulation of breakdown - negative regulation of catabolism - negative regulation of degradation - inhibition of catabolic process - biological_process - GO:0009895 - negative regulation of catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. - positive regulation of breakdown - positive regulation of catabolism - positive regulation of degradation - up regulation of catabolic process - up-regulation of catabolic process - upregulation of catabolic process - activation of catabolic process - stimulation of catabolic process - biological_process - GO:0009896 - positive regulation of catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. - GOC:go_curators - - - - @@ -135383,9 +135336,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. + + The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. https://github.com/geneontology/go-ontology/issues/22557 + https://github.com/geneontology/go-ontology/issues/25419 Wikipedia:Gene_expression biological_process GO:0010467 @@ -135395,7 +135349,7 @@ For example, A and B may be gene products and binding of B by A positively regul - The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. + The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. GOC:txnOH-2018 PMID:25934543 PMID:31580950 @@ -135417,7 +135371,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135500,7 +135454,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135537,9 +135491,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135575,9 +135529,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135783,43 +135737,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells. - biological_process - GO:0010567 - regulation of ketone catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells. - GOC:dph - GOC:tb - - - - @@ -135929,7 +135846,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135966,7 +135883,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -136092,46 +136009,78 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - + + - - + + - Any process in which a lipid is transported to, or maintained in, a specific location. - lipid localisation + Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process - GO:0010876 - lipid localization + GO:0010720 + positive regulation of cell development - + - Any process in which a lipid is transported to, or maintained in, a specific location. + Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. + biological_process + GO:0010721 + negative regulation of cell development + - - - lipid localisation - GOC:mah + + + Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. + GOC:BHF + GOC:dph + GOC:tb @@ -136327,43 +136276,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The lipid bilayer surrounding any membrane-bounded vesicle in the cell. - NIF_Subcellular:sao1153182838 - cellular_component - GO:0012506 - vesicle membrane - - - - - The lipid bilayer surrounding any membrane-bounded vesicle in the cell. - GOC:mah - GOC:vesicle - - - - @@ -136720,25 +136632,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GO:0006724 GO:0044240 @@ -136832,24 +136727,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. vesicle organisation biological_process @@ -136916,47 +136794,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage. - organic acid breakdown - organic acid catabolism - organic acid degradation - biological_process - GO:0016054 - organic acid catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage. - ISBN:0198506732 - - - - @@ -136986,7 +136823,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + RNA metabolic process @@ -137048,25 +136885,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. https://github.com/geneontology/go-ontology/issues/25421 GO:0006899 @@ -137238,7 +137058,6 @@ For example, A and B may be gene products and binding of B by A positively regul - transferase activity @@ -137892,9 +137711,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -137929,42 +137746,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of exocytosis. - biological_process - GO:0017157 - regulation of exocytosis - - - - - Any process that modulates the frequency, rate or extent of exocytosis. - GOC:go_curators - - - - @@ -138049,42 +137830,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. - regulation of lipid metabolism - biological_process - GO:0019216 - regulation of lipid metabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. - GOC:go_curators - - - - @@ -138255,47 +138000,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. - aromatic compound breakdown - aromatic compound catabolism - aromatic compound degradation - aromatic hydrocarbon catabolic process - aromatic hydrocarbon catabolism - biological_process - GO:0019439 - aromatic compound catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. - GOC:ai - - - - @@ -138966,126 +138670,45 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - - + - - + + - Any process that modulates the frequency, rate or extent of endocytosis. + The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. + https://github.com/geneontology/go-ontology/issues/24390 + Wikipedia:Cellular_differentiation biological_process - GO:0030100 - regulation of endocytosis - - - - - Any process that modulates the frequency, rate or extent of endocytosis. - GOC:go_curators - - - - - - - - - - - - - - - Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. - NIF_Subcellular:sao885490876 - constitutive secretory pathway transport vesicle - Golgi to vacuole transport vesicle - Golgi-vacuole transport vesicle - cellular_component - secretory vesicle - GO:0030133 - Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'. - transport vesicle - - - - - Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. - GOC:mah - PMID:22160157 - - - - - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - https://github.com/geneontology/go-ontology/issues/23112 - GO:0044254 - GO:0044257 - Wikipedia:Protein_catabolism - cellular protein breakdown - cellular protein catabolic process - cellular protein catabolism - cellular protein degradation - protein breakdown - protein catabolism - protein degradation - multicellular organismal protein catabolic process - biological_process - pheromone catabolic process - pheromone catabolism - GO:0030163 - + GO:0030154 + + - - - This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children. - protein catabolic process + + + cell differentiation - + - The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - GOC:mah + The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. + ISBN:0198506732 @@ -139306,41 +138929,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The lipid bilayer surrounding a cytoplasmic vesicle. - cellular_component - GO:0030659 - cytoplasmic vesicle membrane - - - - - The lipid bilayer surrounding a cytoplasmic vesicle. - GOC:mah - - - - @@ -139641,134 +139229,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - regulation of cellular breakdown - regulation of cellular catabolism - regulation of cellular degradation - biological_process - GO:0031329 - regulation of cellular catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - down regulation of cellular catabolic process - down-regulation of cellular catabolic process - downregulation of cellular catabolic process - negative regulation of cellular breakdown - negative regulation of cellular catabolism - negative regulation of cellular degradation - inhibition of cellular catabolic process - biological_process - GO:0031330 - negative regulation of cellular catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - positive regulation of cellular breakdown - positive regulation of cellular catabolism - positive regulation of cellular degradation - up regulation of cellular catabolic process - up-regulation of cellular catabolic process - upregulation of cellular catabolic process - activation of cellular catabolic process - stimulation of cellular catabolic process - biological_process - GO:0031331 - positive regulation of cellular catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - GOC:mah - - - - @@ -139853,173 +139313,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of vesicle fusion. - biological_process - GO:0031338 - regulation of vesicle fusion - - - - - Any process that modulates the frequency, rate or extent of vesicle fusion. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion. - down regulation of vesicle fusion - down-regulation of vesicle fusion - downregulation of vesicle fusion - inhibition of vesicle fusion - biological_process - GO:0031339 - negative regulation of vesicle fusion - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of vesicle fusion. - up regulation of vesicle fusion - up-regulation of vesicle fusion - upregulation of vesicle fusion - activation of vesicle fusion - stimulation of vesicle fusion - biological_process - GO:0031340 - positive regulation of vesicle fusion - - - - - Any process that activates or increases the frequency, rate or extent of vesicle fusion. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - A vesicle found in the cytoplasm of a cell. - GO:0016023 - NIF_Subcellular:sao180601769 - cellular_component - cytoplasmic membrane bounded vesicle - cytoplasmic membrane-enclosed vesicle - cytoplasmic, membrane-bounded vesicle - GO:0031410 - - - - - - - cytoplasmic vesicle - - - - - A vesicle found in the cytoplasm of a cell. - GOC:ai - GOC:mah - GOC:vesicles - - - - @@ -140170,32 +139463,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 - NIF_Subcellular:sao221389602 - Wikipedia:Vesicle_(biology) - cellular_component - membrane-bounded vesicle - membrane-enclosed vesicle - GO:0031982 - - vesicle - - - - - Any small, fluid-filled, spherical organelle enclosed by membrane. - GOC:mah - GOC:pz - GOC:vesicles - - - - @@ -140356,278 +139623,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - The directed movement of lipids within cells. - biological_process - GO:0032365 - intracellular lipid transport - - - - - The directed movement of lipids within cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - biological_process - GO:0032368 - regulation of lipid transport - - - - - Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - down regulation of lipid transport - down-regulation of lipid transport - downregulation of lipid transport - inhibition of lipid transport - biological_process - GO:0032369 - negative regulation of lipid transport - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - up regulation of lipid transport - up-regulation of lipid transport - upregulation of lipid transport - activation of lipid transport - stimulation of lipid transport - biological_process - GO:0032370 - positive regulation of lipid transport - - - - - Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells. - biological_process - GO:0032377 - regulation of intracellular lipid transport - - - - - Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells. - down regulation of intracellular lipid transport - down-regulation of intracellular lipid transport - downregulation of intracellular lipid transport - inhibition of intracellular lipid transport - biological_process - GO:0032378 - negative regulation of intracellular lipid transport - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells. - up regulation of intracellular lipid transport - up-regulation of intracellular lipid transport - upregulation of intracellular lipid transport - activation of intracellular lipid transport - stimulation of intracellular lipid transport - biological_process - GO:0032379 - positive regulation of intracellular lipid transport - - - - - Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells. - GOC:mah - - - - @@ -140747,123 +139742,139 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + + - - + - - + + - + - - - - - - - - Any process that modulates the activity of a transporter. - biological_process - GO:0032409 - - regulation of transporter activity - - - - - Any process that modulates the activity of a transporter. - GOC:mah - - - - - - - - + - - + - - + + - + - - - - + - - - - + + + + + + + + - Any process that stops or reduces the activity of a transporter. - down regulation of transporter activity - down-regulation of transporter activity - downregulation of transporter activity - inhibition of transporter activity - biological_process - GO:0032410 - - negative regulation of transporter activity - - - - - Any process that stops or reduces the activity of a transporter. - GOC:mah - - - - - - - - + - - + - - + + - + - - - - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Any process that activates or increases the activity of a transporter. - up regulation of transporter activity - up-regulation of transporter activity - upregulation of transporter activity - activation of transporter activity - stimulation of transporter activity + + + + + + + + + + + + + + + + + + + + + + + + + Any biological process, occurring at the level of a multicellular organism, pertinent to its function. + + + + + jl + 2012-09-19T16:07:47Z + GO:0044707 + GO:0050874 + organismal physiological process biological_process - GO:0032411 - - positive regulation of transporter activity + single-multicellular organism process + GO:0032501 + + + multicellular organismal process - + - Any process that activates or increases the activity of a transporter. - GOC:mah + Any biological process, occurring at the level of a multicellular organism, pertinent to its function. + GOC:curators + GOC:dph + GOC:isa_complete + GOC:tb @@ -140940,7 +139951,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -140992,41 +140003,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion. - biological_process - GO:0032871 - regulation of karyogamy - - - - - Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion. - GOC:mah - - - - @@ -141681,127 +140657,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - regulation of amine breakdown - regulation of amine catabolism - regulation of amine degradation - regulation of cellular amine catabolic process - biological_process - GO:0033241 - regulation of amine catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - negative regulation of amine breakdown - negative regulation of amine catabolism - negative regulation of amine degradation - negative regulation of cellular amine catabolic process - biological_process - GO:0033242 - negative regulation of amine catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - positive regulation of amine breakdown - positive regulation of amine catabolism - positive regulation of amine degradation - biological_process - GO:0033243 - positive regulation of amine catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - GOC:mah - - - - @@ -141903,7 +140758,7 @@ For example, A and B may be gene products and binding of B by A positively regul kinase inhibitor biological_process GO:0033673 - + negative regulation of kinase activity @@ -141946,7 +140801,7 @@ For example, A and B may be gene products and binding of B by A positively regul stimulation of kinase activity biological_process GO:0033674 - + positive regulation of kinase activity @@ -142094,128 +140949,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - regulation of amide breakdown - regulation of amide catabolism - regulation of amide degradation - regulation of cellular amide catabolic process - biological_process - GO:0034251 - regulation of amide catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - negative regulation of amide breakdown - negative regulation of amide catabolism - negative regulation of cellular amide catabolic process - biological_process - negative regulation of amide degradation - GO:0034252 - negative regulation of amide catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - positive regulation of amide breakdown - positive regulation of amide catabolism - positive regulation of cellular amide catabolic process - biological_process - positive regulation of amide degradation - GO:0034253 - positive regulation of amide catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - GOC:mah - - - - @@ -142429,9 +141162,11 @@ For example, A and B may be gene products and binding of B by A positively regul The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. + https://github.com/geneontology/go-ontology/issues/26424 cellular nitrogen compound metabolism biological_process GO:0034641 + cellular nitrogen compound metabolic process @@ -142487,53 +141222,45 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - - - - - + - - + + + + + + + + - The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. - nucleobase, nucleoside, nucleotide and nucleic acid breakdown - nucleobase, nucleoside, nucleotide and nucleic acid catabolism - nucleobase, nucleoside, nucleotide and nucleic acid degradation + The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex. biological_process - nucleobase, nucleoside, nucleotide and nucleic acid catabolic process - GO:0034655 - - nucleobase-containing compound catabolic process + GO:0035190 + syncytial nuclear migration - + - The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. - GOC:mah - - - - - nucleobase, nucleoside, nucleotide and nucleic acid catabolic process - GOC:dph - GOC:tb + The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex. + GOC:bf + ISBN:0879694238 + PMID:8314839 @@ -142676,6 +141403,48 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of embryonic development. + up regulation of embryonic development + up-regulation of embryonic development + upregulation of embryonic development + activation of embryonic development + stimulation of embryonic development + biological_process + GO:0040019 + positive regulation of embryonic development + + + + + Any process that activates or increases the frequency, rate or extent of embryonic development. + GOC:go_curators + + + + @@ -142784,287 +141553,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - https://github.com/geneontology/go-ontology/issues/23112 - kmv - 2014-08-21T15:05:45Z - GO:1903362 - GO:2000598 - regulation of cellular protein breakdown - regulation of cellular protein catabolic process - regulation of cellular protein catabolism - regulation of cellular protein degradation - regulation of protein breakdown - regulation of protein catabolism - regulation of protein degradation - regulation of cyclin breakdown - regulation of cyclin catabolic process - regulation of cyclin catabolism - regulation of cyclin degradation - regulation of degradation of cyclin - biological_process - GO:0042176 - regulation of protein catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - GOC:go_curators - GOC:jl - - - - - regulation of cellular protein breakdown - GOC:TermGenie - - - - - regulation of cellular protein catabolism - GOC:TermGenie - - - - - regulation of cellular protein degradation - GOC:TermGenie - - - - - regulation of cyclin breakdown - GOC:obol - - - - - regulation of cyclin catabolism - GOC:obol - - - - - regulation of cyclin degradation - GOC:obol - - - - - regulation of degradation of cyclin - GOC:obol - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process. - https://github.com/geneontology/go-ontology/issues/23112 - GO:1903363 - GO:2000599 - down regulation of cellular protein breakdown - down regulation of cellular protein catabolic process - down regulation of cellular protein catabolism - down regulation of cellular protein degradation - down regulation of protein catabolic process - down-regulation of cellular protein breakdown - down-regulation of cellular protein catabolic process - down-regulation of cellular protein catabolism - down-regulation of cellular protein degradation - down-regulation of protein catabolic process - downregulation of cellular protein breakdown - downregulation of cellular protein catabolic process - downregulation of cellular protein catabolism - downregulation of cellular protein degradation - downregulation of protein catabolic process - negative regulation of cellular protein breakdown - negative regulation of cellular protein catabolic process - negative regulation of cellular protein catabolism - negative regulation of cellular protein degradation - negative regulation of protein breakdown - negative regulation of protein catabolism - negative regulation of protein degradation - inhibition of cellular protein breakdown - inhibition of cellular protein catabolic process - inhibition of cellular protein catabolism - inhibition of cellular protein degradation - inhibition of protein catabolic process - biological_process - GO:0042177 - negative regulation of protein catabolic process - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process. - GOC:TermGenie - GOC:kmv - GOC:obol - GO_REF:0000058 - PMID:24785082 - - - - - down regulation of cellular protein breakdown - GOC:TermGenie - - - - - down regulation of cellular protein catabolic process - GOC:TermGenie - - - - - down regulation of cellular protein catabolism - GOC:TermGenie - - - - - down regulation of cellular protein degradation - GOC:TermGenie - - - - - down-regulation of cellular protein breakdown - GOC:TermGenie - - - - - down-regulation of cellular protein catabolic process - GOC:TermGenie - - - - - down-regulation of cellular protein catabolism - GOC:TermGenie - - - - - down-regulation of cellular protein degradation - GOC:TermGenie - - - - - downregulation of cellular protein breakdown - GOC:TermGenie - - - - - downregulation of cellular protein catabolic process - GOC:TermGenie - - - - - downregulation of cellular protein catabolism - GOC:TermGenie - - - - - downregulation of cellular protein degradation - GOC:TermGenie - - - - - negative regulation of cellular protein breakdown - GOC:TermGenie - - - - - negative regulation of cellular protein catabolism - GOC:TermGenie - - - - - negative regulation of cellular protein degradation - GOC:TermGenie - - - - - inhibition of cellular protein breakdown - GOC:TermGenie - - - - - inhibition of cellular protein catabolic process - GOC:TermGenie - - - - - inhibition of cellular protein catabolism - GOC:TermGenie - - - - - inhibition of cellular protein degradation - GOC:TermGenie - - - - @@ -143147,47 +141635,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. - ketone breakdown - ketone catabolism - ketone degradation - biological_process - GO:0042182 - ketone catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. - GOC:go_curators - - - - @@ -143410,7 +141857,7 @@ For example, A and B may be gene products and binding of B by A positively regul biological_process GO:0043062 - + extracellular structure organization @@ -143471,8 +141918,8 @@ For example, A and B may be gene products and binding of B by A positively regul upregulation of metalloenzyme activity biological_process GO:0043085 + - positive regulation of catalytic activity @@ -143529,7 +141976,7 @@ For example, A and B may be gene products and binding of B by A positively regul negative regulation of metalloenzyme activity biological_process GO:0043086 - + negative regulation of catalytic activity @@ -143655,46 +142102,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. - peptide breakdown - peptide catabolism - peptide degradation - biological_process - GO:0043171 - peptide catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. - GOC:jl - - - - @@ -143727,7 +142134,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organelle @@ -144281,7 +142687,7 @@ For example, A and B may be gene products and binding of B by A positively regul Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. biological_process GO:0043549 - + regulation of kinase activity @@ -144367,43 +142773,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. - cellular amide catabolic process - biological_process - GO:0043605 - amide catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. - GOC:curators - - - - @@ -144765,7 +143134,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -144774,7 +143143,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -144818,7 +143187,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2009-04-21T04:07:27Z biological_process GO:0044092 - + negative regulation of molecular function @@ -144856,7 +143225,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2009-04-21T04:11:06Z biological_process GO:0044093 - + positive regulation of molecular function @@ -145088,29 +143457,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. - nitrogen compound breakdown - nitrogen compound catabolism - nitrogen compound degradation - biological_process - GO:0044270 - cellular nitrogen compound catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. - GOC:jl - ISBN:0198506732 - - - - @@ -145162,30 +143508,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. - jl - 2010-01-26T12:06:10Z - small molecule catabolism - biological_process - GO:0044282 - Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. - small molecule catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. - GOC:curators - GOC:vw - - - - @@ -145198,7 +143520,6 @@ For example, A and B may be gene products and binding of B by A positively regul biological_process GO:0044283 - Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule biosynthetic process @@ -145472,46 +143793,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. - GO:0006947 - cell fusion - cell-cell fusion - biological_process - GO:0045026 - plasma membrane fusion - - - - - The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. - GOC:elh - GOC:mtg_muscle - - - - @@ -145616,6 +143897,125 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. + biological_process + GO:0045595 + regulation of cell differentiation + + + + + Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. + down regulation of cell differentiation + down-regulation of cell differentiation + downregulation of cell differentiation + inhibition of cell differentiation + biological_process + GO:0045596 + negative regulation of cell differentiation + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of cell differentiation. + up regulation of cell differentiation + up-regulation of cell differentiation + upregulation of cell differentiation + activation of cell differentiation + stimulation of cell differentiation + biological_process + GO:0045597 + positive regulation of cell differentiation + + + + + Any process that activates or increases the frequency, rate or extent of cell differentiation. + GOC:go_curators + + + + @@ -145631,9 +144031,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -145696,217 +144094,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - https://github.com/geneontology/go-ontology/issues/23112 - GO:1903364 - GO:2000600 - positive regulation of cellular protein breakdown - positive regulation of cellular protein catabolic process - positive regulation of cellular protein catabolism - positive regulation of cellular protein degradation - positive regulation of protein breakdown - positive regulation of protein catabolism - positive regulation of protein degradation - up regulation of cellular protein breakdown - up regulation of cellular protein catabolic process - up regulation of cellular protein catabolism - up regulation of cellular protein degradation - up regulation of protein catabolic process - up-regulation of cellular protein breakdown - up-regulation of cellular protein catabolic process - up-regulation of cellular protein catabolism - up-regulation of cellular protein degradation - up-regulation of protein catabolic process - upregulation of cellular protein breakdown - upregulation of cellular protein catabolic process - upregulation of cellular protein catabolism - upregulation of cellular protein degradation - upregulation of protein catabolic process - activation of cellular protein breakdown - activation of cellular protein catabolic process - activation of cellular protein catabolism - activation of cellular protein degradation - activation of protein catabolic process - positive regulation of cyclin breakdown - positive regulation of cyclin catabolic process - positive regulation of cyclin catabolism - positive regulation of cyclin degradation - positive regulation of degradation of cyclin - stimulation of protein catabolic process - biological_process - GO:0045732 - positive regulation of protein catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - GOC:go_curators - - - - - positive regulation of cellular protein breakdown - GOC:TermGenie - - - - - positive regulation of cellular protein catabolism - GOC:TermGenie - - - - - positive regulation of cellular protein degradation - GOC:TermGenie - - - - - up regulation of cellular protein breakdown - GOC:TermGenie - - - - - up regulation of cellular protein catabolic process - GOC:TermGenie - - - - - up regulation of cellular protein catabolism - GOC:TermGenie - - - - - up regulation of cellular protein degradation - GOC:TermGenie - - - - - up-regulation of cellular protein breakdown - GOC:TermGenie - - - - - up-regulation of cellular protein catabolic process - GOC:TermGenie - - - - - up-regulation of cellular protein catabolism - GOC:TermGenie - - - - - up-regulation of cellular protein degradation - GOC:TermGenie - - - - - upregulation of cellular protein breakdown - GOC:TermGenie - - - - - upregulation of cellular protein catabolic process - GOC:TermGenie - - - - - upregulation of cellular protein catabolism - GOC:TermGenie - - - - - upregulation of cellular protein degradation - GOC:TermGenie - - - - - activation of cellular protein breakdown - GOC:TermGenie - - - - - activation of cellular protein catabolic process - GOC:TermGenie - - - - - activation of cellular protein catabolism - GOC:TermGenie - - - - - activation of cellular protein degradation - GOC:TermGenie - - - - - positive regulation of cyclin breakdown - GOC:obol - - - - - positive regulation of cyclin catabolism - GOC:obol - - - - - positive regulation of cyclin degradation - GOC:obol - - - - - positive regulation of degradation of cyclin - GOC:obol - - - - @@ -145922,9 +144109,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -145965,9 +144150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -146089,172 +144272,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. - down regulation of endocytosis - down-regulation of endocytosis - downregulation of endocytosis - inhibition of endocytosis - biological_process - GO:0045806 - negative regulation of endocytosis - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of endocytosis. - up regulation of endocytosis - up-regulation of endocytosis - upregulation of endocytosis - activation of endocytosis - stimulation of endocytosis - biological_process - GO:0045807 - positive regulation of endocytosis - - - - - Any process that activates or increases the frequency, rate or extent of endocytosis. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. - down regulation of lipid metabolic process - down-regulation of lipid metabolic process - downregulation of lipid metabolic process - negative regulation of lipid metabolism - inhibition of lipid metabolic process - biological_process - GO:0045833 - negative regulation of lipid metabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. - positive regulation of lipid metabolism - up regulation of lipid metabolic process - up-regulation of lipid metabolic process - upregulation of lipid metabolic process - activation of lipid metabolic process - stimulation of lipid metabolic process - biological_process - GO:0045834 - positive regulation of lipid metabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. - GOC:go_curators - - - - @@ -146506,87 +144523,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. - down regulation of exocytosis - down-regulation of exocytosis - downregulation of exocytosis - inhibition of exocytosis - biological_process - GO:0045920 - negative regulation of exocytosis - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of exocytosis. - up regulation of exocytosis - up-regulation of exocytosis - upregulation of exocytosis - activation of exocytosis - stimulation of exocytosis - biological_process - GO:0045921 - positive regulation of exocytosis - - - - - Any process that activates or increases the frequency, rate or extent of exocytosis. - GOC:go_curators - - - - @@ -146852,84 +144788,119 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - - - - + + + - - + + - The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. - nucleobase anabolism - nucleobase biosynthesis - nucleobase formation - nucleobase synthesis + Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. + down regulation of embryonic development + down-regulation of embryonic development + downregulation of embryonic development + inhibition of embryonic development biological_process - GO:0046112 - nucleobase biosynthetic process + GO:0045992 + negative regulation of embryonic development - + - The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. - GOC:ai + Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. + GOC:go_curators - + - + - + - + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of embryonic development. + biological_process + GO:0045995 + regulation of embryonic development + + + + + Any process that modulates the frequency, rate or extent of embryonic development. + GOC:go_curators + + + + + + + + + + + + + - - - + + + - + - The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. - nucleobase breakdown - nucleobase catabolism - nucleobase degradation + The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. + nucleobase anabolism + nucleobase biosynthesis + nucleobase formation + nucleobase synthesis biological_process - GO:0046113 - nucleobase catabolic process + GO:0046112 + nucleobase biosynthetic process - + - The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. + The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. GOC:ai @@ -147023,45 +144994,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. - carboxylic acid breakdown - carboxylic acid catabolism - carboxylic acid degradation - biological_process - GO:0046395 - carboxylic acid catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. - ISBN:0198506732 - - - - @@ -147099,145 +145031,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). - heterocycle breakdown - heterocycle catabolism - heterocycle degradation - biological_process - GO:0046700 - heterocycle catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). - GOC:ai - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - positive regulation of lipid anabolism - positive regulation of lipid biosynthesis - positive regulation of lipid formation - positive regulation of lipid synthesis - positive regulation of lipogenesis - up regulation of lipid biosynthetic process - up-regulation of lipid biosynthetic process - upregulation of lipid biosynthetic process - activation of lipid biosynthetic process - stimulation of lipid biosynthetic process - biological_process - GO:0046889 - positive regulation of lipid biosynthetic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - GOC:ai - - - - - positive regulation of lipogenesis - GOC:sl - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - regulation of lipid anabolism - regulation of lipid biosynthesis - regulation of lipid formation - regulation of lipid synthesis - regulation of lipogenesis - biological_process - GO:0046890 - regulation of lipid biosynthetic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - GOC:ai - - - - - regulation of lipogenesis - GOC:sl - - - - @@ -147428,43 +145221,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The creation of a single organelle from two or more organelles. - biological_process - GO:0048284 - - - organelle fusion - - - - - The creation of a single organelle from two or more organelles. - GOC:jid - - - - @@ -147502,49 +145258,81 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - + + - + - The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei. + + + + + + + The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. + https://github.com/geneontology/go-ontology/issues/24390 biological_process - nuclear membrane fusion during karyogamy - GO:0048288 - nuclear membrane fusion involved in karyogamy + terminal differentiation + GO:0048468 + + cell development - + - The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei. - GOC:jid + The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. + GOC:go_curators - + - nuclear membrane fusion during karyogamy + terminal differentiation GOC:dph GOC:tb + + + + + Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + https://github.com/geneontology/go-ontology/issues/25943 + Wikipedia:Organogenesis + development of an organ + organogenesis + biological_process + GO:0048513 + animal organ development + + + + + Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + GOC:dph + GOC:jid + + + + @@ -147717,6 +145505,124 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + biological_process + GO:0048580 + regulation of post-embryonic development + + + + + Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + down regulation of post-embryonic development + down-regulation of post-embryonic development + downregulation of post-embryonic development + inhibition of post-embryonic development + biological_process + GO:0048581 + negative regulation of post-embryonic development + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + up regulation of post-embryonic development + up-regulation of post-embryonic development + upregulation of post-embryonic development + activation of post-embryonic development + stimulation of post-embryonic development + biological_process + GO:0048582 + positive regulation of post-embryonic development + + + + + Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + GOC:jid + + + + @@ -147791,7 +145697,24 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. https://github.com/geneontology/go-ontology/issues/26424 development of an anatomical structure @@ -148090,8 +146013,8 @@ For example, A and B may be gene products and binding of B by A positively regul regulation of metalloenzyme activity biological_process GO:0050790 + - regulation of catalytic activity @@ -148105,6 +146028,41 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + biological_process + GO:0050793 + regulation of developmental process + + + + + Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:go_curators + + + + @@ -148171,134 +146129,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - regulation of lipid breakdown - regulation of lipid catabolism - regulation of lipid degradation - biological_process - GO:0050994 - regulation of lipid catabolic process - - - - - Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - GOC:ai - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - down regulation of lipid catabolic process - down-regulation of lipid catabolic process - downregulation of lipid catabolic process - negative regulation of lipid breakdown - negative regulation of lipid catabolism - negative regulation of lipid degradation - inhibition of lipid catabolic process - biological_process - GO:0050995 - negative regulation of lipid catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - GOC:ai - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - positive regulation of lipid breakdown - positive regulation of lipid catabolism - positive regulation of lipid degradation - up regulation of lipid catabolic process - up-regulation of lipid catabolic process - upregulation of lipid catabolic process - activation of lipid catabolic process - stimulation of lipid catabolic process - biological_process - GO:0050996 - positive regulation of lipid catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - GOC:ai - - - - @@ -148532,58 +146362,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - down regulation of lipid biosynthetic process - down-regulation of lipid biosynthetic process - downregulation of lipid biosynthetic process - negative regulation of lipid anabolism - negative regulation of lipid biosynthesis - negative regulation of lipid formation - negative regulation of lipid synthesis - negative regulation of lipogenesis - inhibition of lipid biosynthetic process - biological_process - GO:0051055 - negative regulation of lipid biosynthetic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - GOC:ai - - - - - negative regulation of lipogenesis - GOC:sl - - - - @@ -148658,6 +146436,87 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + down regulation of developmental process + down-regulation of developmental process + downregulation of developmental process + inhibition of developmental process + biological_process + GO:0051093 + negative regulation of developmental process + + + + + Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + up regulation of developmental process + up-regulation of developmental process + upregulation of developmental process + activation of developmental process + stimulation of developmental process + biological_process + GO:0051094 + positive regulation of developmental process + + + + + Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:ai + + + + @@ -149266,6 +147125,124 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. + biological_process + GO:0051239 + regulation of multicellular organismal process + + + + + Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. + GOC:ai + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. + up regulation of multicellular organismal process + up-regulation of multicellular organismal process + upregulation of multicellular organismal process + activation of multicellular organismal process + stimulation of multicellular organismal process + biological_process + GO:0051240 + positive regulation of multicellular organismal process + + + + + Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. + down regulation of multicellular organismal process + down-regulation of multicellular organismal process + downregulation of multicellular organismal process + inhibition of multicellular organismal process + biological_process + GO:0051241 + negative regulation of multicellular organismal process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. + GOC:ai + + + + @@ -149678,8 +147655,8 @@ For example, A and B may be gene products and binding of B by A positively regul transferase regulator biological_process GO:0051338 + - This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity @@ -149723,8 +147700,8 @@ For example, A and B may be gene products and binding of B by A positively regul stimulation of transferase activity biological_process GO:0051347 + - This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity @@ -149767,8 +147744,8 @@ For example, A and B may be gene products and binding of B by A positively regul inhibition of transferase activity biological_process GO:0051348 + - This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity @@ -149937,49 +147914,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole. - GO:0042146 - biological_process - heterotypic vacuole fusion (non-autophagic) - heterotypic vacuole fusion, non-autophagic - GO:0051469 - vesicle fusion with vacuole - - - - - The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole. - GOC:ai - - - - @@ -150125,50 +148059,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. - cytoplasmic vesicle localization - establishment and maintenance of vesicle localization - vesicle localisation - biological_process - GO:0051648 - vesicle localization - - - - - Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. - GOC:ai - - - - - vesicle localisation - GOC:mah - - - - @@ -150243,44 +148133,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - The directed movement of a vesicle to a specific location. - establishment of vesicle localisation - biological_process - GO:0051650 - establishment of vesicle localization - - - - - The directed movement of a vesicle to a specific location. - GOC:ai - - - - - establishment of vesicle localisation - GOC:mah - - - - @@ -150937,8 +148789,8 @@ For example, A and B may be gene products and binding of B by A positively regul + - nucleobase-containing small molecule metabolic process @@ -150986,6 +148838,42 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. + biological_process + GO:0060284 + regulation of cell development + + + + + Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. + GOC:dph + GOC:tb + + + + @@ -151074,45 +148962,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. - dph - 2009-05-18T02:29:43Z - biological_process - GO:0060627 - regulation of vesicle-mediated transport - - - - - Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. - GOC:dph - GOC:tb - - - - @@ -151152,7 +149001,6 @@ For example, A and B may be gene products and binding of B by A positively regul - membrane organization @@ -151177,50 +149025,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The membrane organization process that joins two lipid bilayers to form a single membrane. - jl - 2010-02-08T02:48:06Z - GO:0006944 - GO:0044801 - Wikipedia:Lipid_bilayer_fusion - cellular membrane fusion - biological_process - single-organism membrane fusion - GO:0061025 - - membrane fusion - - - - - The membrane organization process that joins two lipid bilayers to form a single membrane. - GOC:dph - GOC:tb - - - - @@ -151690,7 +149494,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + protein-containing complex assembly @@ -151755,7 +149559,6 @@ For example, A and B may be gene products and binding of B by A positively regul - regulation of molecular function @@ -151878,45 +149681,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis. - exocytic constitutive secretory pathway transport vesicle - exocytotic vesicle - cellular_component - GO:0070382 - exocytic vesicle - - - - - A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis. - GOC:kad - GOC:mah - - - - - exocytotic vesicle - GOC:kad - - - - @@ -152446,7 +150210,6 @@ For example, A and B may be gene products and binding of B by A positively regul - The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. mah 2010-10-04T01:51:47Z @@ -152455,12 +150218,6 @@ For example, A and B may be gene products and binding of B by A positively regul cell periphery - - - - The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - GOC:pdt - @@ -152567,7 +150324,7 @@ For example, A and B may be gene products and binding of B by A positively regul protein localization in membrane biological_process GO:0072657 - + protein localization to membrane @@ -153052,46 +150809,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The joining of two lipid bilayers to form a single organelle membrane. - tb - 2009-12-11T11:44:58Z - biological_process - GO:0090174 - organelle membrane fusion - - - - - The joining of two lipid bilayers to form a single organelle membrane. - GOC:ascb_2009 - GOC:dph - GOC:tb - - - - @@ -153115,6 +150832,7 @@ For example, A and B may be gene products and binding of B by A positively regul Any cellular metabolic process involving nucleic acids. + https://github.com/geneontology/go-ontology/issues/26133 tb 2010-04-07T10:18:47Z biological_process @@ -153400,78 +151118,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole. - pr - 2014-02-28T09:49:31Z - biological_process - GO:0097576 - vacuole fusion - - - - - Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole. - GOC:pr - GOC:vw - Wikipedia:Vacuole - - - - - - - - - - - - - - - - - - - - - Any vesicle that is part of the intracellular region. - pr - 2016-03-29T17:39:45Z - cellular_component - GO:0097708 - intracellular vesicle - - - - - Any vesicle that is part of the intracellular region. - GOC:vesicles - - - - @@ -153725,135 +151371,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis. - biological_process - GO:0098876 - vesicle-mediated transport to the plasma membrane - - - - - The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space. - biological_process - GO:0099500 - vesicle fusion to plasma membrane - - - - - Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space. - GOC:aruk - GOC:bc - ISBN:0071120009 - PMID:18618940 - - - - - - - - - - - - - - - - - - - - - - - - - - A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. - cellular_component - GO:0099503 - - secretory vesicle - - - - - A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. - GOC:dos - - - - @@ -153975,7 +151492,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -153990,7 +151507,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154070,138 +151587,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate, or extent of lipid transporter activity. - kmv - 2018-07-06T18:53:55Z - biological_process - GO:0110112 - - regulation of lipid transporter activity - - - - - Any process that modulates the frequency, rate, or extent of lipid transporter activity. - GOC:BHF - GOC:BHF_miRNA - GOC:rph - PMID:27365390 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that increases the frequency, rate, or extent of lipid transporter activity. - kmv - 2018-07-06T19:14:13Z - biological_process - GO:0110113 - - positive regulation of lipid transporter activity - - - - - Any process that increases the frequency, rate, or extent of lipid transporter activity. - GOC:BHF - GOC:BHF_miRNA - GOC:rph - PMID:27365390 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that decreases the frequency, rate, or extent of lipid transporter activity. - kmv - 2018-07-06T19:21:44Z - biological_process - GO:0110114 - - negative regulation of lipid transporter activity - - - - - Any process that decreases the frequency, rate, or extent of lipid transporter activity. - GOC:BHF - GOC:BHF_miRNA - GOC:rph - PMID:27365390 - - - - + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 @@ -154337,44 +151727,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The cellular processes that contribute to exocytosis. - pg - 2017-05-15T13:20:45Z - biological_process - GO:0140029 - - exocytic process - - - - - The cellular processes that contribute to exocytosis. - Wikipedia:Exocytosis - - - - @@ -154383,7 +151735,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154392,7 +151744,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154404,7 +151756,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0140096 - catalytic activity, acting on a protein @@ -154425,7 +151776,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154434,7 +151785,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154446,7 +151797,7 @@ For example, A and B may be gene products and binding of B by A positively regul molecular_function GO:0140098 - + catalytic activity, acting on RNA @@ -154480,61 +151831,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Directly binding to a specific protein and delivering it to a specific cellular location. - https://github.com/geneontology/go-ontology/issues/17073 - pg - 2019-04-01T10:41:38Z - Reactome:R-HSA-9662747 - Reactome:R-HSA-9662818 - molecular_function - protein carrier activity - protein transport chaperone - GO:0140318 - Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation. - protein transporter activity - - - - - Directly binding to a specific protein and delivering it to a specific cellular location. - PMID:18706423 - - - - - Reactome:R-HSA-9662747 - iRHOM2 transports ADAM17 from ER to the Golgi-network - - - - - Reactome:R-HSA-9662818 - iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane - - - - @@ -154584,99 +151880,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of a lipid from a cell, into the extracellular region. - pg - 2019-05-22T11:33:07Z - lipid efflux - biological_process - GO:0140353 - lipid export from cell - - - - - The directed movement of a lipid from a cell, into the extracellular region. - GOC:pg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. - pg - 2019-05-22T11:38:15Z - lipid uptake - biological_process - GO:0140354 - lipid import into cell - - - - - The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. - GOC:pg - - - - @@ -154783,7 +151986,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154792,7 +151995,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154894,6 +152097,7 @@ For example, A and B may be gene products and binding of B by A positively regul + The chemical reactions and pathways resulting in the formation of L-amino acids, the L-enantiomers of amino acids. @@ -154948,6 +152152,8 @@ For example, A and B may be gene products and binding of B by A positively regul + + The chemical reactions and pathways involving any amino acid that is incorporated into protein naturally by ribosomal translation of mRNA, and that has a specific codon for translation from mRNA to protein. https://github.com/geneontology/go-ontology/issues/23268 ew @@ -155657,65 +152863,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. - bf - 2012-09-14T09:05:04Z - organic cyclic compound breakdown - organic cyclic compound catabolism - organic cyclic compound degradation - biological_process - GO:1901361 - organic cyclic compound catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. - GOC:TermGenie - - - - - organic cyclic compound breakdown - GOC:TermGenie - - - - - organic cyclic compound catabolism - GOC:TermGenie - - - - - organic cyclic compound degradation - GOC:TermGenie - - - - @@ -155880,66 +153027,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. - pr - 2012-11-04T15:17:56Z - organonitrogen compound breakdown - organonitrogen compound catabolism - organonitrogen compound degradation - biological_process - GO:1901565 - organonitrogen compound catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. - GOC:TermGenie - GOC:pr - - - - - organonitrogen compound breakdown - GOC:TermGenie - - - - - organonitrogen compound catabolism - GOC:TermGenie - - - - - organonitrogen compound degradation - GOC:TermGenie - - - - @@ -156010,25 +153097,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:36Z @@ -156158,6 +153228,8 @@ For example, A and B may be gene products and binding of B by A positively regul + + @@ -156187,65 +153259,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid. - tb - 2012-11-08T17:39:54Z - alpha-amino acid breakdown - alpha-amino acid catabolism - alpha-amino acid degradation - biological_process - GO:1901606 - alpha-amino acid catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid. - GOC:TermGenie - - - - - alpha-amino acid breakdown - GOC:TermGenie - - - - - alpha-amino acid catabolism - GOC:TermGenie - - - - - alpha-amino acid degradation - GOC:TermGenie - - - - @@ -156260,7 +153273,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + @@ -156564,179 +153578,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process. - bf - 2013-08-22T14:59:39Z - down regulation of RNA breakdown - down regulation of RNA catabolic process - down regulation of RNA catabolism - down regulation of RNA degradation - down-regulation of RNA breakdown - down-regulation of RNA catabolic process - down-regulation of RNA catabolism - down-regulation of RNA degradation - downregulation of RNA breakdown - downregulation of RNA catabolic process - downregulation of RNA catabolism - downregulation of RNA degradation - negative regulation of RNA breakdown - negative regulation of RNA catabolism - negative regulation of RNA degradation - inhibition of RNA breakdown - inhibition of RNA catabolic process - inhibition of RNA catabolism - inhibition of RNA degradation - biological_process - GO:1902369 - negative regulation of RNA catabolic process - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process. - GOC:TermGenie - GOC:bf - PMID:16640457 - - - - - down regulation of RNA breakdown - GOC:TermGenie - - - - - down regulation of RNA catabolic process - GOC:TermGenie - - - - - down regulation of RNA catabolism - GOC:TermGenie - - - - - down regulation of RNA degradation - GOC:TermGenie - - - - - down-regulation of RNA breakdown - GOC:TermGenie - - - - - down-regulation of RNA catabolic process - GOC:TermGenie - - - - - down-regulation of RNA catabolism - GOC:TermGenie - - - - - down-regulation of RNA degradation - GOC:TermGenie - - - - - downregulation of RNA breakdown - GOC:TermGenie - - - - - downregulation of RNA catabolic process - GOC:TermGenie - - - - - downregulation of RNA catabolism - GOC:TermGenie - - - - - downregulation of RNA degradation - GOC:TermGenie - - - - - negative regulation of RNA breakdown - GOC:TermGenie - - - - - negative regulation of RNA catabolism - GOC:TermGenie - - - - - negative regulation of RNA degradation - GOC:TermGenie - - - - - inhibition of RNA breakdown - GOC:TermGenie - - - - - inhibition of RNA catabolic process - GOC:TermGenie - - - - - inhibition of RNA catabolism - GOC:TermGenie - - - - - inhibition of RNA degradation - GOC:TermGenie - - - - @@ -156883,7 +153724,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -157093,7 +153933,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -158451,48 +155290,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - Any vesicle that is part of the extracellular region. - jl - 2014-10-22T14:26:11Z - cellular_component - microparticle - GO:1903561 - extracellular vesicle - - - - - Any vesicle that is part of the extracellular region. - GOC:TermGenie - GOC:pm - GO_REF:0000064 - PMID:24769233 - - - - - microparticle - GOC:vesicles - - - - @@ -158742,495 +155539,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole. - rl - 2015-06-12T09:10:36Z - biological_process - regulation of vacuolar protein breakdown - regulation of vacuolar protein catabolic process - regulation of vacuolar protein catabolism - regulation of vacuolar protein degradation - GO:1904350 - regulation of protein catabolic process in the vacuole - - - - - Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole. - GOC:BHF - GOC:TermGenie - GOC:rl - GO_REF:0000058 - PMID:25635054 - - - - - regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - regulation of vacuolar protein degradation - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole. - rl - 2015-06-12T09:10:42Z - down regulation of protein catabolic process in the vacuole - down-regulation of protein catabolic process in the vacuole - downregulation of protein catabolic process in the vacuole - inhibition of protein catabolic process in the vacuole - biological_process - down regulation of vacuolar protein breakdown - down regulation of vacuolar protein catabolic process - down regulation of vacuolar protein catabolism - down regulation of vacuolar protein degradation - down-regulation of vacuolar protein breakdown - down-regulation of vacuolar protein catabolic process - down-regulation of vacuolar protein catabolism - down-regulation of vacuolar protein degradation - downregulation of vacuolar protein breakdown - downregulation of vacuolar protein catabolic process - downregulation of vacuolar protein catabolism - downregulation of vacuolar protein degradation - inhibition of vacuolar protein breakdown - inhibition of vacuolar protein catabolic process - inhibition of vacuolar protein catabolism - inhibition of vacuolar protein degradation - negative regulation of vacuolar protein breakdown - negative regulation of vacuolar protein catabolic process - negative regulation of vacuolar protein catabolism - negative regulation of vacuolar protein degradation - GO:1904351 - negative regulation of protein catabolic process in the vacuole - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole. - GOC:BHF - GOC:TermGenie - GOC:rl - GO_REF:0000058 - PMID:25635054 - - - - - down regulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - down-regulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - downregulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - inhibition of protein catabolic process in the vacuole - GOC:TermGenie - - - - - down regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - down regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - down regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - down regulation of vacuolar protein degradation - GOC:TermGenie - - - - - down-regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - down-regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - down-regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - down-regulation of vacuolar protein degradation - GOC:TermGenie - - - - - downregulation of vacuolar protein breakdown - GOC:TermGenie - - - - - downregulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - downregulation of vacuolar protein catabolism - GOC:TermGenie - - - - - downregulation of vacuolar protein degradation - GOC:TermGenie - - - - - inhibition of vacuolar protein breakdown - GOC:TermGenie - - - - - inhibition of vacuolar protein catabolic process - GOC:TermGenie - - - - - inhibition of vacuolar protein catabolism - GOC:TermGenie - - - - - inhibition of vacuolar protein degradation - GOC:TermGenie - - - - - negative regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - negative regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - negative regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - negative regulation of vacuolar protein degradation - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole. - rl - 2015-06-12T09:10:49Z - up regulation of protein catabolic process in the vacuole - up-regulation of protein catabolic process in the vacuole - upregulation of protein catabolic process in the vacuole - activation of protein catabolic process in the vacuole - biological_process - activation of vacuolar protein breakdown - activation of vacuolar protein catabolic process - activation of vacuolar protein catabolism - activation of vacuolar protein degradation - positive regulation of vacuolar protein breakdown - positive regulation of vacuolar protein catabolic process - positive regulation of vacuolar protein catabolism - positive regulation of vacuolar protein degradation - up regulation of vacuolar protein breakdown - up regulation of vacuolar protein catabolic process - up regulation of vacuolar protein catabolism - up regulation of vacuolar protein degradation - up-regulation of vacuolar protein breakdown - up-regulation of vacuolar protein catabolic process - up-regulation of vacuolar protein catabolism - up-regulation of vacuolar protein degradation - upregulation of vacuolar protein breakdown - upregulation of vacuolar protein catabolic process - upregulation of vacuolar protein catabolism - upregulation of vacuolar protein degradation - GO:1904352 - positive regulation of protein catabolic process in the vacuole - - - - - Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole. - GOC:BHF - GOC:TermGenie - GOC:rl - GO_REF:0000058 - PMID:25635054 - - - - - up regulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - up-regulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - upregulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - activation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - activation of vacuolar protein breakdown - GOC:TermGenie - - - - - activation of vacuolar protein catabolic process - GOC:TermGenie - - - - - activation of vacuolar protein catabolism - GOC:TermGenie - - - - - activation of vacuolar protein degradation - GOC:TermGenie - - - - - positive regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - positive regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - positive regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - positive regulation of vacuolar protein degradation - GOC:TermGenie - - - - - up regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - up regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - up regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - up regulation of vacuolar protein degradation - GOC:TermGenie - - - - - up-regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - up-regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - up-regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - up-regulation of vacuolar protein degradation - GOC:TermGenie - - - - - upregulation of vacuolar protein breakdown - GOC:TermGenie - - - - - upregulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - upregulation of vacuolar protein catabolism - GOC:TermGenie - - - - - upregulation of vacuolar protein degradation - GOC:TermGenie - - - - @@ -160050,186 +156358,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of membrane invagination. - bf - 2016-04-18T15:43:54Z - biological_process - GO:1905153 - regulation of membrane invagination - - - - - Any process that modulates the frequency, rate or extent of membrane invagination. - GOC:PARL - GOC:TermGenie - GOC:bf - GO_REF:0000058 - PMID:26589353 - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination. - bf - 2016-04-18T15:44:04Z - down regulation of membrane invagination - down-regulation of membrane invagination - downregulation of membrane invagination - inhibition of membrane invagination - biological_process - GO:1905154 - negative regulation of membrane invagination - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination. - GOC:PARL - GOC:TermGenie - GOC:bf - GO_REF:0000058 - PMID:26589353 - - - - - down regulation of membrane invagination - GOC:TermGenie - - - - - down-regulation of membrane invagination - GOC:TermGenie - - - - - downregulation of membrane invagination - GOC:TermGenie - - - - - inhibition of membrane invagination - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of membrane invagination. - bf - 2016-04-18T15:44:12Z - up regulation of membrane invagination - up-regulation of membrane invagination - upregulation of membrane invagination - activation of membrane invagination - biological_process - GO:1905155 - positive regulation of membrane invagination - - - - - Any process that activates or increases the frequency, rate or extent of membrane invagination. - GOC:PARL - GOC:TermGenie - GOC:bf - GO_REF:0000058 - - - - - up regulation of membrane invagination - GOC:TermGenie - - - - - up-regulation of membrane invagination - GOC:TermGenie - - - - - upregulation of membrane invagination - GOC:TermGenie - - - - - activation of membrane invagination - GOC:TermGenie - - - - @@ -160613,258 +156741,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of lipid localization. - rz - 2017-02-21T12:12:22Z - regulation of lipid localisation - biological_process - GO:1905952 - regulation of lipid localization - - - - - Any process that modulates the frequency, rate or extent of lipid localization. - GOC:TermGenie - GO_REF:0000058 - PMID:17564681 - - - - - regulation of lipid localisation - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. - rz - 2017-02-21T12:12:41Z - down regulation of lipid localisation - down regulation of lipid localization - down-regulation of lipid localisation - down-regulation of lipid localization - downregulation of lipid localisation - downregulation of lipid localization - negative regulation of lipid localisation - inhibition of lipid localisation - inhibition of lipid localization - biological_process - GO:1905953 - negative regulation of lipid localization - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. - GOC:TermGenie - GO_REF:0000058 - PMID:17564681 - - - - - down regulation of lipid localisation - GOC:TermGenie - - - - - down regulation of lipid localization - GOC:TermGenie - - - - - down-regulation of lipid localisation - GOC:TermGenie - - - - - down-regulation of lipid localization - GOC:TermGenie - - - - - downregulation of lipid localisation - GOC:TermGenie - - - - - downregulation of lipid localization - GOC:TermGenie - - - - - negative regulation of lipid localisation - GOC:TermGenie - - - - - inhibition of lipid localisation - GOC:TermGenie - - - - - inhibition of lipid localization - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of lipid localization. - rz - 2017-02-21T12:12:49Z - positive regulation of lipid localisation - up regulation of lipid localisation - up regulation of lipid localization - up-regulation of lipid localisation - up-regulation of lipid localization - upregulation of lipid localisation - upregulation of lipid localization - activation of lipid localisation - activation of lipid localization - biological_process - GO:1905954 - positive regulation of lipid localization - - - - - Any process that activates or increases the frequency, rate or extent of lipid localization. - GOC:TermGenie - GO_REF:0000058 - PMID:17564681 - - - - - positive regulation of lipid localisation - GOC:TermGenie - - - - - up regulation of lipid localisation - GOC:TermGenie - - - - - up regulation of lipid localization - GOC:TermGenie - - - - - up-regulation of lipid localisation - GOC:TermGenie - - - - - up-regulation of lipid localization - GOC:TermGenie - - - - - upregulation of lipid localisation - GOC:TermGenie - - - - - upregulation of lipid localization - GOC:TermGenie - - - - - activation of lipid localisation - GOC:TermGenie - - - - - activation of lipid localization - GOC:TermGenie - - - - @@ -160903,45 +156779,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells. - bhm - 2014-03-26T14:23:27Z - cellular_component - GO:1990351 - An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay). - transporter complex - - - - - A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells. - GOC:bhm - PMID:15449578 - - - - @@ -161056,6 +156893,44 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of multicellular organismal development. + tb + 2010-08-05T11:25:59Z + biological_process + GO:2000026 + regulation of multicellular organismal development + + + + + Any process that modulates the frequency, rate or extent of multicellular organismal development. + GOC:obol + + + + @@ -161183,8 +157058,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + @@ -161257,7 +157133,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + @@ -161331,7 +157208,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + @@ -161405,7 +157283,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -161665,6 +157542,8 @@ For example, A and B may be gene products and binding of B by A positively regul GC_ID:1 + PMID:30365038 + PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -161679,6 +157558,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1206794 + Ecdysozoa + + + + @@ -161698,6 +157590,289 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + true yeasts + ncbi_taxonomy + NCBITaxon:147537 + Saccharomycotina + + + + + true yeasts + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Archiascomycota + NCBITaxon:147554 + Schizosaccharomycetes + + + + + Archiascomycota + + + + + + + + + + + GC_ID:1 + PMID:10874751 + PMID:11557979 + ncbi_taxonomy + NCBITaxon:197562 + Pancrustacea + + + + + + + + + + GC_ID:1 + PMID:11557979 + PMID:9727836 + mandibulates + ncbi_taxonomy + NCBITaxon:197563 + Mandibulata + + + + + mandibulates + + + + + + + + + + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11542017 + PMID:11542087 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:270744 + PMID:32628106 + PMID:36748408 + PMID:7520741 + PMID:8123559 + PMID:8186100 + PMID:8590690 + PMID:9103655 + PMID:9336922 + eubacteria + ncbi_taxonomy + Monera + Procaryotae + Prokaryota + Prokaryotae + bacteria + prokaryote + prokaryotes + NCBITaxon:2 + Bacteria + + + + + eubacteria + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + bacteria + + + + + + prokaryote + + + + + + prokaryotes + + + + + + + + + + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11541975 + PMID:11542064 + PMID:11542149 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:25527841 + PMID:270744 + PMID:32628106 + PMID:36748408 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + ncbi_taxonomy + Archaebacteria + Mendosicutes + Metabacteria + Monera + Procaryotae + Prokaryota + Prokaryotae + archaea + prokaryote + prokaryotes + NCBITaxon:2157 + Archaea + + + + + Archaebacteria + + + + + + Mendosicutes + + + + + + Metabacteria + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + archaea + + + + + + prokaryote + + + + + + prokaryotes + + + + + @@ -161727,7 +157902,7 @@ For example, A and B may be gene products and binding of B by A positively regul eukaryotes - + @@ -161789,6 +157964,117 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + metazoans + multicellular animals + ncbi_taxonomy + Animalia + animals + NCBITaxon:33208 + Metazoa + + + + + metazoans + + + + + + multicellular animals + + + + + + Animalia + + + + + + animals + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33213 + Bilateria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33317 + Protostomia + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:34346 + Schizosaccharomycetales + + + + + + + + + + GC_ID:1 + PMID:15689432 + PMID:16151185 + PMID:17010206 + PMID:17051209 + PMID:17572334 + ncbi_taxonomy + NCBITaxon:451864 + Dikarya + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:451866 + Taphrinomycotina + + + + @@ -161818,6 +158104,417 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + PMID:17572334 + ascomycetes + sac fungi + ncbi_taxonomy + ascomycete fungi + NCBITaxon:4890 + Ascomycota + + + + + ascomycetes + + + + + + sac fungi + + + + + + ascomycete fungi + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Hemiascomycetes + NCBITaxon:4891 + Saccharomycetes + + + + + Hemiascomycetes + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Endomycetales + budding yeasts + NCBITaxon:4892 + Saccharomycetales + + + + + Endomycetales + + + + + + budding yeasts + + + + + + + + + + + NCBITaxon:221665 + NCBITaxon:44280 + GC_ID:1 + ncbi_taxonomy + NCBITaxon:4893 + Saccharomycetaceae + + + + + + + + + + GC_ID:1 + fission yeasts + ncbi_taxonomy + Schizosaccharomycetoideae + NCBITaxon:4894 + Schizosaccharomycetaceae + + + + + fission yeasts + + + + + + Schizosaccharomycetoideae + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:4895 + Schizosaccharomyces + + + + + + + + + + NCBITaxon:45042 + GC_ID:1 + fission yeast + ncbi_taxonomy + Schizosaccharomyces malidevorans + NCBITaxon:4896 + Schizosaccharomyces pombe + + + + + fission yeast + + + + + + Schizosaccharomyces malidevorans + + + + + + + + + + + NCBITaxon:36915 + GC_ID:1 + ncbi_taxonomy + Pachytichospora + NCBITaxon:4930 + Saccharomyces + + + + + Pachytichospora + + + + + + + + + + + NCBITaxon:41870 + GC_ID:1 + Saccharomyces cerevisiae 'var. diastaticus' + baker's yeast + brewer's yeast + ncbi_taxonomy + Candida robusta + Mycoderma cerevisiae + Saccharomyces capensis + Saccharomyces diastaticus + Saccharomyces italicus + Saccharomyces oviformis + Saccharomyces uvarum var. melibiosus + NCBITaxon:4932 + Saccharomyces cerevisiae + + + + + Saccharomyces cerevisiae 'var. diastaticus' + + + + + + baker's yeast + + + + + + brewer's yeast + + + + + + Candida robusta + + + + + + Mycoderma cerevisiae + + + + + + Saccharomyces capensis + + + + + + Saccharomyces diastaticus + + + + + + Saccharomyces italicus + + + + + + Saccharomyces oviformis + + + + + + Saccharomyces uvarum var. melibiosus + + + + + + + + + + + GC_ID:1 + true insects + ncbi_taxonomy + insects + NCBITaxon:50557 + Insecta + + + + + true insects + + + + + + insects + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:6072 + Eumetazoa + + + + + + + + + + GC_ID:1 + arthropods + ncbi_taxonomy + arthropods + NCBITaxon:6656 + Arthropoda + + + + + arthropods + + + + + + arthropods + + + + + + + + + + + GC_ID:1 + insects + ncbi_taxonomy + Atelocerata + Tracheata + Uniramia + hexapods + NCBITaxon:6960 + Hexapoda + + + + + insects + + + + + + Atelocerata + + + + + + Tracheata + + + + + + Uniramia + + + + + + hexapods + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:716545 + saccharomyceta + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:88770 + Panarthropoda + + + + @@ -163355,6 +160052,45 @@ See https://github.com/pato-ontology/pato/issues/331. + + + + + An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. + quality + PATO:0001992 + + + cellularity + + + + + An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. + PATOC:GVG + + + + + + + + + A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. + quality + PATO:0001993 + + multicellular + + + + + A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. + PATOC:GVG + + + + @@ -203315,7 +200051,7 @@ See https://github.com/pato-ontology/pato/issues/331. - + A single species cell morphology phenotype in which fungal hyphae form an increased number of branches. alaynecuzick 2020-03-04T14:33:49Z @@ -206889,6 +203625,394 @@ occurs to a lesser extent than normal. + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001411 + resistance to dalfopristin + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001412 + sensitive to dalfopristin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001413 + normal growth on dalfopristin + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001414 + resistance to thifluzamide + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001415 + sensitive to thifluzamide + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001416 + normal growth on thifluzamide + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001417 + resistance to penflufen + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001418 + sensitive to penflufen + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001419 + normal growth on penflufen + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001420 + resistance to flutolanil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001421 + sensitive to flutolanil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001422 + normal growth on flutolanil + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001423 + resistance to imazalil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001424 + sensitive to imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001425 + normal growth on imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-28T09:44:54Z + single_species_phenotype + normal growth on fludioxonil + + + + + + + + + A single species cell morphology phenotype in which fungal hyphae branching is abnormal. + alaynecuzick + 2024-03-04T15:00:58Z + single_species_phenotype + abnormal hyphal branching + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:12:17Z + single_species_phenotype + normal growth on brefeldin A + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:14:22Z + single_species_phenotype + normal growth on fluconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001430 + resistance to ipconazole + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001431 + sensitive to ipconazole + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001432 + normal growth on ipconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001433 + resistance to cyprodinil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001434 + sensitive to cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001435 + normal growth on cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001436 + normal growth on caspofungin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001437 + normal growth on terbinafine + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001438 + normal growth on bifonazole + + + + @@ -207100,6 +204224,7 @@ occurs to a lesser extent than normal. + BFO:0000003 uberon UBERON:0000000 @@ -207163,6 +204288,12 @@ occurs to a lesser extent than normal. Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 + + + + FBbt:00007001 + + @@ -207172,6 +204303,107 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + adult stage + BTO:0001043 + BilaDO:0000004 + EFO:0001272 + FBdv:00005369 + WBls:0000041 + XtroDO:0000084 + fully formed animal stage + juvenile-adult stage + uberon + UBERON:0000066 + + fully formed stage + https://github.com/obophenotype/uberon/issues/566 + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + BilaDO:0000002 + EV:0300001 + FBdv:00005289 + FMA:72652 + HsapDv:0000002 + MmusDv:0000002 + OGES:000000 + OGES:000022 + SCTID:296280003 + WBls:0000003 + WBls:0000092 + WBls:0000102 + XAO:1000012 + embryonic stage + uberon + embryogenesis + UBERON:0000068 + embryo stage + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + http://orcid.org/0000-0002-6601-2165 + + + + @@ -207211,6 +204443,49 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + Stage succeeding embryo, including mature structure. + In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) + BilaDO:0000003 + OGES:000010 + OGES:000014 + OGES:000024 + WBls:0000022 + WBls:0000093 + WBls:0000103 + postembryonic stage + post-hatching stage + uberon + postembryonic + UBERON:0000092 + post-embryonic stage + https://github.com/obophenotype/uberon/issues/344 + + + + + Stage succeeding embryo, including mature structure. + https://orcid.org/0000-0002-6601-2165 + + + + @@ -207306,6 +204581,149 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + BILS:0000106 + BilaDO:0000005 + EFO:0001322 + EHDAA:27 + FBdv:00005288 + IDOMAL:0000302 + NCIT:C12601 + PdumDv:0000100 + VHOG:0000745 + Wikipedia:Zygote + XAO:1000001 + ZFS:0000001 + 1-cell stage + fertilized egg stage + one cell stage + uberon + fertilized egg stage + one-cell stage + zygote + zygotum + UBERON:0000106 + + zygote stage + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + Wikipedia:Zygote + + + + + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + 2012-09-17 + VHOG:0000745 + VHOG + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 + http://bgee.unil.ch/ + + + + + IDOMAL:0000302 + + + https://github.com/biopragmatics/biomappings + + + + + fertilized egg stage + BTO:0000854 + + + + + one-cell stage + VHOG:0000745 + + + + + zygote + VHOG:0000745 + + + + + zygotum + Wikipedia:Zygote + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + BILS:0000111 + BilaDO:0000010 + HsapDv:0000015 + MmusDv:0000018 + OGES:000005 + OGES:000032 + Wikipedia:Organogenesis + uberon + segmentation stage + UBERON:0000111 + organogenesis stage + https://github.com/obophenotype/developmental-stage-ontologies/issues/84 + https://github.com/obophenotype/uberon/issues/533 + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + Wikipedia:Organogenesis + + + + @@ -207338,6 +204756,248 @@ occurs to a lesser extent than normal. Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 + + + + FBbt:00007016 + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + TODO - split body and mc organism? body continues after death stage + + + + organismal + organism + AAO:0010026 + AEO:0000191 + BILA:0000012 + BIRNLEX:18 + BSA:0000038 + BTO:0000042 + CARO:0000012 + EFO:0002906 + EHDAA2:0003103 + EHDAA2:0003191 + EHDAA:1 + EMAPA:25765 + EV:0100016 + FBbt:00000001 + FMA:256135 + HAO:0000012 + NCIT:C13041 + SCTID:243928005 + TADS:0000001 + TAO:0001094 + TGMA:0001832 + VHOG:0000671 + WBbt:0007833 + Wikipedia:Multi-cellular_organism + XAO:0003004 + ZFA:0001094 + galen:Organism + ncithesaurus:Whole_Organism + multi-cellular organism + uberon + Koerper + body + whole body + whole organism + UBERON:0000468 + + + + + + multicellular organism + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + CARO:0000012 + Wikipedia:Multi-cellular_organism + http://orcid.org/0000-0001-9114-8737 + + + + + organism + FBbt:00000001 + VHOG:0000671 + WBbt:0007833 + + + + + FBbt:00000001 + + + + + + multi-cellular organism + CARO:0000012 + + + + + Koerper + BTO:0001489 + + + + + body + AEO:0000103 + BIRNLEX:18 + FMA:256135 + NCIT:C13041 + + + + + whole body + BTO:0001489 + + + + + whole organism + FBbt:00000001 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + embryonic + Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo + AAO:0011035 + AEO:0000169 + BILA:0000056 + BSA:0000039 + BTO:0000379 + CALOHA:TS-0229 + EFO:0001367 + EHDAA2:0000002 + EHDAA2_RETIRED:0003236 + EHDAA:38 + EMAPA:16039 + FBbt:00000052 + FMA:69068 + GAID:963 + IDOMAL:0000646 + MAT:0000226 + MESH:D004622 + MIAA:0000019 + NCIT:C28147 + OGEM:000001 + SCTID:57991002 + UMLS:C0013935 + VHOG:0001766 + Wikipedia:Embryo + XAO:0000113 + ZFA:0000103 + http://neurolex.org/wiki/Category:Embryonic_organism + embryonic organism + uberon + developing organism + developmental tissue + UBERON:0000922 + + + + + embryo + https://github.com/obophenotype/uberon/issues/503 + https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg + + + + + Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + BTO:0000379 + FB:FBrf0039741 + FB:FBrf0041814 + GO:0009790 + Wikipedia:Embryo + + + + + Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo + ZFA + + + + + FBbt:00000052 + + + + + + IDOMAL:0000646 + + + https://github.com/biopragmatics/biomappings + + + + + UMLS:C0013935 + ncithesaurus:Embryo + + + + + embryonic organism + BILA:0000056 + + + + + developing organism + BILA:0000056 + @@ -207351,6 +205011,7 @@ occurs to a lesser extent than normal. AAO:0010841 AEO:0000000 + BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 @@ -207379,6 +205040,12 @@ occurs to a lesser extent than normal. FMA:62955 http://orcid.org/0000-0001-9114-8737 + + + + FBbt:10000000 + + @@ -207388,6 +205055,133 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + + + + + A multicellular organism that existence_starts_with a post-embryonic stage. + MA:0002405 + postnatal organism + TS28 mouse + post-hatching organism + post-natal organism + postnatal mouse + uberon + UBERON:0009953 + post-embryonic organism + https://github.com/obophenotype/uberon/issues/667 + + + + + A multicellular organism that existence_starts_with a post-embryonic stage. + OBOL:automatic + + + + + TS28 mouse + MA:0002405 + + + + + post-hatching organism + https://orcid.org/0000-0002-6601-2165 + + + + + post-natal organism + https://orcid.org/0000-0002-6601-2165 + + + + + postnatal mouse + MA:0002405 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that has more than one cell as a part. + + + + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + + multicellular anatomical structure + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + + + + + FBbt:00100313 + + + + + + multicellular structure + FBbt:00100313 + + + + @@ -207743,6 +205537,36 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -207814,6 +205638,16 @@ occurs to a lesser extent than normal. + + + + + + + + + + @@ -207847,10 +205681,10 @@ occurs to a lesser extent than normal. /////////////////////////////////////////////////////////////////////////////////////// --> - + - + @@ -207868,66 +205702,54 @@ occurs to a lesser extent than normal. - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - + - - - - - - - - - @@ -207940,8 +205762,8 @@ occurs to a lesser extent than normal. - - + + @@ -207951,7 +205773,7 @@ occurs to a lesser extent than normal. - + @@ -207961,7 +205783,7 @@ occurs to a lesser extent than normal. - + @@ -207978,8 +205800,8 @@ occurs to a lesser extent than normal. - - + + @@ -208241,7 +206063,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208251,8 +206073,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208262,8 +206084,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208280,8 +206102,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208300,7 +206122,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208310,8 +206132,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208321,8 +206143,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208339,8 +206161,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208356,8 +206178,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208367,7 +206189,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208377,8 +206199,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208388,8 +206210,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208408,8 +206230,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208427,8 +206249,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208438,8 +206260,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208449,8 +206271,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208467,8 +206289,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208485,8 +206307,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208496,8 +206318,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208507,8 +206329,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208525,8 +206347,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208543,8 +206365,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208554,8 +206376,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208565,8 +206387,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208583,8 +206405,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208600,9 +206422,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208611,9 +206433,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208628,8 +206450,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208645,9 +206467,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208656,9 +206478,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208673,8 +206495,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208690,9 +206512,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208701,9 +206523,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208718,8 +206540,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208735,9 +206557,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208746,9 +206568,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208763,8 +206585,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208780,9 +206602,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208791,9 +206613,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208808,8 +206630,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208825,9 +206647,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208836,9 +206658,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208853,7 +206675,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208863,7 +206685,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208881,9 +206703,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208892,9 +206714,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208909,7 +206731,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208919,7 +206741,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208936,7 +206758,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208947,7 +206769,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208980,9 +206802,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208991,9 +206813,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209008,8 +206830,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -209024,9 +206846,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209035,9 +206857,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209051,9 +206873,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209068,7 +206890,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -209079,7 +206901,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -209095,7 +206917,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -209112,9 +206934,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209123,9 +206945,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209157,8 +206979,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -209168,8 +206990,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + diff --git a/phipo-simple-non-classified.json b/phipo-simple-non-classified.json index d5500a4..be74222 100644 --- a/phipo-simple-non-classified.json +++ b/phipo-simple-non-classified.json @@ -19,9 +19,9 @@ "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-01-31" + "val" : "2024-04-04" } ], - "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-01-31/phipo-simple-non-classified.json" + "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-04-04/phipo-simple-non-classified.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/PHIPO_0000001", @@ -27240,6 +27240,538 @@ "val" : "single_species_phenotype" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001411", + "lbl" : "resistance to dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001412", + "lbl" : "sensitive to dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001413", + "lbl" : "normal growth on dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001414", + "lbl" : "resistance to thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001415", + "lbl" : "sensitive to thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001416", + "lbl" : "normal growth on thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001417", + "lbl" : "resistance to penflufen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. 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"http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001419", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001420", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001421", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001422", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001423", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001424", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001425", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001426", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001427", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001205" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001428", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001429", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001431", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001432", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001433", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001434", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001435", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001436", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001437", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001438", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" } ] } ] } \ No newline at end of file diff --git a/phipo-simple-non-classified.obo b/phipo-simple-non-classified.obo index 2c03eb9..9698003 100644 --- a/phipo-simple-non-classified.obo +++ b/phipo-simple-non-classified.obo @@ -1,12 +1,12 @@ format-version: 1.2 -data-version: phipo/releases/2024-01-31/phipo-simple-non-classified.owl +data-version: phipo/releases/2024-04-04/phipo-simple-non-classified.owl ontology: phipo/phipo-simple-non-classified property_value: created:by "alaynecuzick" xsd:string property_value: creation:date "2018-07-09T13:43:00Z" xsd:string property_value: http://purl.org/dc/elements/1.1/description "Ontology of species-neutral phenotypes observed in pathogen-host interactions." xsd:string property_value: http://purl.org/dc/elements/1.1/title "Pathogen Host Interactions Phenotype Ontology" xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/3.0/" xsd:string -property_value: owl:versionInfo "2024-01-31" xsd:string +property_value: owl:versionInfo "2024-04-04" xsd:string [Term] id: PHIPO:0000001 @@ -10155,7 +10155,7 @@ namespace: single_species_phenotype def: "A single species cell morphology phenotype in which fungal hyphae form an increased number of branches." [] synonym: "increased branching of hyphae" EXACT [] synonym: "increased hyphal branching" EXACT [] -is_a: PHIPO:0001205 ! abnormal filament morphology +is_a: PHIPO:0001427 ! abnormal hyphal branching created_by: alaynecuzick creation_date: 2020-03-04T14:33:49Z @@ -12594,6 +12594,258 @@ is_a: PHIPO:0001308 ! normal growth on chemical created_by: alaynecuzick creation_date: 2024-01-30T14:16:53Z +[Term] +id: PHIPO:0001411 +name: resistance to dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001412 +name: sensitive to dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001413 +name: normal growth on dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001414 +name: resistance to thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001415 +name: sensitive to thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001416 +name: normal growth on thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001417 +name: resistance to penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001418 +name: sensitive to penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001419 +name: normal growth on penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001420 +name: resistance to flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001421 +name: sensitive to flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001422 +name: normal growth on flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001423 +name: resistance to imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001424 +name: sensitive to imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001425 +name: normal growth on imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001426 +name: normal growth on fludioxonil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-28T09:44:54Z + +[Term] +id: PHIPO:0001427 +name: abnormal hyphal branching +namespace: single_species_phenotype +def: "A single species cell morphology phenotype in which fungal hyphae branching is abnormal." [] +is_a: PHIPO:0001205 ! abnormal filament morphology +created_by: alaynecuzick +creation_date: 2024-03-04T15:00:58Z + +[Term] +id: PHIPO:0001428 +name: normal growth on brefeldin A +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-12T15:12:17Z + +[Term] +id: PHIPO:0001429 +name: normal growth on fluconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-12T15:14:22Z + +[Term] +id: PHIPO:0001430 +name: resistance to ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001431 +name: sensitive to ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001432 +name: normal growth on ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001433 +name: resistance to cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001434 +name: sensitive to cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001435 +name: normal growth on cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001436 +name: normal growth on caspofungin +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + +[Term] +id: PHIPO:0001437 +name: normal growth on terbinafine +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + +[Term] +id: PHIPO:0001438 +name: normal growth on bifonazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + [Typedef] id: PHIPO:0000304 name: qualifier diff --git a/phipo-simple-non-classified.owl b/phipo-simple-non-classified.owl index 2a5bf50..b8ac4e3 100644 --- a/phipo-simple-non-classified.owl +++ b/phipo-simple-non-classified.owl @@ -11,13 +11,13 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + alaynecuzick 2018-07-09T13:43:00Z Ontology of species-neutral phenotypes observed in pathogen-host interactions. Pathogen Host Interactions Phenotype Ontology https://creativecommons.org/licenses/by/3.0/ - 2024-01-31 + 2024-04-04 @@ -14530,7 +14530,7 @@ - + A single species cell morphology phenotype in which fungal hyphae form an increased number of branches. alaynecuzick 2020-03-04T14:33:49Z @@ -18021,6 +18021,394 @@ occurs to a lesser extent than normal. PHIPO:0001410 normal growth on iprovalicarb + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001411 + resistance to dalfopristin + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001412 + sensitive to dalfopristin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001413 + normal growth on dalfopristin + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001414 + resistance to thifluzamide + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001415 + sensitive to thifluzamide + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001416 + normal growth on thifluzamide + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001417 + resistance to penflufen + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001418 + sensitive to penflufen + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001419 + normal growth on penflufen + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001420 + resistance to flutolanil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001421 + sensitive to flutolanil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001422 + normal growth on flutolanil + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001423 + resistance to imazalil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001424 + sensitive to imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001425 + normal growth on imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-28T09:44:54Z + single_species_phenotype + normal growth on fludioxonil + + + + + + + + + A single species cell morphology phenotype in which fungal hyphae branching is abnormal. + alaynecuzick + 2024-03-04T15:00:58Z + single_species_phenotype + abnormal hyphal branching + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:12:17Z + single_species_phenotype + normal growth on brefeldin A + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:14:22Z + single_species_phenotype + normal growth on fluconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001430 + resistance to ipconazole + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001431 + sensitive to ipconazole + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001432 + normal growth on ipconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001433 + resistance to cyprodinil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001434 + sensitive to cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001435 + normal growth on cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001436 + normal growth on caspofungin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001437 + normal growth on terbinafine + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001438 + normal growth on bifonazole + diff --git a/phipo-simple.json b/phipo-simple.json index 8a1b742..8b0a352 100644 --- a/phipo-simple.json +++ b/phipo-simple.json @@ -19,9 +19,9 @@ "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-01-31" + "val" : "2024-04-04" } ], - "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-01-31/phipo-simple.json" + "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-04-04/phipo-simple.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -92,9 +92,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -160,9 +157,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -27453,273 +27447,741 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "inheres in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001411", + "lbl" : "resistance to dalfopristin", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "inheres in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this fragility inheres in this vase" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this fragility is a characteristic of this vase" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this red color inheres in this apple" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001412", + "lbl" : "sensitive to dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this red color is a characteristic of this apple" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A dependent inheres in its bearer at all times for which the dependent exists." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001413", + "lbl" : "normal growth on dalfopristin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres_in" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-05T09:44:00Z" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002314", - "lbl" : "characteristic of part of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001414", + "lbl" : "resistance to thifluzamide", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001415", + "lbl" : "sensitive to thifluzamide", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002503", - "lbl" : "towards", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001416", + "lbl" : "normal growth on thifluzamide", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type)." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002573", - "lbl" : "has modifier", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001417", + "lbl" : "resistance to penflufen", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relation that holds between an attribute or a qualifier and another attribute." + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001418", + "lbl" : "sensitive to penflufen", + "type" : "CLASS", "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001419", + "lbl" : "normal growth on penflufen", + "type" : "CLASS", "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type)." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001420", + "lbl" : "resistance to flutolanil", + "type" : "CLASS", "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001421", + "lbl" : "sensitive to flutolanil", + "type" : "CLASS", "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", - "lbl" : "has_broad_synonym", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001422", + "lbl" : "normal growth on flutolanil", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type)." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-07T11:32:37Z" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", - "lbl" : "has_exact_synonym", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001423", + "lbl" : "resistance to imazalil", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-12T10:06:39Z" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", - "lbl" : "has_narrow_synonym", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001424", + "lbl" : "sensitive to imazalil", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-12T10:06:39Z" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "lbl" : "has_obo_namespace", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", - "lbl" : "has_related_synonym", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001425", + "lbl" : "normal growth on imazalil", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type)." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-12T10:06:39Z" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" } ] } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001426", + "lbl" : "normal growth on fludioxonil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-28T09:44:54Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001427", + "lbl" : "abnormal hyphal branching", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A single species cell morphology phenotype in which fungal hyphae branching is abnormal." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-04T15:00:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001428", + "lbl" : "normal growth on brefeldin A", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-12T15:12:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001429", + "lbl" : "normal growth on fluconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-12T15:14:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001430", + "lbl" : "resistance to ipconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. 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Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001432", + "lbl" : "normal growth on ipconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001433", + "lbl" : "resistance to cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001434", + "lbl" : "sensitive to cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001435", + "lbl" : "normal growth on cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001436", + "lbl" : "normal growth on caspofungin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001437", + "lbl" : "normal growth on terbinafine", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001438", + "lbl" : "normal growth on bifonazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "inheres in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility inheres in this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color inheres in this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A dependent inheres in its bearer at all times for which the dependent exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "lbl" : "towards", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "lbl" : "has modifier", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between an attribute or a qualifier and another attribute." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + } ] + } + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "lbl" : "created by", + "type" : "PROPERTY" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "lbl" : "creation date", + "type" : "PROPERTY" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "lbl" : "has_alternative_id", + "type" : "PROPERTY" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", + "lbl" : "has_broad_synonym", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0001-5208-3432" + }, { + "pred" : 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"https://github.com/information-artifact-ontology/ontology-metadata/issues/20" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" + } ] + } + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", + "lbl" : "has_narrow_synonym", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0001-5208-3432" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" + } ] + } + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "lbl" : "has_obo_namespace", + "type" : "PROPERTY" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", + "lbl" : "has_related_synonym", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0001-5208-3432" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" + } ] + } + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#id", + "lbl" : "id", + "type" : "PROPERTY" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", "type" : "PROPERTY" } ], @@ -31310,7 +31772,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001153", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001205" + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001427" }, { "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001154", "pred" : "is_a", @@ -32251,6 +32713,118 @@ "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001410", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001411", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001412", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001413", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001414", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001415", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001416", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001417", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001418", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001419", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001420", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001421", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001422", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001423", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001424", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001425", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001426", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001427", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001205" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001428", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001429", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001431", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001432", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001433", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001434", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0000021" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001435", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001436", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001437", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" + }, { + "sub" : "http://purl.obolibrary.org/obo/PHIPO_0001438", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PHIPO_0001308" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000052", "pred" : "subPropertyOf", diff --git a/phipo-simple.obo b/phipo-simple.obo index 9e510cc..0789573 100644 --- a/phipo-simple.obo +++ b/phipo-simple.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: phipo/releases/2024-03-27/phipo-simple.owl +data-version: phipo/releases/2024-04-04/phipo-simple.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -8,10 +8,10 @@ subsetdef: ro-eco "" ontology: phipo/phipo-simple property_value: created:by "alaynecuzick" xsd:string property_value: creation:date "2018-07-09T13:43:00Z" xsd:string -property_value: dc-description "Ontology of species-neutral phenotypes observed in pathogen-host interactions." xsd:string -property_value: dc-title "Pathogen Host Interactions Phenotype Ontology" xsd:string -property_value: dcterms-license "https://creativecommons.org/licenses/by/3.0/" xsd:string -property_value: owl:versionInfo "2024-03-27" xsd:string +property_value: http://purl.org/dc/elements/1.1/description "Ontology of species-neutral phenotypes observed in pathogen-host interactions." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Pathogen Host Interactions Phenotype Ontology" xsd:string +property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/3.0/" xsd:string +property_value: owl:versionInfo "2024-04-04" xsd:string [Term] id: PHIPO:0000001 @@ -12934,41 +12934,12 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - [Typedef] id: has_part name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -13011,7 +12982,6 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/phipo-simple.owl b/phipo-simple.owl index be666d6..378ec8b 100644 --- a/phipo-simple.owl +++ b/phipo-simple.owl @@ -12,13 +12,13 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + alaynecuzick 2018-07-09T13:43:00Z Ontology of species-neutral phenotypes observed in pathogen-host interactions. Pathogen Host Interactions Phenotype Ontology https://creativecommons.org/licenses/by/3.0/ - 2024-01-31 + 2024-04-04 @@ -203,53 +203,25 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - + @@ -267,13 +239,17 @@ We also have the outstanding issue of how to aim different definitions to differ - + + created by + - + + creation date + @@ -355,7 +331,9 @@ We also have the outstanding issue of how to aim different definitions to differ - + + id + @@ -367,12 +345,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -424,7 +396,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An BFO:0000050 external quality - uberon part_of @@ -462,7 +433,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. BFO:0000051 external quality - uberon has_part @@ -14923,7 +14893,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + A single species cell morphology phenotype in which fungal hyphae form an increased number of branches. alaynecuzick 2020-03-04T14:33:49Z @@ -18414,6 +18384,394 @@ occurs to a lesser extent than normal. PHIPO:0001410 normal growth on iprovalicarb + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001411 + resistance to dalfopristin + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001412 + sensitive to dalfopristin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001413 + normal growth on dalfopristin + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001414 + resistance to thifluzamide + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001415 + sensitive to thifluzamide + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001416 + normal growth on thifluzamide + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001417 + resistance to penflufen + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001418 + sensitive to penflufen + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001419 + normal growth on penflufen + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001420 + resistance to flutolanil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001421 + sensitive to flutolanil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001422 + normal growth on flutolanil + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001423 + resistance to imazalil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001424 + sensitive to imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001425 + normal growth on imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-28T09:44:54Z + single_species_phenotype + normal growth on fludioxonil + + + + + + + + + A single species cell morphology phenotype in which fungal hyphae branching is abnormal. + alaynecuzick + 2024-03-04T15:00:58Z + single_species_phenotype + abnormal hyphal branching + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:12:17Z + single_species_phenotype + normal growth on brefeldin A + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:14:22Z + single_species_phenotype + normal growth on fluconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001430 + resistance to ipconazole + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001431 + sensitive to ipconazole + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001432 + normal growth on ipconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001433 + resistance to cyprodinil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001434 + sensitive to cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001435 + normal growth on cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001436 + normal growth on caspofungin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001437 + normal growth on terbinafine + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001438 + normal growth on bifonazole + diff --git a/phipo.json b/phipo.json index a61a2f5..0d6e983 100644 --- a/phipo.json +++ b/phipo.json @@ -19,9 +19,9 @@ "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-01-31" + "val" : "2024-04-04" } ], - "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-01-31/phipo.json" + "version" : "http://purl.obolibrary.org/obo/phipo/releases/2024-04-04/phipo.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", @@ -741,6 +741,12 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/OBOFoundry/COB/issues/65" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -938,9 +944,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -1006,9 +1009,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -1096,18 +1096,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -1131,9 +1125,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -1187,18 +1178,9 @@ "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -15033,6 +15015,49 @@ "val" : "chebi_ontology" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CHEBI_228364", + "lbl" : "NMR chemical shift reference compound", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "NMR chemical shift reference compounds", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR chemical shift standard", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR chemical shift standards", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR internal standard", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR internal standards", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR reference standard", + "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "NMR reference standards", + "xrefs" : [ "ChEBI" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "chebi_ontology" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CHEBI_22888", "lbl" : "biphenyls", @@ -36198,13 +36223,35 @@ "lbl" : "alpha-amino-acid residue", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "An amino-acid residue derived from an alpha-amino acid." + }, "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "alpha-amino-acid residues", "xrefs" : [ "ChEBI" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "an alpha-amino acid residue", + "xrefs" : [ "UniProt" ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/chebi/charge", + "val" : "0" + }, { + "pred" : "http://purl.obolibrary.org/obo/chebi/formula", + "val" : "C2H2NOR" + }, { + "pred" : "http://purl.obolibrary.org/obo/chebi/mass", + "val" : "56.043" + }, { + "pred" : "http://purl.obolibrary.org/obo/chebi/monoisotopicmass", + "val" : "56.01364" + }, { + "pred" : "http://purl.obolibrary.org/obo/chebi/smiles", + "val" : "*-NC([*])C(-*)=O" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "chebi_ontology" } ] @@ -86884,11 +86931,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs" : [ "CARO:mah" ] + "val" : "A material entity that has a plasma membrane and results from cellular division." }, - "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "comments" : [ "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.", "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).", "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -86913,6 +86959,96 @@ "val" : "http://purl.obolibrary.org/obo/cl.owl" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000151", + "lbl" : "secretory cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell that specializes in controlled release of one or more substances.", + "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "BTO:0003659" + }, { + "val" : "FMA:86916" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000154", + "lbl" : "protein secreting cell", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000225", + "lbl" : "anucleate cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell that lacks a nucleus.", + "xrefs" : [ "FB:ma" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "non-nucleated cell" + } ], + "xrefs" : [ { + "val" : "FMA:68647" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000226", + "lbl" : "single nucleate cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell with a single nucleus.", + "xrefs" : [ "FB:ma", "GOC:tfm" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000227", + "lbl" : "binucleate cell", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000228", + "lbl" : "multinucleate cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell with more than one nucleus.", + "xrefs" : [ "FB:ma" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "syncitium" + }, { + "pred" : "hasExactSynonym", + "val" : "syncytial cell" + }, { + "pred" : "hasExactSynonym", + "val" : "syncytium" + } ], + "xrefs" : [ { + "val" : "AEO:0000203" + }, { + "val" : "WBbt:0008074" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000255", + "lbl" : "eukaryotic cell", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "MESH:D005057" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000521", + "lbl" : "fungal cell", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/CL_0001061", "lbl" : "abnormal cell", @@ -86923,6 +87059,7 @@ "xrefs" : [ "GOC:add", "GOC:cg", "GOC:wdd" ] }, "comments" : [ "https://github.com/obophenotype/cell-ontology/issues/448" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913" } ], @@ -86935,22 +87072,37 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CL_0017505", - "lbl" : "increased nucleus size", + "id" : "http://purl.obolibrary.org/obo/CL_0002242", + "lbl" : "nucleate cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.", + "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "xrefs" : [ { + "val" : "FMA:67513" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-12-23T10:53:24Z" + "val" : "2010-09-07T03:32:33Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0011115", + "lbl" : "precursor cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cell that, by division or terminal differentiation, can give rise to other cell types.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + } }, { "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", "lbl" : "results_in_fission_of", @@ -87073,59 +87225,32 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0000740", - "lbl" : "nuclear membrane fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The joining of 2 or more lipid bilayer membranes that surround the nucleus.", - "xrefs" : [ "GOC:elh" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0000741", - "lbl" : "karyogamy", + "id" : "http://purl.obolibrary.org/obo/GO_0001677", + "lbl" : "formation of translation initiation ternary complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei.", - "xrefs" : [ "GOC:elh" ] + "val" : "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).", + "xrefs" : [ "GOC:hjd" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "nuclear fusion" - }, { - "pred" : "hasExactSynonym", - "val" : "nuclear fusion during karyogamy" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Karyogamy" + "val" : "translation initiation ternary complex assembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007335" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0001677", - "lbl" : "formation of translation initiation ternary complex", + "id" : "http://purl.obolibrary.org/obo/GO_0001700", + "lbl" : "embryonic development via the syncytial blastoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).", - "xrefs" : [ "GOC:hjd" ] + "val" : "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster.", + "xrefs" : [ "GOC:go_curators", "GOC:mtg_sensu" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "translation initiation ternary complex assembly" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -87301,7 +87426,7 @@ "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -87538,7 +87663,7 @@ "xrefs" : [ "GOC:ai", "GOC:dgf" ] }, "comments" : [ "Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "carrier" @@ -87556,50 +87681,6 @@ "val" : "molecular_function" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005319", - "lbl" : "lipid transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Enables the directed movement of lipids into, out of or within a cell, or between cells.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "lipophorin" - }, { - "pred" : "hasRelatedSynonym", - "val" : "apolipoprotein" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-1369028" - }, { - "val" : "Reactome:R-HSA-1369052" - }, { - "val" : "Reactome:R-HSA-174786" - }, { - "val" : "Reactome:R-HSA-5682285" - }, { - "val" : "Reactome:R-HSA-5682311" - }, { - "val" : "Reactome:R-HSA-5683672" - }, { - "val" : "Reactome:R-HSA-5683714" - }, { - "val" : "Reactome:R-HSA-5688397" - }, { - "val" : "Reactome:R-HSA-6801250" - }, { - "val" : "Reactome:R-HSA-8848053" - }, { - "val" : "Reactome:R-HSA-8866329" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0005488", "lbl" : "binding", @@ -87660,7 +87741,7 @@ "val" : "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -87697,7 +87778,7 @@ "xrefs" : [ "GOC:go_curators" ] }, "comments" : [ "Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "extracellular" @@ -87807,7 +87888,7 @@ "val" : "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.", "xrefs" : [ "ISBN:0198547684" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "xrefs" : [ { "val" : "Wikipedia:Cytoplasm" } ], @@ -87902,7 +87983,7 @@ "val" : "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.", "xrefs" : [ "ISBN:0716731363" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "juxtamembrane" @@ -88078,31 +88159,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0006401", - "lbl" : "RNA catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RNA breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "RNA catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "RNA degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006403", "lbl" : "RNA localization", @@ -88135,7 +88191,7 @@ "val" : "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "protein anabolism" @@ -88385,7 +88441,7 @@ "val" : "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.", "xrefs" : [ "ISBN:0198506732" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular amino acid metabolic process" @@ -88458,7 +88514,7 @@ "val" : "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.", "xrefs" : [ "GOC:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "lipid metabolism" @@ -88637,7 +88693,7 @@ "xrefs" : [ "GOC:dos", "GOC:dph", "GOC:jl", "GOC:mah" ] }, "comments" : [ "Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "single-organism transport" @@ -88729,21 +88785,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0006869", - "lbl" : "lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006886", "lbl" : "intracellular protein transport", @@ -88753,7 +88794,7 @@ "val" : "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "copper-induced intracellular protein transport", @@ -88767,37 +88808,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0006887", - "lbl" : "exocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", - "xrefs" : [ "GOC:mah", "ISBN:0716731363", "PMID:22323285" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "vesicle exocytosis" - }, { - "pred" : "hasRelatedSynonym", - "val" : "nonselective vesicle exocytosis" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Exocytosis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016195" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006897", "lbl" : "endocytosis", @@ -88893,20 +88903,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0006906", - "lbl" : "vesicle fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Fusion of the membrane of a transport vesicle with its target membrane.", - "xrefs" : [ "GOC:jid" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006914", "lbl" : "autophagy", @@ -89195,33 +89191,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0007039", - "lbl" : "protein catabolic process in the vacuole", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.", - "xrefs" : [ "GOC:mah", "GOC:vw" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar protein breakdown" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar protein catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar protein catabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar protein degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007049", "lbl" : "cell cycle", @@ -89351,6 +89320,25 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0007275", + "lbl" : "multicellular organism development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", + "xrefs" : [ "GOC:dph", "GOC:ems", "GOC:isa_complete", "GOC:tb" ] + }, + "comments" : [ "Note that this term was 'developmental process'." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_plant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/21234" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0008061", "lbl" : "chitin binding", @@ -89430,7 +89418,7 @@ "definition" : { "val" : "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -89900,53 +89888,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009057", - "lbl" : "macromolecule catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "biopolymer catabolic process", - "xrefs" : [ "GOC:mtg_chebi_dec09" ] - }, { - "pred" : "hasExactSynonym", - "val" : "macromolecule breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "macromolecule catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "macromolecule degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organismal macromolecule catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cellular macromolecule catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cellular macromolecule catabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cellular macromolecule degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043285" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044266" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009058", "lbl" : "biosynthetic process", @@ -90025,7 +89966,10 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "http://amigo.geneontology.org/amigo/term/GO:0070589" + "val" : "https://github.com/geneontology/go-ontology/issues/15249" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/25418" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0043284" @@ -90034,36 +89978,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009063", - "lbl" : "amino acid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "amino acid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "amino acid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "amino acid degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular amino acid catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/17904" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009066", "lbl" : "aspartate family amino acid metabolic process", @@ -90245,30 +90159,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009310", - "lbl" : "amine catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.", - "xrefs" : [ "GOC:jl", "ISBN:0198506732" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "amine breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "amine catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "amine degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009403", "lbl" : "toxin biosynthetic process", @@ -90408,6 +90298,70 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0009790", + "lbl" : "embryo development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", + "xrefs" : [ "GOC:go_curators", "GOC:isa_complete", "GOC:mtg_sensu" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_plant" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "embryogenesis and morphogenesis" + }, { + "pred" : "hasExactSynonym", + "val" : "embryogenesis" + }, { + "pred" : "hasExactSynonym", + "val" : "embryonal development" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Embryogenesis" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0009795" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0009791", + "lbl" : "post-embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.", + "xrefs" : [ "GOC:go_curators" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_plant" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0009792", + "lbl" : "embryo development ending in birth or egg hatching", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.", + "xrefs" : [ "GOC:go_curators", "GOC:isa_complete", "GOC:mtg_sensu" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "embryogenesis" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009847", "lbl" : "spore germination", @@ -90630,105 +90584,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009894", - "lbl" : "regulation of catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009895", - "lbl" : "negative regulation of catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0009896", - "lbl" : "positive regulation of catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0009987", "lbl" : "cellular process", @@ -90830,7 +90685,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.", + "val" : "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.", "xrefs" : [ "GOC:txnOH-2018", "PMID:25934543", "PMID:31580950" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], @@ -90840,6 +90695,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22557" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/25419" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -91003,20 +90861,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0010567", - "lbl" : "regulation of ketone catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells.", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0010604", "lbl" : "positive regulation of macromolecule metabolic process", @@ -91149,19 +90993,28 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0010876", - "lbl" : "lipid localization", + "id" : "http://purl.obolibrary.org/obo/GO_0010720", + "lbl" : "positive regulation of cell development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any process in which a lipid is transported to, or maintained in, a specific location.", + "val" : "Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.", + "xrefs" : [ "GOC:BHF", "GOC:dph", "GOC:tb" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0010721", + "lbl" : "negative regulation of cell development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.", "xrefs" : [ "GOC:BHF", "GOC:dph", "GOC:tb" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "lipid localisation", - "xrefs" : [ "GOC:mah" ] - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -91286,23 +91139,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0012506", - "lbl" : "vesicle membrane", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The lipid bilayer surrounding any membrane-bounded vesicle in the cell.", - "xrefs" : [ "GOC:mah", "GOC:vesicle" ] - }, - "xrefs" : [ { - "val" : "NIF_Subcellular:sao1153182838" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0015031", "lbl" : "protein transport", @@ -91628,30 +91464,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016054", - "lbl" : "organic acid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic acid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "organic acid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic acid degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0016070", "lbl" : "RNA metabolic process", @@ -91661,7 +91473,7 @@ "val" : "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.", "xrefs" : [ "ISBN:0198506732" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "RNA metabolism" @@ -91862,7 +91674,7 @@ "val" : "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.", "xrefs" : [ "ISBN:0198506732" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "xrefs" : [ { "val" : "EC:2.-.-.-" }, { @@ -92329,20 +92141,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0017157", - "lbl" : "regulation of exocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of exocytosis.", - "xrefs" : [ "GOC:go_curators" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0018130", "lbl" : "heterocycle biosynthetic process", @@ -92416,24 +92214,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0019216", - "lbl" : "regulation of lipid metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid metabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0019219", "lbl" : "regulation of nucleobase-containing compound metabolic process", @@ -92536,36 +92316,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0019439", - "lbl" : "aromatic compound catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "aromatic compound breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "aromatic compound catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "aromatic compound degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "aromatic hydrocarbon catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "aromatic hydrocarbon catabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0019538", "lbl" : "protein metabolic process", @@ -93084,104 +92834,21 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030100", - "lbl" : "regulation of endocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of endocytosis.", - "xrefs" : [ "GOC:go_curators" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030133", - "lbl" : "transport vesicle", + "id" : "http://purl.obolibrary.org/obo/GO_0030154", + "lbl" : "cell differentiation", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.", - "xrefs" : [ "GOC:mah", "PMID:22160157" ] + "val" : "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.", + "xrefs" : [ "ISBN:0198506732" ] }, - "comments" : [ "Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "constitutive secretory pathway transport vesicle" - }, { - "pred" : "hasNarrowSynonym", - "val" : "Golgi to vacuole transport vesicle" - }, { - "pred" : "hasNarrowSynonym", - "val" : "Golgi-vacuole transport vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "secretory vesicle" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_plant" ], "xrefs" : [ { - "val" : "NIF_Subcellular:sao885490876" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030163", - "lbl" : "protein catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular protein breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular protein catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular protein degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "protein breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "protein catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "protein degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organismal protein catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "pheromone catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "pheromone catabolism" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Protein_catabolism" + "val" : "Wikipedia:Cellular_differentiation" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044254" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044257" + "val" : "https://github.com/geneontology/go-ontology/issues/24390" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -93396,20 +93063,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030659", - "lbl" : "cytoplasmic vesicle membrane", - 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}, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031331", - "lbl" : "positive regulation of cellular catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of cellular catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of cellular catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of cellular catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of cellular catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of cellular catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0031333", "lbl" : "negative regulation of protein-containing complex assembly", @@ -93786,108 +93340,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031338", - "lbl" : "regulation of vesicle fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of vesicle fusion.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031339", - "lbl" : "negative regulation of vesicle fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of vesicle fusion" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of vesicle fusion" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of vesicle fusion" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of vesicle fusion" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031340", - "lbl" : "positive regulation of vesicle fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of vesicle fusion.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "up regulation of vesicle fusion" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of vesicle fusion" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of vesicle fusion" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of vesicle fusion" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of vesicle fusion" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031410", - "lbl" : "cytoplasmic vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A vesicle found in the cytoplasm of a cell.", - "xrefs" : [ "GOC:ai", "GOC:mah", "GOC:vesicles" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic membrane bounded vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic membrane-enclosed vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic, membrane-bounded vesicle" - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao180601769" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0031503", "lbl" : "protein-containing complex localization", @@ -93978,36 +93430,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031982", - "lbl" : "vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any small, fluid-filled, spherical organelle enclosed by membrane.", - "xrefs" : [ "GOC:mah", "GOC:pz", "GOC:vesicles" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "membrane-bounded vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "membrane-enclosed vesicle" - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao221389602" - }, { - "val" : "Wikipedia:Vesicle_(biology)" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032179", "lbl" : "germ tube", @@ -94110,162 +93532,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032365", - "lbl" : "intracellular lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of lipids within cells.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032368", - "lbl" : "regulation of lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032369", - "lbl" : "negative regulation of lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of lipid transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032370", - 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"type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032378", - "lbl" : "negative regulation of intracellular lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of intracellular lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of intracellular lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of intracellular lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of intracellular lipid transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032379", - "lbl" : "positive regulation of intracellular lipid transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "up regulation of intracellular lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of intracellular lipid transport" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of intracellular lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of intracellular lipid transport" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of intracellular lipid transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032386", "lbl" : "regulation of intracellular transport", @@ -94338,75 +93604,47 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032409", - "lbl" : "regulation of transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the activity of a transporter.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032410", - "lbl" : "negative regulation of transporter activity", + "id" : "http://purl.obolibrary.org/obo/GO_0032501", + "lbl" : "multicellular organismal process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any process that stops or reduces the activity of a transporter.", - "xrefs" : [ "GOC:mah" ] + "val" : "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.", + "xrefs" : [ "GOC:curators", "GOC:dph", "GOC:isa_complete", "GOC:tb" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "down regulation of transporter activity" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of transporter activity" + "val" : "organismal physiological process" }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of transporter activity" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of transporter activity" + "pred" : "hasRelatedSynonym", + "val" : "single-multicellular organism process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032411", - "lbl" : "positive regulation of transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the activity of a transporter.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "up regulation of transporter activity" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of transporter activity" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of transporter activity" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of transporter activity" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "jl" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-09-19T16:07:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044707" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0050874" }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of transporter activity" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -94511,20 +93749,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032871", - "lbl" : "regulation of karyogamy", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion.", - "xrefs" : [ "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032879", "lbl" : "regulation of localization", @@ -94959,84 +94183,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0033241", - "lbl" : "regulation of amine catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of amine breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of amine catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of amine degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular amine catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0033242", - "lbl" : "negative regulation of amine catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amine breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amine catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amine degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular amine catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0033243", - "lbl" : "positive regulation of amine catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amine breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amine catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amine degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0033365", "lbl" : "protein localization to organelle", @@ -95085,7 +94231,7 @@ "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "down regulation of kinase activity" @@ -95116,7 +94262,7 @@ "val" : "Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "up regulation of kinase activity" @@ -95226,87 +94372,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0034251", - "lbl" : "regulation of amide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of amide breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of amide catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of amide degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular amide catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0034252", - "lbl" : "negative regulation of amide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amide breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of amide catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular amide catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "negative regulation of amide degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0034253", - "lbl" : "positive regulation of amide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amide breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of amide catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular amide catabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "positive regulation of amide degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0034293", "lbl" : "sexual sporulation", @@ -95474,12 +94539,15 @@ "val" : "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular nitrogen compound metabolism" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/26424" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -95512,29 +94580,14 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0034655", - "lbl" : "nucleobase-containing compound catabolic process", + "id" : "http://purl.obolibrary.org/obo/GO_0035190", + "lbl" : "syncytial nuclear migration", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.", - "xrefs" : [ "GOC:mah" ] + "val" : "The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex.", + "xrefs" : [ "GOC:bf", "ISBN:0879694238", "PMID:8314839" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "nucleobase, nucleoside, nucleotide and nucleic acid degradation" - }, { - "pred" : "hasRelatedSynonym", - "val" : "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -95655,6 +94708,36 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0040019", + "lbl" : "positive regulation of embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the frequency, rate or extent of embryonic development.", + "xrefs" : [ "GOC:go_curators" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of embryonic development" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0040020", "lbl" : "regulation of meiotic nuclear division", @@ -95695,203 +94778,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0042176", - "lbl" : "regulation of protein catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.", - "xrefs" : [ "GOC:go_curators", "GOC:jl" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of protein breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of protein catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of protein degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of cyclin breakdown", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of cyclin catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of cyclin catabolism", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of cyclin degradation", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "regulation of degradation of cyclin", - "xrefs" : [ "GOC:obol" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - 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}, { - "pred" : "hasExactSynonym", - "val" : "down regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down regulation of protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of protein breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of protein catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of protein degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of protein catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1903363" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:2000599" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0042180", "lbl" : "cellular ketone metabolic process", @@ -95938,30 +94824,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0042182", - "lbl" : "ketone catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ketone breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "ketone catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "ketone degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0042325", "lbl" : "regulation of phosphorylation", @@ -96084,7 +94946,7 @@ "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite.", "xrefs" : [ "GOC:ai", "GOC:dph", "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "extracellular structure organisation" @@ -96107,7 +94969,7 @@ "val" : "Any process that activates or increases the activity of an enzyme.", "xrefs" : [ "GOC:ebc", "GOC:jl", "GOC:tb", "GOC:vw" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "positive regulation of enzyme activity", @@ -96163,7 +95025,7 @@ "val" : "Any process that stops or reduces the activity of an enzyme.", "xrefs" : [ "GOC:ebc", "GOC:jl", "GOC:tb", "GOC:vw" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "down regulation of enzyme activity" @@ -96277,30 +95139,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0043171", - "lbl" : "peptide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.", - "xrefs" : [ "GOC:jl" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "peptide breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "peptide catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "peptide degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043207", "lbl" : "response to external biotic stimulus", @@ -96324,7 +95162,7 @@ "val" : "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "xrefs" : [ { "val" : "NIF_Subcellular:sao1539965131" }, { @@ -96703,7 +95541,7 @@ "val" : "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", "xrefs" : [ "GOC:bf" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -96745,24 +95583,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0043605", - "lbl" : "amide catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.", - "xrefs" : [ "GOC:curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular amide catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043933", "lbl" : "protein-containing complex organization", @@ -97016,7 +95836,7 @@ "val" : "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.", "xrefs" : [ "GO:jl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" @@ -97037,7 +95857,7 @@ "val" : "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.", "xrefs" : [ "GO:jl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" @@ -97277,30 +96097,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044270", - "lbl" : "cellular nitrogen compound catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.", - "xrefs" : [ "GOC:jl", "ISBN:0198506732" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "nitrogen compound breakdown" - }, { - "pred" : "hasBroadSynonym", - "val" : "nitrogen compound catabolism" - }, { - "pred" : "hasBroadSynonym", - "val" : "nitrogen compound degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044271", "lbl" : "cellular nitrogen compound biosynthetic process", @@ -97354,31 +96150,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044282", - "lbl" : "small molecule catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.", - "xrefs" : [ "GOC:curators", "GOC:vw" ] - }, - "comments" : [ "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "small molecule catabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-01-26T12:06:10Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044283", "lbl" : "small molecule biosynthetic process", @@ -97389,7 +96160,7 @@ "xrefs" : [ "GOC:curators", "GOC:pde", "GOC:vw" ] }, "comments" : [ "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "small molecule biosynthesis" @@ -97721,30 +96492,6 @@ "val" : "molecular_function" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045026", - "lbl" : "plasma membrane fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.", - "xrefs" : [ "GOC:elh", "GOC:mtg_muscle" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cell fusion" - }, { - "pred" : "hasBroadSynonym", - "val" : "cell-cell fusion" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045087", "lbl" : "innate immune response", @@ -97824,6 +96571,77 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045595", + "lbl" : "regulation of cell differentiation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.", + "xrefs" : [ "GOC:go_curators" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045596", + "lbl" : "negative regulation of cell differentiation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.", + "xrefs" : [ "GOC:go_curators" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "down regulation of cell differentiation" + }, { + "pred" : "hasExactSynonym", + "val" : "down-regulation of cell differentiation" + }, { + "pred" : "hasExactSynonym", + "val" : "downregulation of cell differentiation" + }, { + "pred" : "hasNarrowSynonym", + "val" : "inhibition of cell differentiation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045597", + "lbl" : "positive regulation of cell differentiation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the frequency, rate or extent of cell differentiation.", + "xrefs" : [ "GOC:go_curators" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of cell differentiation" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of cell differentiation" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of cell differentiation" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of cell differentiation" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of cell differentiation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045727", "lbl" : "positive regulation of translation", @@ -97897,152 +96715,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045732", - "lbl" : "positive regulation of protein catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of protein breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of protein catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of protein degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of protein catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of protein catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of cellular protein breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of cellular protein catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of cellular protein catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of cellular protein degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of protein catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation of cyclin breakdown", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation of cyclin catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation of cyclin catabolism", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation of cyclin degradation", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation of degradation of cyclin", - "xrefs" : [ "GOC:obol" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of protein catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1903364" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:2000600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045763", "lbl" : "negative regulation of cellular amino acid metabolic process", @@ -98179,126 +96851,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045806", - "lbl" : "negative regulation of endocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of endocytosis" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of endocytosis" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of endocytosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of endocytosis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045807", - "lbl" : "positive regulation of endocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of endocytosis.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "up regulation of endocytosis" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of endocytosis" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of endocytosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of endocytosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of endocytosis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045833", - "lbl" : "negative regulation of lipid metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of lipid metabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045834", - "lbl" : "positive regulation of lipid metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid metabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of lipid metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of lipid metabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of lipid metabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of lipid metabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045835", "lbl" : "negative regulation of meiotic nuclear division", @@ -98476,63 +97028,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045920", - "lbl" : "negative regulation of exocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of exocytosis" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of exocytosis" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of exocytosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of exocytosis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045921", - "lbl" : "positive regulation of exocytosis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of exocytosis.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "up regulation of exocytosis" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of exocytosis" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of exocytosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of exocytosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of exocytosis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045934", "lbl" : "negative regulation of nucleobase-containing compound metabolic process", @@ -98725,26 +97220,26 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046112", - "lbl" : "nucleobase biosynthetic process", + "id" : "http://purl.obolibrary.org/obo/GO_0045992", + "lbl" : "negative regulation of embryonic development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.", - "xrefs" : [ "GOC:ai" ] + "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development.", + "xrefs" : [ "GOC:go_curators" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "nucleobase anabolism" + "val" : "down regulation of embryonic development" }, { "pred" : "hasExactSynonym", - "val" : "nucleobase biosynthesis" + "val" : "down-regulation of embryonic development" }, { "pred" : "hasExactSynonym", - "val" : "nucleobase formation" + "val" : "downregulation of embryonic development" }, { - "pred" : "hasExactSynonym", - "val" : "nucleobase synthesis" + "pred" : "hasNarrowSynonym", + "val" : "inhibition of embryonic development" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -98752,23 +97247,40 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046113", - "lbl" : "nucleobase catabolic process", + "id" : "http://purl.obolibrary.org/obo/GO_0045995", + "lbl" : "regulation of embryonic development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.", + "val" : "Any process that modulates the frequency, rate or extent of embryonic development.", + "xrefs" : [ "GOC:go_curators" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0046112", + "lbl" : "nucleobase biosynthetic process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.", "xrefs" : [ "GOC:ai" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "nucleobase breakdown" + "val" : "nucleobase anabolism" }, { "pred" : "hasExactSynonym", - "val" : "nucleobase catabolism" + "val" : "nucleobase biosynthesis" + }, { + "pred" : "hasExactSynonym", + "val" : "nucleobase formation" }, { "pred" : "hasExactSynonym", - "val" : "nucleobase degradation" + "val" : "nucleobase synthesis" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -98859,30 +97371,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046395", - "lbl" : "carboxylic acid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "carboxylic acid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "carboxylic acid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "carboxylic acid degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0046483", "lbl" : "heterocycle metabolic process", @@ -98902,107 +97390,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046700", - "lbl" : "heterocycle catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heterocycle breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "heterocycle catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "heterocycle degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046889", - "lbl" : "positive regulation of lipid biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid formation" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid synthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipogenesis", - "xrefs" : [ "GOC:sl" ] - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of lipid biosynthetic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of lipid biosynthetic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of lipid biosynthetic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0046890", - "lbl" : "regulation of lipid biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid formation" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid synthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipogenesis", - "xrefs" : [ "GOC:sl" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0046903", "lbl" : "secretion", @@ -99113,12 +97500,12 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0048284", - "lbl" : "organelle fusion", + "id" : "http://purl.obolibrary.org/obo/GO_0048285", + "lbl" : "organelle fission", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The creation of a single organelle from two or more organelles.", + "val" : "The creation of two or more organelles by division of one organelle.", "xrefs" : [ "GOC:jid" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -99128,35 +97515,51 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0048285", - "lbl" : "organelle fission", + "id" : "http://purl.obolibrary.org/obo/GO_0048468", + "lbl" : "cell development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The creation of two or more organelles by division of one organelle.", - "xrefs" : [ "GOC:jid" ] + "val" : "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place.", + "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "terminal differentiation", + "xrefs" : [ "GOC:dph", "GOC:tb" ] + } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/24390" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0048288", - "lbl" : "nuclear membrane fusion involved in karyogamy", + "id" : "http://purl.obolibrary.org/obo/GO_0048513", + "lbl" : "animal organ development", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei.", - "xrefs" : [ "GOC:jid" ] + "val" : "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.", + "xrefs" : [ "GOC:dph", "GOC:jid" ] }, "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "nuclear membrane fusion during karyogamy", - "xrefs" : [ "GOC:dph", "GOC:tb" ] + "pred" : "hasExactSynonym", + "val" : "development of an organ" + }, { + "pred" : "hasExactSynonym", + "val" : "organogenesis" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Organogenesis" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/25943" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -99303,6 +97706,77 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0048580", + "lbl" : "regulation of post-embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.", + "xrefs" : [ "GOC:jid" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0048581", + "lbl" : "negative regulation of post-embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.", + "xrefs" : [ "GOC:jid" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "down regulation of post-embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "down-regulation of post-embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "downregulation of post-embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "inhibition of post-embryonic development" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0048582", + "lbl" : "positive regulation of post-embryonic development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.", + "xrefs" : [ "GOC:jid" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of post-embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of post-embryonic development" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of post-embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of post-embryonic development" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of post-embryonic development" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0048589", "lbl" : "developmental growth", @@ -99504,7 +97978,7 @@ "val" : "Any process that modulates the activity of an enzyme.", "xrefs" : [ "GOC:ai", "GOC:ebc", "GOC:vw" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "regulation of enzyme activity" @@ -99520,6 +97994,20 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0050793", + "lbl" : "regulation of developmental process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", + "xrefs" : [ "GOC:go_curators" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0050794", "lbl" : "regulation of cellular process", @@ -99565,105 +98053,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0050994", - "lbl" : "regulation of lipid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of lipid degradation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0050995", - "lbl" : "negative regulation of lipid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid degradation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of lipid catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0050996", - "lbl" : "positive regulation of lipid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid breakdown" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid catabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation of lipid degradation" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation of lipid catabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation of lipid catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation of lipid catabolic process" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation of lipid catabolic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051046", "lbl" : "regulation of secretion", @@ -99807,49 +98196,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051055", - "lbl" : "negative regulation of lipid biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "down regulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of lipid biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid formation" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipid synthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "negative regulation of lipogenesis", - "xrefs" : [ "GOC:sl" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "inhibition of lipid biosynthetic process" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051078", "lbl" : "meiotic nuclear membrane disassembly", @@ -99904,6 +98250,63 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051093", + "lbl" : "negative regulation of developmental process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", + "xrefs" : [ "GOC:ai" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "down regulation of developmental process" + }, { + "pred" : "hasExactSynonym", + "val" : "down-regulation of developmental process" + }, { + "pred" : "hasExactSynonym", + "val" : "downregulation of developmental process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "inhibition of developmental process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051094", + "lbl" : "positive regulation of developmental process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", + "xrefs" : [ "GOC:ai" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of developmental process" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of developmental process" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of developmental process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of developmental process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of developmental process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051128", "lbl" : "regulation of cellular component organization", @@ -100309,6 +98712,77 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051239", + "lbl" : "regulation of multicellular organismal process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.", + "xrefs" : [ "GOC:ai", "GOC:dph", "GOC:tb" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051240", + "lbl" : "positive regulation of multicellular organismal process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.", + "xrefs" : [ "GOC:ai" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "up regulation of multicellular organismal process" + }, { + "pred" : "hasExactSynonym", + "val" : "up-regulation of multicellular organismal process" + }, { + "pred" : "hasExactSynonym", + "val" : "upregulation of multicellular organismal process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "activation of multicellular organismal process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stimulation of multicellular organismal process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051241", + "lbl" : "negative regulation of multicellular organismal process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.", + "xrefs" : [ "GOC:ai" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "down regulation of multicellular organismal process" + }, { + "pred" : "hasExactSynonym", + "val" : "down-regulation of multicellular organismal process" + }, { + "pred" : "hasExactSynonym", + "val" : "downregulation of multicellular organismal process" + }, { + "pred" : "hasNarrowSynonym", + "val" : "inhibition of multicellular organismal process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051246", "lbl" : "regulation of protein metabolic process", @@ -100612,7 +99086,7 @@ "xrefs" : [ "GOC:ai" ] }, "comments" : [ "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "transferase regulator" @@ -100632,7 +99106,7 @@ "xrefs" : [ "GOC:ai" ] }, "comments" : [ "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "transferase activator" @@ -100667,7 +99141,7 @@ "xrefs" : [ "GOC:ai" ] }, "comments" : [ "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "down regulation of transferase activity" @@ -100794,30 +99268,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051469", - "lbl" : "vesicle fusion with vacuole", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "heterotypic vacuole fusion (non-autophagic)" - }, { - "pred" : "hasRelatedSynonym", - "val" : "heterotypic vacuole fusion, non-autophagic" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042146" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051640", "lbl" : "organelle localization", @@ -100920,31 +99370,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051648", - "lbl" : "vesicle localization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cytoplasmic vesicle localization" - }, { - "pred" : "hasExactSynonym", - "val" : "establishment and maintenance of vesicle localization" - }, { - "pred" : "hasExactSynonym", - "val" : "vesicle localisation", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051649", "lbl" : "establishment of localization in cell", @@ -100977,25 +99402,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051650", - "lbl" : "establishment of vesicle localization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of a vesicle to a specific location.", - "xrefs" : [ "GOC:ai" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "establishment of vesicle localisation", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051656", "lbl" : "establishment of organelle localization", @@ -101484,7 +99890,7 @@ "val" : "The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.", "xrefs" : [ "GOC:vw" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nucleobase, nucleoside and nucleotide metabolism" @@ -101511,6 +99917,20 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0060284", + "lbl" : "regulation of cell development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.", + "xrefs" : [ "GOC:dph", "GOC:tb" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0060341", "lbl" : "regulation of cellular localization", @@ -101555,26 +99975,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0060627", - "lbl" : "regulation of vesicle-mediated transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-05-18T02:29:43Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0061024", "lbl" : "membrane organization", @@ -101584,7 +99984,7 @@ "val" : "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.", "xrefs" : [ "GOC:dph", "GOC:tb" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular membrane organisation" @@ -101620,43 +100020,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0061025", - "lbl" : "membrane fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The membrane organization process that joins two lipid bilayers to form a single membrane.", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular membrane fusion" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism membrane fusion" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Lipid_bilayer_fusion" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-02-08T02:48:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006944" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044801" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0061650", "lbl" : "ubiquitin-like protein conjugating enzyme activity", @@ -101976,7 +100339,7 @@ "val" : "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.", "xrefs" : [ "GOC:jl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular protein complex assembly" @@ -102047,7 +100410,7 @@ "val" : "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.", "xrefs" : [ "GOC:isa_complete" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "regulation of a molecular function" @@ -102122,28 +100485,6 @@ } ], "deprecated" : true } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0070382", - "lbl" : "exocytic vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.", - "xrefs" : [ "GOC:kad", "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "exocytic constitutive secretory pathway transport vesicle" - }, { - "pred" : "hasExactSynonym", - "val" : "exocytotic vesicle", - "xrefs" : [ "GOC:kad" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0070727", "lbl" : "cellular macromolecule localization", @@ -102592,7 +100933,7 @@ "val" : "A process in which a protein is transported to, or maintained in, a specific location in a membrane.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "protein localisation in membrane", @@ -102942,26 +101283,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0090174", - "lbl" : "organelle membrane fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The joining of two lipid bilayers to form a single organelle membrane.", - "xrefs" : [ "GOC:ascb_2009", "GOC:dph", "GOC:tb" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-12-11T11:44:58Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0090304", "lbl" : "nucleic acid metabolic process", @@ -102972,6 +101293,9 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/26133" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "tb" }, { @@ -103163,46 +101487,6 @@ "val" : "molecular_function" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0097576", - "lbl" : "vacuole fusion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole.", - "xrefs" : [ "GOC:pr", "GOC:vw", "Wikipedia:Vacuole" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2014-02-28T09:49:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0097708", - "lbl" : "intracellular vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any vesicle that is part of the intracellular region.", - "xrefs" : [ "GOC:vesicles" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2016-03-29T17:39:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0098542", "lbl" : "defense response to other organism", @@ -103348,49 +101632,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0098876", - "lbl" : "vesicle-mediated transport to the plasma membrane", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis.", - "xrefs" : [ "GOC:dos" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099500", - "lbl" : "vesicle fusion to plasma membrane", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "ISBN:0071120009", "PMID:18618940" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099503", - "lbl" : "secretory vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.", - "xrefs" : [ "GOC:dos" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0099568", "lbl" : "cytoplasmic region", @@ -103512,69 +101753,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0110112", - "lbl" : "regulation of lipid transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates the frequency, rate, or extent of lipid transporter activity.", - "xrefs" : [ "GOC:BHF", "GOC:BHF_miRNA", "GOC:rph", "PMID:27365390" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-07-06T18:53:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0110113", - "lbl" : "positive regulation of lipid transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that increases the frequency, rate, or extent of lipid transporter activity.", - "xrefs" : [ "GOC:BHF", "GOC:BHF_miRNA", "GOC:rph", "PMID:27365390" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-07-06T19:14:13Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0110114", - "lbl" : "negative regulation of lipid transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that decreases the frequency, rate, or extent of lipid transporter activity.", - "xrefs" : [ "GOC:BHF", "GOC:BHF_miRNA", "GOC:rph", "PMID:27365390" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#term_scheduled_for_obsoletion" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-07-06T19:21:44Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", "lbl" : "cellular anatomical entity", @@ -103704,27 +101882,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140029", - "lbl" : "exocytic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The cellular processes that contribute to exocytosis.", - "xrefs" : [ "Wikipedia:Exocytosis" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-15T13:20:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140096", "lbl" : "catalytic activity, acting on a protein", @@ -103734,7 +101891,7 @@ "val" : "Catalytic activity that acts to modify a protein.", "xrefs" : [ "GOC:molecular_function_refactoring", "GOC:pdt" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14225" @@ -103758,7 +101915,7 @@ "val" : "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.", "xrefs" : [ "GOC:molecular_function_refactoring", "GOC:pdt" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14225" @@ -103797,42 +101954,6 @@ "val" : "molecular_function" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140318", - "lbl" : "protein transporter activity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Directly binding to a specific protein and delivering it to a specific cellular location.", - "xrefs" : [ "PMID:18706423" ] - }, - "comments" : [ "Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "protein carrier activity" - }, { - "pred" : "hasRelatedSynonym", - "val" : "protein transport chaperone" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-9662747" - }, { - "val" : "Reactome:R-HSA-9662818" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/17073" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2019-04-01T10:41:38Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140352", "lbl" : "export from cell", @@ -103857,54 +101978,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140353", - "lbl" : "lipid export from cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of a lipid from a cell, into the extracellular region.", - "xrefs" : [ "GOC:pg" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "lipid efflux" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2019-05-22T11:33:07Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140354", - "lbl" : "lipid import into cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.", - "xrefs" : [ "GOC:pg" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "lipid uptake" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2019-05-22T11:38:15Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140513", "lbl" : "nuclear protein-containing complex", @@ -104560,39 +102633,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901361", - "lbl" : "organic cyclic compound catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.", - "xrefs" : [ "GOC:TermGenie" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic cyclic compound breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic cyclic compound catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic cyclic compound degradation", - "xrefs" : [ "GOC:TermGenie" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-09-14T09:05:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1901362", "lbl" : "organic cyclic compound biosynthetic process", @@ -104696,39 +102736,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901565", - "lbl" : "organonitrogen compound catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organonitrogen compound breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organonitrogen compound catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organonitrogen compound degradation", - "xrefs" : [ "GOC:TermGenie" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-04T15:17:56Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1901566", "lbl" : "organonitrogen compound biosynthetic process", @@ -104888,39 +102895,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901606", - "lbl" : "alpha-amino acid catabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid.", - "xrefs" : [ "GOC:TermGenie" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "alpha-amino acid breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "alpha-amino acid catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "alpha-amino acid degradation", - "xrefs" : [ "GOC:TermGenie" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { - "pred" : 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: "hasExactSynonym", - "val" : "down regulation of RNA catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down regulation of RNA degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of RNA breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of RNA catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of RNA catabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "down-regulation of RNA degradation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of RNA breakdown", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of RNA catabolic process", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "downregulation of RNA 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Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-12T10:06:39Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001425", + "lbl" : "normal growth on imazalil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-12T10:06:39Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001426", + "lbl" : "normal growth on fludioxonil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-02-28T09:44:54Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001427", + "lbl" : "abnormal hyphal branching", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A single species cell morphology phenotype in which fungal hyphae branching is abnormal." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-04T15:00:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001428", + "lbl" : "normal growth on brefeldin A", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-12T15:12:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001429", + "lbl" : "normal growth on fluconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-12T15:14:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001430", + "lbl" : "resistance to ipconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001431", + "lbl" : "sensitive to ipconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001432", + "lbl" : "normal growth on ipconazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001433", + "lbl" : "resistance to cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001434", + "lbl" : "sensitive to cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001435", + "lbl" : "normal growth on cyprodinil", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-18T13:26:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001436", + "lbl" : "normal growth on caspofungin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001437", + "lbl" : "normal growth on terbinafine", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/PHIPO_0001438", + "lbl" : "normal growth on bifonazole", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "alaynecuzick" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2024-03-27T11:45:23Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "single_species_phenotype" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000000001", "lbl" : "protein", @@ -137772,6 +136512,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "bearer_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -137803,9 +136546,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "participates_in" @@ -137840,9 +136580,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" @@ -137950,9 +136687,6 @@ "definition" : { "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, - "xrefs" : [ { - "val" : "RO:0000086" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple has quality this red color" @@ -137962,12 +136696,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_quality" } ] } }, { @@ -138023,9 +136751,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -138052,9 +136777,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -138078,9 +136800,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -138095,9 +136814,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -138114,9 +136830,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -138127,13 +136840,10 @@ "lbl" : "directly regulated by", "type" : "PROPERTY", "meta" : { - "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.", "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -138146,14 +136856,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -138166,14 +136873,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -138186,20 +136890,50 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002086", "lbl" : "ends after", @@ -138230,9 +136964,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "immediately_preceded_by" @@ -138327,9 +137058,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -138343,9 +137071,6 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" @@ -138364,12 +137089,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -138385,9 +137104,6 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -138403,12 +137119,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -138441,9 +137151,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -138596,9 +137303,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -138624,9 +137328,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -138668,9 +137369,6 @@ "val" : "inverse of starts with" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -138683,12 +137381,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" } ] } }, { @@ -138721,9 +137413,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -138738,9 +137427,6 @@ "val" : "inverse of ends with" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -138750,12 +137436,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" } ] } }, { @@ -138785,9 +137465,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -138910,6 +137587,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -138945,9 +137625,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" @@ -138984,9 +137661,41 @@ "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -139106,6 +137815,35 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002315" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002320", "lbl" : "evolutionarily related to", @@ -139203,21 +137941,12 @@ "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" } ] } }, { @@ -139253,9 +137982,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "enables part of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" @@ -139443,18 +138169,9 @@ "val" : "inverse of has input" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" } ] } }, { @@ -139475,9 +138192,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -139781,7 +138495,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -139992,6 +138706,88 @@ "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", "lbl" : "existence ends during or before", @@ -140001,18 +138797,9 @@ "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" } ] } }, { @@ -140481,9 +139268,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -140510,9 +139294,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -140551,7 +139332,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -140578,7 +139359,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -140629,9 +139410,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:30Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" @@ -140675,9 +139453,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:14Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" @@ -140701,9 +139476,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:22Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" @@ -140760,29 +139532,6 @@ "val" : "https://orcid.org/0000-0003-4639-4431" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012008", - "lbl" : "results in fusion of", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0012008" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-02-26T07:28:29Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fusion_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012011", "lbl" : "indirectly causally upstream of", @@ -140794,9 +139543,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0003-1813-6857" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -140813,9 +139559,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0003-1813-6857" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -140898,9 +139641,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-11-08T12:00:00Z" } ] } }, { @@ -141004,6 +139744,9 @@ "xrefs" : [ "span:ProcessualEntity" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "BFO:0000003" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" @@ -141091,6 +139834,95 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000066", + "lbl" : "fully formed stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "adult stage" + }, { + "pred" : "hasExactSynonym", + "val" : "fully formed animal stage" + }, { + "pred" : "hasExactSynonym", + "val" : "juvenile-adult stage" + } ], + "xrefs" : [ { + "val" : "BTO:0001043" + }, { + "val" : "BilaDO:0000004" + }, { + "val" : "EFO:0001272" + }, { + "val" : "FBdv:00005369" + }, { + "val" : "WBls:0000041" + }, { + "val" : "XtroDO:0000084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/566" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000068", + "lbl" : "embryo stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A life cycle stage that starts with fertilization and ends with the fully formed embryo.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "embryogenesis" + } ], + "xrefs" : [ { + "val" : "BilaDO:0000002" + }, { + "val" : "EV:0300001" + }, { + "val" : "FBdv:00005289" + }, { + "val" : "FMA:72652" + }, { + "val" : "HsapDv:0000002" + }, { + "val" : "MmusDv:0000002" + }, { + "val" : "OGES:000000" + }, { + "val" : "OGES:000022" + }, { + "val" : "SCTID:296280003" + }, { + "val" : "WBls:0000003" + }, { + "val" : "WBls:0000092" + }, { + "val" : "WBls:0000102" + }, { + "val" : "XAO:1000012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000071", "lbl" : "death stage", @@ -141127,6 +139959,51 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000092", + "lbl" : "post-embryonic stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Stage succeeding embryo, including mature structure.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "postembryonic stage" + }, { + "pred" : "hasNarrowSynonym", + "val" : "post-hatching stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "postembryonic" + } ], + "xrefs" : [ { + "val" : "BilaDO:0000003" + }, { + "val" : "OGES:000010" + }, { + "val" : "OGES:000014" + }, { + "val" : "OGES:000024" + }, { + "val" : "WBls:0000022" + }, { + "val" : "WBls:0000093" + }, { + "val" : "WBls:0000103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", + "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/344" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000104", "lbl" : "life cycle", @@ -141247,6 +140124,118 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000106", + "lbl" : "zygote stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A stage at which the organism is a single cell produced by means of sexual reproduction.", + "xrefs" : [ "Wikipedia:Zygote" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "1-cell stage" + }, { + "pred" : "hasExactSynonym", + "val" : "fertilized egg stage", + "xrefs" : [ "BTO:0000854" ] + }, { + "pred" : "hasExactSynonym", + "val" : "one cell stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "fertilized egg stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "one-cell stage", + "xrefs" : [ "VHOG:0000745" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "zygote", + "xrefs" : [ "VHOG:0000745" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "zygotum", + "xrefs" : [ "Wikipedia:Zygote" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000106" + }, { + "val" : "BilaDO:0000005" + }, { + "val" : "EFO:0001322" + }, { + "val" : "EHDAA:27" + }, { + "val" : "FBdv:00005288" + }, { + "val" : "IDOMAL:0000302" + }, { + "val" : "NCIT:C12601" + }, { + "val" : "PdumDv:0000100" + }, { + "val" : "VHOG:0000745" + }, { + "val" : "Wikipedia:Zygote" + }, { + "val" : "XAO:1000001" + }, { + "val" : "ZFS:0000001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", + "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/EMAPA_16033" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" + }, { + "val" : "BilaDO:0000010" + }, { + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/533" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", "lbl" : "material anatomical entity", @@ -141294,6 +140283,212 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000468", + "lbl" : "multicellular organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical structure that is an individual member of a species and consists of more than one cell.", + "xrefs" : [ "CARO:0000012", "Wikipedia:Multi-cellular_organism", "http://orcid.org/0000-0001-9114-8737" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "organism", + "xrefs" : [ "FBbt:00000001", "VHOG:0000671", "WBbt:0007833" ] + }, { + "pred" : "hasExactSynonym", + "val" : "multi-cellular organism", + "xrefs" : [ "CARO:0000012" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Koerper", + "xrefs" : [ "BTO:0001489" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "body", + "xrefs" : [ "AEO:0000103", "BIRNLEX:18", "FMA:256135", "NCIT:C13041" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole body", + "xrefs" : [ "BTO:0001489" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole organism", + "xrefs" : [ "FBbt:00000001" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010026" + }, { + "val" : "AEO:0000191" + }, { + "val" : "BILA:0000012" + }, { + "val" : "BIRNLEX:18" + }, { + "val" : "BSA:0000038" + }, { + "val" : "BTO:0000042" + }, { + "val" : "CARO:0000012" + }, { + "val" : "EFO:0002906" + }, { + "val" : "EHDAA2:0003103" + }, { + "val" : "EHDAA2:0003191" + }, { + "val" : "EHDAA:1" + }, { + "val" : "EMAPA:25765" + }, { + "val" : "EV:0100016" + }, { + "val" : "FBbt:00000001" + }, { + "val" : "FMA:256135" + }, { + "val" : "HAO:0000012" + }, { + "val" : "NCIT:C13041" + }, { + "val" : "SCTID:243928005" + }, { + "val" : "TADS:0000001" + }, { + "val" : "TAO:0001094" + }, { + "val" : "TGMA:0001832" + }, { + "val" : "VHOG:0000671" + }, { + "val" : "WBbt:0007833" + }, { + "val" : "Wikipedia:Multi-cellular_organism" + }, { + "val" : "XAO:0003004" + }, { + "val" : "ZFA:0001094" + }, { + "val" : "galen:Organism" + }, { + "val" : "ncithesaurus:Whole_Organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - split body and mc organism? body continues after death stage" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", + "val" : "organismal" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000922", + "lbl" : "embryo", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", + "xrefs" : [ "BTO:0000379", "FB:FBrf0039741", "FB:FBrf0041814", "GO:0009790", "Wikipedia:Embryo" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic organism", + "xrefs" : [ "BILA:0000056" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "developing organism", + "xrefs" : [ "BILA:0000056" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "developmental tissue" + } ], + "xrefs" : [ { + "val" : "AAO:0011035" + }, { + "val" : "AEO:0000169" + }, { + "val" : "BILA:0000056" + }, { + "val" : "BSA:0000039" + }, { + "val" : "BTO:0000379" + }, { + "val" : "CALOHA:TS-0229" + }, { + "val" : "EFO:0001367" + }, { + "val" : "EHDAA2:0000002" + }, { + "val" : "EHDAA2_RETIRED:0003236" + }, { + "val" : "EHDAA:38" + }, { + "val" : "EMAPA:16039" + }, { + "val" : "FBbt:00000052" + }, { + "val" : "FMA:69068" + }, { + "val" : "GAID:963" + }, { + "val" : "IDOMAL:0000646" + }, { + "val" : "MAT:0000226" + }, { + "val" : "MESH:D004622" + }, { + "val" : "MIAA:0000019" + }, { + "val" : "NCIT:C28147" + }, { + "val" : "OGEM:000001" + }, { + "val" : "SCTID:57991002" + }, { + "val" : "UMLS:C0013935" + }, { + "val" : "VHOG:0001766" + }, { + "val" : "Wikipedia:Embryo" + }, { + "val" : "XAO:0000113" + }, { + "val" : "ZFA:0000103" + }, { + "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", + "val" : "embryonic" + }, { + "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", + "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/503" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", "lbl" : "anatomical entity", @@ -141308,6 +140503,8 @@ "val" : "AAO:0010841" }, { "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" }, { "val" : "BILA:0000000" }, { @@ -141353,6 +140550,80 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009953", + "lbl" : "post-embryonic organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multicellular organism that existence_starts_with a post-embryonic stage.", + "xrefs" : [ "OBOL:automatic" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "postnatal organism" + }, { + "pred" : "hasNarrowSynonym", + "val" : "TS28 mouse", + "xrefs" : [ "MA:0002405" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "post-hatching organism", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "post-natal organism", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "postnatal mouse", + "xrefs" : [ "MA:0002405" ] + } ], + "xrefs" : [ { + "val" : "MA:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/667" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "lbl" : "multicellular anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] + } ], + "xrefs" : [ { + "val" : "CARO:0010000" + }, { + "val" : "FBbt:00100313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "lbl" : "obsolete decreased_in_magnitude_relative_to", @@ -141437,81 +140708,13 @@ } ] } }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "lbl" : "created by", + "type" : "PROPERTY" }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "lbl" : "creation date", + "type" : "PROPERTY" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", @@ -141600,6 +140803,10 @@ "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" } ] } + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#id", + "lbl" : "id", + "type" : "PROPERTY" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", @@ -141640,7 +140847,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000023", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_50906" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", "pred" : "is_a", @@ -142513,6 +141720,10 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_16134", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CHEBI_37176" + }, { + "sub" : "http://purl.obolibrary.org/obo/CHEBI_16134", + "pred" : "http://purl.obolibrary.org/obo/RO_0000087", + "obj" : "http://purl.obolibrary.org/obo/CHEBI_228364" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_16134", "pred" : "http://purl.obolibrary.org/obo/RO_0000087", @@ -144273,6 +143484,14 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_22728", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CHEBI_38180" + }, { + "sub" : "http://purl.obolibrary.org/obo/CHEBI_228364", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CHEBI_33232" + }, { + "sub" : "http://purl.obolibrary.org/obo/CHEBI_228364", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CHEBI_51086" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_22888", "pred" : "is_a", @@ -144701,10 +143920,6 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_24431", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/CHEBI_24432", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_24432", "pred" : "is_a", @@ -145489,6 +144704,10 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_26078", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CHEBI_59698" + }, { + "sub" : "http://purl.obolibrary.org/obo/CHEBI_26078", + "pred" : "http://purl.obolibrary.org/obo/RO_0000087", + "obj" : "http://purl.obolibrary.org/obo/CHEBI_228364" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_26078", "pred" : "http://purl.obolibrary.org/obo/RO_0000087", @@ -148085,10 +147304,6 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_33231", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CHEBI_64912" - }, { - "sub" : "http://purl.obolibrary.org/obo/CHEBI_33232", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_33232", "pred" : "is_a", @@ -153584,7 +152799,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_50906", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_50908", "pred" : "is_a", @@ -153657,10 +152872,6 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_51061", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CHEBI_90710" - }, { - "sub" : "http://purl.obolibrary.org/obo/CHEBI_51086", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_51086", "pred" : "is_a", @@ -159197,6 +158408,70 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000000", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000151", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000151", + "pred" : "http://purl.obolibrary.org/obo/RO_0002215", + "obj" : "http://purl.obolibrary.org/obo/GO_0032940" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000154", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000151" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000154", + "pred" : "http://purl.obolibrary.org/obo/RO_0002215", + "obj" : "http://purl.obolibrary.org/obo/GO_0009306" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000225", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000225", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001405" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000226", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0002242" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000226", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001407" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000227", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000227", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001406" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000228", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0002242" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000228", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001908" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000255", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000255", + "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000521", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000521", + "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001061", "pred" : "is_a", @@ -159206,13 +158481,21 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/PATO_0000460" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0017505", + "sub" : "http://purl.obolibrary.org/obo/CL_0002242", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0005634" + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0017505", + "sub" : "http://purl.obolibrary.org/obo/CL_0002242", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000586" + "obj" : "http://purl.obolibrary.org/obo/PATO_0002505" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011115", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011115", + "pred" : "http://purl.obolibrary.org/obo/RO_0002215", + "obj" : "http://purl.obolibrary.org/obo/GO_0030154" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000003", "pred" : "is_a", @@ -159253,34 +158536,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0000280", "pred" : "http://purl.obolibrary.org/obo/GOREL_0002004", "obj" : "http://purl.obolibrary.org/obo/GO_0005634" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000740", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071763" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000740", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0090174" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000740", - "pred" : "http://purl.obolibrary.org/obo/RO_0012008", - "obj" : "http://purl.obolibrary.org/obo/GO_0031965" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000741", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0006997" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000741", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0048284" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000741", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GO_0006997" - }, { - "sub" 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"propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0030154" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000280", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048285" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GOREL_0002004", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] }, { @@ -172538,13 +171181,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016887" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0005319", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005215" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0005938", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], @@ -172566,13 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"http://purl.obolibrary.org/obo/GO_0006886", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -172712,20 +171327,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006887", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0070382" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006906", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0012506" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006996", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -172775,13 +171376,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002344", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007039", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0030163" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007097", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0046907" ], @@ -172789,6 +171383,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007275", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002295", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000468" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0008104", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], @@ -172810,13 +171411,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0008283" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0008610", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0008652", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -172824,13 +171418,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_37022" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009057", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33694" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009059", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -172838,13 +171425,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33694" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009063", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_37022" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009112", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -172874,11 +171454,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_32952" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009310", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009790", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_32952" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000922" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009889", @@ -172915,27 +171495,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0008152" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009894", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009056" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009895", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009056" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009896", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009056" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010256", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -173013,13 +171572,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0042181" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010567", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0042182" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010604", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173063,11 +171615,18 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0006996" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010876", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0033036" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010720", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0048468" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010721", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0048468" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010927", @@ -173090,13 +171649,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006817" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0012506", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0015031", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -173153,13 +171705,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_61120" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016042", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016043", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], @@ -173167,13 +171712,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005575" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016050", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016053", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -173181,13 +171719,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_64709" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016054", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_64709" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016070", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -173195,13 +171726,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016192", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0017148", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173209,13 +171733,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006412" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0017157", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0018130", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -173223,13 +171740,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_5686" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019216", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006629" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019219", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173258,13 +171768,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33655" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019439", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33655" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019538", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -173322,18 +171825,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_1990904" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030100", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006897" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030163", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030154", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048869" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002315", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000000" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030397", @@ -173342,13 +171838,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030659", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031410" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031090", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], @@ -173398,27 +171887,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0044249" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031329", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0044248" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031330", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0044248" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031331", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0044248" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031333", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173433,34 +171901,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0065003" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031338", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006906" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031339", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006906" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031340", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006906" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031410", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005737" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031503", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], @@ -173496,58 +171936,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0015931" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032365", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032368", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006869" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032369", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006869" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032370", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006869" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032377", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032365" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032378", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032365" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032379", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032365" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032386", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173569,27 +171957,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0046907" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032409", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005215" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032410", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005215" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032411", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005215" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032594", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0015031" ], @@ -173599,18 +171966,11 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032774", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009059" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032871", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0000741" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032879", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173695,27 +172055,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0009308" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033241", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009310" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033242", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009310" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033243", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009310" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033365", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008104" ], @@ -173758,27 +172097,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043603" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034251", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043605" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034252", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043605" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034253", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043605" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034293", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0043934" ], @@ -173801,11 +172119,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_61120" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034655", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035190", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007097" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_61120" + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000228" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035592", @@ -173815,32 +172133,25 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0040020", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0040019", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0140013" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009790" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042127", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0040020", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0008283" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0140013" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042176", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042127", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0030163" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042177", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0030163" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0008283" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042180", @@ -173856,13 +172167,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_17087" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042182", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_17087" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042325", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -173933,13 +172237,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33694" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043171", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_16670" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043227", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0043226" ], @@ -174031,13 +172328,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_32988" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043605", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_32988" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043933", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -174084,7 +172374,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/GO_0044091", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0044085" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002234", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] }, { @@ -174101,13 +172391,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0003674" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045026", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045184", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], @@ -174116,74 +172399,60 @@ "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_36080" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045727", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045595", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006412" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045732", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0030163" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0030154" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045763", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045596", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0030154" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045764", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045597", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0030154" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045786", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007049" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045787", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045727", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007049" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0006412" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045806", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045763", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006897" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045807", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045764", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006897" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0006520" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045833", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045786", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006629" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007049" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045834", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045787", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006629" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007049" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045835", @@ -174227,20 +172496,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006415" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045920", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045921", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045934", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -174284,31 +172539,31 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0006413" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046112", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045992", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18282" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009790" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046113", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045995", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18282" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009790" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046394", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046112", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_29067" + "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18282" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046395", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046394", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_29067" } ] }, { @@ -174318,27 +172573,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_5686" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046700", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_5686" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046889", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0008610" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046890", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0008610" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046907", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -174360,13 +172594,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016236" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048284", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048285", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], @@ -174375,11 +172602,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048288", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0000740" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048468", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0000741" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000000" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048518", @@ -174409,6 +172636,27 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0009987" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048580", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009791" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048581", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009791" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048582", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009791" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048589", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0040007" ], @@ -174416,6 +172664,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032502" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048856", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032502" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000061" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050657", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -174466,32 +172721,18 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0003824" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050794", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050793", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0009987" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032502" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050994", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050794", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016042" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050995", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016042" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050996", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016042" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0009987" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051046", @@ -174535,13 +172776,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006810" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051055", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0008610" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051078", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051081" ], @@ -174556,6 +172790,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", "fillerId" : "http://purl.obolibrary.org/obo/GO_0031965" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051093", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032502" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051094", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032502" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051128", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -174636,6 +172884,27 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0015031" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051239", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032501" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051240", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032501" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051241", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032501" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051246", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -174734,16 +173003,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0051321" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051469", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051640", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], @@ -174758,13 +173017,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051648", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051649", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], @@ -174772,13 +173024,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000000" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051650", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051656", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], @@ -174877,6 +173122,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043170" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060284", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0048468" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060341", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -174891,13 +173143,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0009653" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060627", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016192" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0061024", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -174905,13 +173150,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0061025", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0061024" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0061695", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], @@ -174985,13 +173223,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0045184" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0070382", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0030133" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0099500" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0070925", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -175121,13 +173352,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0090174", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0061025" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031090" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0090304", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], @@ -175170,20 +173394,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_28938" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0097576", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0097708", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098590", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], @@ -175225,36 +173435,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098876", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099500", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0061025" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0012506" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0098590" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099503", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0099500" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099568", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], @@ -175283,30 +173463,9 @@ "definedClassId" : "http://purl.obolibrary.org/obo/GO_0101025", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0044085" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002234", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/GO_0031965" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0110112", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005319" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0110113", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005319" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0110114", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005319" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140013", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0000280" ], @@ -175314,33 +173473,19 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0051321" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140029", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006887" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140096", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0003824" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002233", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140098", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0003824" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002233", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140318", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005215" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" + "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33697" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140352", @@ -175352,32 +173497,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140353", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002338", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140354", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002338", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_18059" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140513", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], @@ -175396,7 +173515,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/GO_0140640", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0003824" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002233", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33696" } ] }, { @@ -175455,13 +173574,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33832" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901361", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_33832" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901362", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -175476,13 +173588,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_35352" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901565", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_35352" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901566", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -175490,13 +173595,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004008", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_35352" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901575", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_50860" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901576", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -175511,13 +173609,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_78608" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901606", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009056" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/CHEBI_78608" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1901607", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009058" ], @@ -175546,13 +173637,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0070925" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1902369", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0006401" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1902494", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], @@ -175658,13 +173742,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032940" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1903561", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1903729", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -175686,27 +173763,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0008104" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1904350", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007039" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1904351", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007039" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1904352", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007039" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1904375", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -175763,27 +173819,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0045184" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905153", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010324" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905154", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010324" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905155", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010324" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905475", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -175812,27 +173847,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905952", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010876" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905953", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010876" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905954", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0010876" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1990234", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_1902494" ], @@ -175840,13 +173854,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016740" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1990351", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032991" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005215" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_1990778", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008104" ], @@ -175861,6 +173868,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005773" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_2000026", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007275" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_2000241", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0065007" ], @@ -176235,6 +174249,30 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000922", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000468" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002489", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000068" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002493", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000068" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0009953", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000468" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002489", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000092" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001993" + } ] } ], "domainRangeAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -176250,6 +174288,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -176263,12 +174305,28 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/GO_0001700", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" + }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005634", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0009792", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051321", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", @@ -176300,7 +174358,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -176308,7 +174366,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -176354,7 +174412,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002334", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -176449,6 +174508,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000086", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ], "propertyChainAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", @@ -176468,6 +174530,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] @@ -176498,9 +174563,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0002025" ] @@ -176654,12 +174716,30 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/RO_0002082" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] @@ -176675,12 +174755,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] } ] } ] } \ No newline at end of file diff --git a/phipo.obo b/phipo.obo index 8c1bbba..f455282 100644 --- a/phipo.obo +++ b/phipo.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-01-31 +data-version: releases/2024-04-04 subsetdef: 1_STAR "" subsetdef: 2_STAR "" subsetdef: 3_STAR "" @@ -7,6 +7,7 @@ subsetdef: abnormal_slim "" subsetdef: absent_slim "" subsetdef: attribute_slim "" subsetdef: cell_quality "" +subsetdef: cellxgene_subset "" subsetdef: common_anatomy "" subsetdef: disposition_slim "" subsetdef: efo_slim "" @@ -31,29 +32,33 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: mpath_slim "" -subsetdef: prokaryote_subset "" +subsetdef: pheno_slim "" subsetdef: relational_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" -subsetdef: term_scheduled_for_obsoletion "" +subsetdef: uberon_slim "" subsetdef: ubprop:upper_level "" subsetdef: upper_level "" subsetdef: value_slim "" +subsetdef: vertebrate_core "" synonymtypedef: blast_name "" synonymtypedef: BRAND_NAME "" -synonymtypedef: common_name "" +synonymtypedef: equivalent_name "" synonymtypedef: genbank_common_name "" +synonymtypedef: in_part "" synonymtypedef: INN "" synonymtypedef: IUPAC_NAME "" +synonymtypedef: OMO:0003003 "" +synonymtypedef: OMO:0003011 "" synonymtypedef: synonym "" ontology: phipo property_value: created:by "alaynecuzick" xsd:string property_value: creation:date "2018-07-09T13:43:00Z" xsd:string -property_value: dc-description "Ontology of species-neutral phenotypes observed in pathogen-host interactions." xsd:string -property_value: dc-title "Pathogen Host Interactions Phenotype Ontology" xsd:string -property_value: dcterms-license "https://creativecommons.org/licenses/by/3.0/" xsd:string -property_value: owl:versionInfo "2024-01-31" xsd:string +property_value: http://purl.org/dc/elements/1.1/description "Ontology of species-neutral phenotypes observed in pathogen-host interactions." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Pathogen Host Interactions Phenotype Ontology" xsd:string +property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/3.0/" xsd:string +property_value: owl:versionInfo "2024-04-04" xsd:string [Term] id: BFO:0000001 @@ -116,8 +121,8 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000020 ! characteristic +disjoint_from: BFO:0000020 ! characteristic disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant property_value: BFO:0000179 "ic" xsd:string @@ -146,6 +151,7 @@ def: "An occurrent that has temporal proper parts and for some time t, p s-depen def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent +relationship: part_of BFO:0000015 {all_only="true"} ! process property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string @@ -179,9 +185,10 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 +name: realizable name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity property_value: BFO:0000179 "realizable" xsd:string @@ -200,11 +207,12 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic relationship: part_of BFO:0000019 {all_only="true"} ! quality [Term] id: BFO:0000020 +name: characteristic name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} @@ -212,7 +220,8 @@ def: "b is a specifically dependent continuant = Def. b is a continuant & there comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant +relationship: has_part BFO:0000020 {all_only="true"} ! characteristic +relationship: part_of BFO:0000020 {all_only="true"} ! characteristic property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string @@ -230,13 +239,14 @@ property_value: IAO:0000116 "Specifically dependent continuant doesn't have a cl property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string [Term] id: BFO:0000023 name: role def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] -is_a: CHEBI:50906 ! role -equivalent_to: CHEBI:50906 ! role +is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000031 @@ -2255,6 +2265,7 @@ is_a: CHEBI:35107 ! azane is_a: CHEBI:37176 ! mononuclear parent hydride relationship: is_conjugate_acid_of CHEBI:29337 ! azanide relationship: is_conjugate_base_of CHEBI:28938 ! ammonium +relationship: RO:0000087 CHEBI:228364 ! has role NMR chemical shift reference compound relationship: RO:0000087 CHEBI:50910 ! has role neurotoxin relationship: RO:0000087 CHEBI:59740 ! has role nucleophilic reagent relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite @@ -5968,6 +5979,22 @@ is_a: CHEBI:27171 ! organic heterobicyclic compound is_a: CHEBI:38101 ! organonitrogen heterocyclic compound is_a: CHEBI:38180 ! polycyclic heteroarene +[Term] +id: CHEBI:228364 +name: NMR chemical shift reference compound +namespace: chebi_ontology +def: "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing." [] +subset: 3_STAR +synonym: "NMR chemical shift reference compounds" RELATED [ChEBI] +synonym: "NMR chemical shift standard" RELATED [ChEBI] +synonym: "NMR chemical shift standards" RELATED [ChEBI] +synonym: "NMR internal standard" RELATED [ChEBI] +synonym: "NMR internal standards" RELATED [ChEBI] +synonym: "NMR reference standard" RELATED [ChEBI] +synonym: "NMR reference standards" RELATED [ChEBI] +is_a: CHEBI:33232 ! application +is_a: CHEBI:51086 ! chemical role + [Term] id: CHEBI:22888 name: biphenyls @@ -6753,7 +6780,6 @@ namespace: chebi_ontology def: "A role played by the molecular entity or part thereof within a biological context." [] subset: 3_STAR synonym: "biological function" RELATED [ChEBI] -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -8097,6 +8123,7 @@ xref: Reaxys:1921286 {source="Reaxys"} xref: Wikipedia:Phosphoric_Acid is_a: CHEBI:59698 ! phosphoric acids relationship: is_conjugate_acid_of CHEBI:39745 ! dihydrogenphosphate +relationship: RO:0000087 CHEBI:228364 ! has role NMR chemical shift reference compound relationship: RO:0000087 CHEBI:33287 ! has role fertilizer relationship: RO:0000087 CHEBI:46787 ! has role solvent relationship: RO:0000087 CHEBI:77746 ! has role human metabolite @@ -13497,7 +13524,6 @@ name: application namespace: chebi_ontology def: "Intended use of the molecular entity or part thereof by humans." [] subset: 3_STAR -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -14910,10 +14936,17 @@ property_value: http://purl.obolibrary.org/obo/chebi/smiles "NC1NC(CC=N1)[C@@H]1 id: CHEBI:33710 name: alpha-amino-acid residue namespace: chebi_ontology +def: "An amino-acid residue derived from an alpha-amino acid." [] subset: 3_STAR synonym: "alpha-amino-acid residues" RELATED [ChEBI] +synonym: "an alpha-amino acid residue" RELATED [UniProt] is_a: CHEBI:33708 ! amino-acid residue relationship: is_substituent_group_from CHEBI:33704 ! alpha-amino acid +property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string +property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H2NOR" xsd:string +property_value: http://purl.obolibrary.org/obo/chebi/mass "56.043" xsd:string +property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "56.01364" xsd:string +property_value: http://purl.obolibrary.org/obo/chebi/smiles "*-NC([*])C(-*)=O" xsd:string [Term] id: CHEBI:33719 @@ -24463,7 +24496,7 @@ name: role namespace: chebi_ontology def: "A role is particular behaviour which a material entity may exhibit." [] subset: 3_STAR -is_a: BFO:0000023 ! role +is_a: PATO:0000001 ! quality [Term] id: CHEBI:50908 @@ -24617,7 +24650,6 @@ name: chemical role namespace: chebi_ontology def: "A role played by the molecular entity or part thereof within a chemical context." [] subset: 3_STAR -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -35840,7 +35872,11 @@ property_value: http://purl.obolibrary.org/obo/chebi/smiles "CC(C)[C@H]1OC(=O)C2 id: CL:0000000 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +def: "A material entity that has a plasma membrane and results from cellular division." [] +comment: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. +subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 @@ -35855,16 +35891,98 @@ is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: has_part GO:0005634 {gci_filler="PATO:0001407", gci_relation="bearer_of"} ! nucleus -relationship: has_part GO:0005634 {gci_filler="PATO:0001908", gci_relation="bearer_of"} ! nucleus -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: has_part GO:0005634 {gci_filler="PATO:0001407", gci_relation="bearer_of"} ! cell nucleus +relationship: has_part GO:0005634 {gci_filler="PATO:0001908", gci_relation="bearer_of"} ! cell nucleus +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl +[Term] +id: CL:0000151 +name: secretory cell +def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] +subset: cellxgene_subset +xref: BTO:0003659 +xref: FMA:86916 +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: capable_of GO:0032940 ! secretion by cell +relationship: capable_of GO:0032940 ! secretion by cell + +[Term] +id: CL:0000154 +name: protein secreting cell +is_a: CL:0000151 ! secretory cell +intersection_of: CL:0000151 ! secretory cell +intersection_of: capable_of GO:0009306 ! protein secretion +relationship: capable_of GO:0009306 ! protein secretion + +[Term] +id: CL:0000225 +name: anucleate cell +def: "A cell that lacks a nucleus." [FB:ma] +synonym: "non-nucleated cell" EXACT [] +xref: FMA:68647 +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001405 ! anucleate +disjoint_from: CL:0002242 ! nucleate cell +relationship: bearer_of PATO:0001405 ! anucleate + +[Term] +id: CL:0000226 +name: single nucleate cell +def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +is_a: CL:0002242 ! nucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001407 ! mononucleate +relationship: bearer_of PATO:0001407 ! mononucleate + +[Term] +id: CL:0000227 +name: binucleate cell +is_a: CL:0000228 ! multinucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001406 ! binucleate +relationship: bearer_of PATO:0001406 ! binucleate + +[Term] +id: CL:0000228 +name: multinucleate cell +def: "A cell with more than one nucleus." [FB:ma] +synonym: "syncitium" EXACT [] +synonym: "syncytial cell" EXACT [] +synonym: "syncytium" EXACT [] +xref: AEO:0000203 +xref: WBbt:0008074 +is_a: CL:0002242 ! nucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001908 ! multinucleate +relationship: bearer_of PATO:0001908 ! multinucleate + +[Term] +id: CL:0000255 +name: eukaryotic cell +subset: cellxgene_subset +xref: MESH:D005057 +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota + +[Term] +id: CL:0000521 +name: fungal cell +is_a: CL:0000255 ! eukaryotic cell +intersection_of: CL:0000000 ! cell +intersection_of: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi +relationship: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi + [Term] id: CL:0001061 name: abnormal cell def: "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models." [GOC:add, GOC:cg, GOC:wdd] comment: https://github.com/obophenotype/cell-ontology/issues/448 +subset: cellxgene_subset xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -35874,15 +35992,27 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001 property_value: http://purl.org/dc/terms/date "2017-01-30T18:53:32Z" xsd:dateTime [Term] -id: CL:0017505 -name: increased nucleus size -def: "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." [GOC:tfm] -is_a: GO:0005634 ! nucleus -intersection_of: GO:0005634 ! nucleus -intersection_of: bearer_of PATO:0000586 ! increased size -relationship: bearer_of PATO:0000586 ! increased size +id: CL:0002242 +name: nucleate cell +def: "A cell containing at least one nucleus." [GOC:tfm] +xref: FMA:67513 +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0002505 ! nucleated +relationship: bearer_of PATO:0002505 ! nucleated property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2009-12-23T10:53:24Z +creation_date: 2010-09-07T03:32:33Z + +[Term] +id: CL:0011115 +name: precursor cell +def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] +comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. +subset: cellxgene_subset +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: capable_of GO:0030154 ! cell differentiation +relationship: capable_of GO:0030154 ! cell differentiation [Term] id: GO:0000003 @@ -35898,7 +36028,7 @@ subset: goslim_pir subset: goslim_plant synonym: "reproductive physiological process" EXACT [] xref: Wikipedia:Reproduction -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl @@ -35939,35 +36069,8 @@ subset: goslim_pir synonym: "karyokinesis" RELATED [] is_a: GO:0048285 ! organelle fission intersection_of: GO:0048285 ! organelle fission -intersection_of: results_in_fission_of GO:0005634 ! nucleus -relationship: results_in_fission_of GO:0005634 ! nucleus - -[Term] -id: GO:0000740 -name: nuclear membrane fusion -namespace: biological_process -def: "The joining of 2 or more lipid bilayer membranes that surround the nucleus." [GOC:elh] -is_a: GO:0071763 ! nuclear membrane organization -is_a: GO:0090174 ! organelle membrane fusion -intersection_of: GO:0061025 ! membrane fusion -intersection_of: results_in_fusion_of GO:0031965 ! nuclear membrane -relationship: results_in_fusion_of GO:0031965 ! nuclear membrane - -[Term] -id: GO:0000741 -name: karyogamy -namespace: biological_process -alt_id: GO:0007335 -def: "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei." [GOC:elh] -synonym: "nuclear fusion" EXACT [] -synonym: "nuclear fusion during karyogamy" EXACT [] -xref: Wikipedia:Karyogamy -is_a: GO:0006997 ! nucleus organization -is_a: GO:0048284 ! organelle fusion -intersection_of: GO:0048284 ! organelle fusion -intersection_of: results_in_fusion_of GO:0005634 ! nucleus -relationship: part_of GO:0006997 ! nucleus organization -relationship: results_in_fusion_of GO:0005634 ! nucleus +intersection_of: results_in_fission_of GO:0005634 ! cell nucleus +relationship: results_in_fission_of GO:0005634 ! cell nucleus [Term] id: GO:0001677 @@ -35981,6 +36084,15 @@ intersection_of: results_in_assembly_of GO:0044207 ! translation initiation tern relationship: part_of GO:0006413 ! translational initiation relationship: results_in_assembly_of GO:0044207 ! translation initiation ternary complex +[Term] +id: GO:0001700 +name: embryonic development via the syncytial blastoderm +namespace: biological_process +def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster." [GOC:go_curators, GOC:mtg_sensu] +is_a: GO:0009792 ! embryo development ending in birth or egg hatching +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta + [Term] id: GO:0002252 name: immune effector process @@ -36002,7 +36114,7 @@ subset: goslim_generic subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase property_value: RO:0002161 NCBITaxon:4895 @@ -36083,12 +36195,14 @@ intersection_of: part_of GO:0000003 ! reproduction [Term] id: GO:0003674 +name: gene product or complex activity name: molecular_function namespace: molecular_function alt_id: GO:0005554 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +comment: This is the same as GO molecular function subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics @@ -36098,7 +36212,7 @@ subset: goslim_yeast synonym: "molecular function" EXACT [] is_a: BFO:0000015 ! process disjoint_from: GO:0005575 ! cellular_component -disjoint_from: GO:0008150 ! biological_process +disjoint_from: GO:0008150 ! biological process [Term] id: GO:0003676 @@ -36235,36 +36349,11 @@ subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote -subset: prokaryote_subset synonym: "carrier" RELATED [] xref: Reactome:R-HSA-168313 "Virion-associated M2 protein mediated ion infusion" xref: Reactome:R-HSA-178215 "SMAD7:SMURF1 complex is exported to the cytosol" is_a: GO:0003674 ! molecular_function -[Term] -id: GO:0005319 -name: lipid transporter activity -namespace: molecular_function -def: "Enables the directed movement of lipids into, out of or within a cell, or between cells." [GOC:ai] -synonym: "apolipoprotein" RELATED [] -synonym: "lipophorin" NARROW [] -xref: Reactome:R-HSA-1369028 "ABCAs mediate lipid efflux" -xref: Reactome:R-HSA-1369052 "ABCAs mediate lipid influx" -xref: Reactome:R-HSA-174786 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex" -xref: Reactome:R-HSA-5682285 "ABCA12 transports lipids from cytosol to extracellular region" -xref: Reactome:R-HSA-5682311 "Defective ABCA12 does not transport lipids from cytosol to extracellular region" -xref: Reactome:R-HSA-5683672 "Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body" -xref: Reactome:R-HSA-5683714 "ABCA3 transports PC, PG from ER membrane to lamellar body" -xref: Reactome:R-HSA-5688397 "Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body" -xref: Reactome:R-HSA-6801250 "TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane" -xref: Reactome:R-HSA-8848053 "ABCA5 transports CHOL from lysosomal lumen to cytosol" -xref: Reactome:R-HSA-8866329 "MTTP lipidates APOB-100, forming a pre-VLDL" -is_a: GO:0005215 ! transporter activity -intersection_of: GO:0005215 ! transporter activity -intersection_of: has_primary_input CHEBI:18059 ! lipid -relationship: has_primary_input CHEBI:18059 ! lipid -relationship: part_of GO:0006869 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! lipid transport - [Term] id: GO:0005488 name: binding @@ -36299,10 +36388,8 @@ id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 -def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao1337158144] def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. -comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics @@ -36314,7 +36401,7 @@ synonym: "cellular component" EXACT [] synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315] xref: NIF_Subcellular:sao1337158144 is_a: BFO:0000040 ! material entity -disjoint_from: GO:0008150 ! biological_process +disjoint_from: GO:0008150 ! biological process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17729" xsd:anyURI [Term] @@ -36332,8 +36419,8 @@ subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant +subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular is_a: GO:0110165 ! cellular anatomical entity @@ -36359,6 +36446,7 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ [Term] id: GO:0005634 +name: cell nucleus name: nucleus namespace: cellular_component def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] @@ -36379,8 +36467,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005635 @@ -36393,7 +36481,7 @@ subset: goslim_generic subset: goslim_plant xref: Wikipedia:Nuclear_envelope is_a: GO:0031967 ! organelle envelope -relationship: part_of GO:0005634 ! nucleus +relationship: part_of GO:0005634 ! cell nucleus relationship: part_of GO:0012505 ! endomembrane system [Term] @@ -36408,7 +36496,6 @@ subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset xref: Wikipedia:Cytoplasm is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005622 ! intracellular anatomical structure @@ -36474,7 +36561,6 @@ subset: goslim_mouse subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "bacterial inner membrane" NARROW [] synonym: "cell membrane" EXACT [] synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645] @@ -36563,22 +36649,6 @@ intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:61120 ! nucleobase-containing molecular entity relationship: has_primary_input_or_output CHEBI:61120 ! nucleobase-containing molecular entity -[Term] -id: GO:0006401 -name: RNA catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732] -subset: goslim_yeast -synonym: "RNA breakdown" EXACT [] -synonym: "RNA catabolism" EXACT [] -synonym: "RNA degradation" EXACT [] -is_a: GO:0009057 ! macromolecule catabolic process -is_a: GO:0016070 ! RNA metabolic process -is_a: GO:0034655 ! nucleobase-containing compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33697 ! ribonucleic acid -relationship: has_primary_input CHEBI:33697 ! ribonucleic acid - [Term] id: GO:0006403 name: RNA localization @@ -36603,7 +36673,7 @@ subset: goslim_drosophila subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "protein anabolism" EXACT [] synonym: "protein biosynthesis" EXACT [] synonym: "protein biosynthetic process" EXACT [] @@ -36676,9 +36746,7 @@ synonym: "regulation of protein anabolism" EXACT [] synonym: "regulation of protein biosynthesis" EXACT [] synonym: "regulation of protein formation" EXACT [] synonym: "regulation of protein synthesis" EXACT [] -is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010608 ! post-transcriptional regulation of gene expression -is_a: GO:0031326 ! regulation of cellular biosynthetic process is_a: GO:0034248 ! regulation of amide metabolic process is_a: GO:0051246 ! regulation of protein metabolic process intersection_of: GO:0065007 ! biological regulation @@ -36753,17 +36821,15 @@ subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "amino acid and derivative metabolism" RELATED [] synonym: "cellular amino acid and derivative metabolic process" RELATED [] synonym: "cellular amino acid metabolic process" EXACT [] synonym: "cellular amino acid metabolism" EXACT [] -is_a: GO:0019752 ! carboxylic acid metabolic process is_a: GO:0044238 ! primary metabolic process -is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process -intersection_of: has_primary_input_or_output CHEBI:37022 ! amino-acid anion -relationship: has_primary_input_or_output CHEBI:37022 ! amino-acid anion +intersection_of: has_primary_input_or_output CHEBI:35238 ! amino acid zwitterion +relationship: has_primary_input_or_output CHEBI:35238 ! amino acid zwitterion property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI [Term] @@ -36805,14 +36871,10 @@ subset: goslim_plant subset: goslim_pombe subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "lipid metabolism" EXACT [] xref: Wikipedia:Lipid_metabolism is_a: GO:0044238 ! primary metabolic process is_a: GO:0071704 ! organic substance metabolic process -intersection_of: GO:0008152 ! metabolic process -intersection_of: has_primary_input_or_output CHEBI:18059 ! lipid -relationship: has_primary_input_or_output CHEBI:18059 ! lipid [Term] id: GO:0006714 @@ -36912,7 +36974,6 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote -subset: prokaryote_subset synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI @@ -36964,20 +37025,6 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:33709 ! amino acid relationship: has_primary_input CHEBI:33709 ! amino acid -[Term] -id: GO:0006869 -name: lipid transport -namespace: biological_process -def: "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732] -subset: goslim_drosophila -subset: goslim_pir -subset: goslim_yeast -is_a: GO:0071702 ! organic substance transport -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:18059 ! lipid -relationship: has_primary_input CHEBI:18059 ! lipid -relationship: part_of GO:0010876 ! lipid localization - [Term] id: GO:0006886 name: intracellular protein transport @@ -36986,7 +37033,6 @@ alt_id: GO:0032779 def: "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah] subset: goslim_generic subset: goslim_prokaryote -subset: prokaryote_subset synonym: "copper-induced intracellular protein transport" RELATED [GOC:al] is_a: GO:0015031 ! protein transport is_a: GO:0046907 ! intracellular transport @@ -36995,24 +37041,6 @@ intersection_of: has_primary_input PR:000000001 ! protein intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure relationship: part_of GO:0008104 ! protein localization -[Term] -id: GO:0006887 -name: exocytosis -namespace: biological_process -alt_id: GO:0016194 -alt_id: GO:0016195 -def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] -subset: goslim_yeast -synonym: "nonselective vesicle exocytosis" RELATED [] -synonym: "vesicle exocytosis" EXACT [] -xref: Wikipedia:Exocytosis -is_a: GO:0016192 ! vesicle-mediated transport -is_a: GO:0032940 ! secretion by cell -intersection_of: GO:0006810 ! transport -intersection_of: process_has_causal_agent GO:0070382 ! exocytic vesicle -relationship: has_part GO:0099500 ! vesicle fusion to plasma membrane -relationship: process_has_causal_agent GO:0070382 ! exocytic vesicle - [Term] id: GO:0006897 name: endocytosis @@ -37031,7 +37059,6 @@ is_a: GO:0016192 ! vesicle-mediated transport is_a: GO:0098657 ! import into cell relationship: has_part GO:0006900 ! vesicle budding from membrane relationship: has_part GO:0010324 ! membrane invagination -relationship: has_target_end_location GO:0031410 ! cytoplasmic vesicle property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24907" xsd:anyURI property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25268" xsd:anyURI @@ -37055,18 +37082,6 @@ relationship: part_of GO:0016192 ! vesicle-mediated transport created_by: jl creation_date: 2013-12-19T15:26:17Z -[Term] -id: GO:0006906 -name: vesicle fusion -namespace: biological_process -def: "Fusion of the membrane of a transport vesicle with its target membrane." [GOC:jid] -is_a: GO:0016050 ! vesicle organization -is_a: GO:0090174 ! organelle membrane fusion -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0012506 ! vesicle membrane -relationship: part_of GO:0016192 ! vesicle-mediated transport -relationship: results_in_fusion_of GO:0012506 ! vesicle membrane - [Term] id: GO:0006914 name: autophagy @@ -37157,8 +37172,8 @@ synonym: "nuclear organization and biogenesis" RELATED [GOC:mah] synonym: "nucleus organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0005634 ! nucleus -relationship: results_in_organization_of GO:0005634 ! nucleus +intersection_of: results_in_organization_of GO:0005634 ! cell nucleus +relationship: results_in_organization_of GO:0005634 ! cell nucleus [Term] id: GO:0006998 @@ -37230,20 +37245,6 @@ intersection_of: GO:0046907 ! intracellular transport intersection_of: results_in_transport_to_from_or_in GO:0005773 ! vacuole relationship: results_in_transport_to_from_or_in GO:0005773 ! vacuole -[Term] -id: GO:0007039 -name: protein catabolic process in the vacuole -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases." [GOC:mah, GOC:vw] -synonym: "vacuolar protein breakdown" RELATED [] -synonym: "vacuolar protein catabolic process" RELATED [] -synonym: "vacuolar protein catabolism" RELATED [] -synonym: "vacuolar protein degradation" RELATED [] -is_a: GO:0030163 ! protein catabolic process -intersection_of: GO:0030163 ! protein catabolic process -intersection_of: occurs_in GO:0005773 ! vacuole -relationship: occurs_in GO:0005773 ! vacuole - [Term] id: GO:0007049 name: cell cycle @@ -37280,7 +37281,7 @@ is_a: GO:0046907 ! intracellular transport is_a: GO:0051647 ! nucleus localization is_a: GO:0051656 ! establishment of organelle localization intersection_of: GO:0046907 ! intracellular transport -intersection_of: has_primary_input GO:0005634 ! nucleus +intersection_of: has_primary_input GO:0005634 ! cell nucleus [Term] id: GO:0007127 @@ -37313,6 +37314,22 @@ xref: Wikipedia:Meiosis#Meiosis_II is_a: GO:0061983 ! meiosis II cell cycle process is_a: GO:0140013 ! meiotic nuclear division +[Term] +id: GO:0007275 +name: multicellular organism development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb] +comment: Note that this term was 'developmental process'. +subset: gocheck_do_not_annotate +subset: goslim_chembl +subset: goslim_plant +is_a: GO:0032501 ! multicellular organismal process +is_a: GO:0048856 ! anatomical structure development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_developmental_progression_of UBERON:0000468 ! multicellular organism +relationship: results_in_developmental_progression_of UBERON:0000468 ! multicellular organism +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21234" xsd:anyURI + [Term] id: GO:0008061 name: chitin binding @@ -37346,13 +37363,16 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ [Term] id: GO:0008150 +name: biological process name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [] +comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -37368,6 +37388,7 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process +relationship: has_part GO:0003674 ! molecular_function property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl created_by: jl @@ -37392,7 +37413,7 @@ synonym: "metabolism resulting in cell growth" NARROW [] synonym: "multicellular organism metabolic process" NARROW [] synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase disjoint_from: GO:0051179 ! localization created_by: jl @@ -37531,9 +37552,6 @@ synonym: "lipid synthesis" EXACT [] synonym: "lipogenesis" EXACT [GOC:sl] is_a: GO:0006629 ! lipid metabolic process is_a: GO:1901576 ! organic substance biosynthetic process -intersection_of: GO:0009058 ! biosynthetic process -intersection_of: has_primary_output CHEBI:18059 ! lipid -relationship: has_primary_output CHEBI:18059 ! lipid [Term] id: GO:0008641 @@ -37559,7 +37577,6 @@ synonym: "amino acid formation" EXACT [] synonym: "amino acid synthesis" EXACT [] synonym: "cellular amino acid biosynthetic process" EXACT [] xref: Wikipedia:Amino_acid_synthesis -is_a: GO:0006520 ! amino acid metabolic process is_a: GO:0046394 ! carboxylic acid biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process @@ -37587,28 +37604,6 @@ is_a: GO:0008152 ! metabolic process created_by: jl creation_date: 2012-10-17T15:52:35Z -[Term] -id: GO:0009057 -name: macromolecule catabolic process -namespace: biological_process -alt_id: GO:0043285 -alt_id: GO:0044266 -def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] -subset: goslim_pir -synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] -synonym: "cellular macromolecule catabolic process" RELATED [] -synonym: "cellular macromolecule catabolism" RELATED [] -synonym: "cellular macromolecule degradation" RELATED [] -synonym: "macromolecule breakdown" EXACT [] -synonym: "macromolecule catabolism" EXACT [] -synonym: "macromolecule degradation" EXACT [] -synonym: "multicellular organismal macromolecule catabolic process" NARROW [] -is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33694 ! biomacromolecule -relationship: has_primary_input CHEBI:33694 ! biomacromolecule - [Term] id: GO:0009058 name: biosynthetic process @@ -37643,28 +37638,13 @@ synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33694 ! biomacromolecule relationship: has_primary_output CHEBI:33694 ! biomacromolecule -property_value: IAO:0000233 "http://amigo.geneontology.org/amigo/term/GO:0070589" xsd:anyURI - -[Term] -id: GO:0009063 -name: amino acid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents." [GOC:ai] -synonym: "amino acid breakdown" EXACT [] -synonym: "amino acid catabolism" EXACT [] -synonym: "amino acid degradation" EXACT [] -synonym: "cellular amino acid catabolic process" EXACT [] -is_a: GO:0006520 ! amino acid metabolic process -is_a: GO:0046395 ! carboxylic acid catabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:37022 ! amino-acid anion -relationship: has_primary_input CHEBI:37022 ! amino-acid anion -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI [Term] id: GO:0009066 @@ -37762,20 +37742,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:32952 ! amine relationship: has_primary_output CHEBI:32952 ! amine -[Term] -id: GO:0009310 -name: amine catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl, ISBN:0198506732] -synonym: "amine breakdown" EXACT [] -synonym: "amine catabolism" EXACT [] -synonym: "amine degradation" EXACT [] -is_a: GO:0009308 ! amine metabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:32952 ! amine -relationship: has_primary_input CHEBI:32952 ! amine - [Term] id: GO:0009403 name: toxin biosynthetic process @@ -37849,6 +37815,43 @@ xref: Wikipedia:Morphogenesis is_a: GO:0032502 ! developmental process relationship: part_of GO:0048856 ! anatomical structure development +[Term] +id: GO:0009790 +name: embryo development +namespace: biological_process +alt_id: GO:0009795 +def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] +subset: gocheck_do_not_manually_annotate +subset: goslim_chembl +subset: goslim_plant +synonym: "embryogenesis" EXACT [] +synonym: "embryogenesis and morphogenesis" BROAD [] +synonym: "embryonal development" EXACT [] +xref: Wikipedia:Embryogenesis +is_a: GO:0007275 ! multicellular organism development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_development_of UBERON:0000922 ! embryo +relationship: results_in_development_of UBERON:0000922 ! embryo + +[Term] +id: GO:0009791 +name: post-embryonic development +namespace: biological_process +def: "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC:go_curators] +subset: goslim_plant +is_a: GO:0032501 ! multicellular organismal process +relationship: part_of GO:0007275 ! multicellular organism development + +[Term] +id: GO:0009792 +name: embryo development ending in birth or egg hatching +namespace: biological_process +def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] +synonym: "embryogenesis" BROAD [] +is_a: GO:0009790 ! embryo development +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa + [Term] id: GO:0009847 name: spore germination @@ -37954,56 +37957,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008152 ! metabolic process relationship: positively_regulates GO:0008152 ! metabolic process -[Term] -id: GO:0009894 -name: regulation of catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] -synonym: "regulation of breakdown" EXACT [] -synonym: "regulation of catabolism" EXACT [] -synonym: "regulation of degradation" EXACT [] -is_a: GO:0019222 ! regulation of metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0009056 ! catabolic process -relationship: regulates GO:0009056 ! catabolic process - -[Term] -id: GO:0009895 -name: negative regulation of catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] -synonym: "down regulation of catabolic process" EXACT [] -synonym: "down-regulation of catabolic process" EXACT [] -synonym: "downregulation of catabolic process" EXACT [] -synonym: "inhibition of catabolic process" NARROW [] -synonym: "negative regulation of breakdown" EXACT [] -synonym: "negative regulation of catabolism" EXACT [] -synonym: "negative regulation of degradation" EXACT [] -is_a: GO:0009892 ! negative regulation of metabolic process -is_a: GO:0009894 ! regulation of catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0009056 ! catabolic process -relationship: negatively_regulates GO:0009056 ! catabolic process - -[Term] -id: GO:0009896 -name: positive regulation of catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] -synonym: "activation of catabolic process" NARROW [] -synonym: "positive regulation of breakdown" EXACT [] -synonym: "positive regulation of catabolism" EXACT [] -synonym: "positive regulation of degradation" EXACT [] -synonym: "stimulation of catabolic process" NARROW [] -synonym: "up regulation of catabolic process" EXACT [] -synonym: "up-regulation of catabolic process" EXACT [] -synonym: "upregulation of catabolic process" EXACT [] -is_a: GO:0009893 ! positive regulation of metabolic process -is_a: GO:0009894 ! regulation of catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0009056 ! catabolic process -relationship: positively_regulates GO:0009056 ! catabolic process - [Term] id: GO:0009987 name: cellular process @@ -38019,7 +37972,7 @@ synonym: "cell growth and/or maintenance" NARROW [] synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase created_by: jl creation_date: 2012-12-11T16:56:55Z @@ -38053,11 +38006,12 @@ creation_date: 2013-12-02T13:58:34Z id: GO:0010467 name: gene expression namespace: biological_process -def: "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes." [GOC:txnOH-2018, PMID:25934543, PMID:31580950] +def: "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes." [GOC:txnOH-2018, PMID:25934543, PMID:31580950] subset: goslim_flybase_ribbon xref: Wikipedia:Gene_expression -is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0009059 ! macromolecule biosynthetic process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22557" xsd:anyURI +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25419" xsd:anyURI [Term] id: GO:0010468 @@ -38069,7 +38023,7 @@ synonym: "gene regulation" RELATED [GOC:cjm] synonym: "regulation of gene product expression" RELATED [] synonym: "regulation of protein expression" NARROW [] xref: Wikipedia:Regulation_of_gene_expression -is_a: GO:0060255 ! regulation of macromolecule metabolic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010467 ! gene expression relationship: regulates GO:0010467 ! gene expression @@ -38090,7 +38044,7 @@ id: GO:0010556 name: regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] -is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009059 ! macromolecule biosynthetic process @@ -38101,9 +38055,9 @@ id: GO:0010557 name: positive regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] -is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: positively_regulates GO:0009059 ! macromolecule biosynthetic process @@ -38113,9 +38067,9 @@ id: GO:0010558 name: negative regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] -is_a: GO:0009890 ! negative regulation of biosynthetic process is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: negatively_regulates GO:0009059 ! macromolecule biosynthetic process @@ -38174,17 +38128,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042181 ! ketone biosynthetic process relationship: regulates GO:0042181 ! ketone biosynthetic process -[Term] -id: GO:0010567 -name: regulation of ketone catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells." [GOC:dph, GOC:tb] -is_a: GO:0010565 ! regulation of cellular ketone metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0042182 ! ketone catabolic process -relationship: regulates GO:0042182 ! ketone catabolic process - [Term] id: GO:0010604 name: positive regulation of macromolecule metabolic process @@ -38221,7 +38164,7 @@ name: positive regulation of gene expression namespace: biological_process def: "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." [GOC:txnOH-2018] is_a: GO:0010468 ! regulation of gene expression -is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010467 ! gene expression relationship: positively_regulates GO:0010467 ! gene expression @@ -38235,7 +38178,7 @@ def: "Any process that decreases the frequency, rate or extent of gene expressio comment: This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. synonym: "gene silencing" RELATED [] is_a: GO:0010468 ! regulation of gene expression -is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010467 ! gene expression relationship: negatively_regulates GO:0010467 ! gene expression @@ -38268,15 +38211,26 @@ intersection_of: negatively_regulates GO:0006996 ! organelle organization relationship: negatively_regulates GO:0006996 ! organelle organization [Term] -id: GO:0010876 -name: lipid localization +id: GO:0010720 +name: positive regulation of cell development namespace: biological_process -def: "Any process in which a lipid is transported to, or maintained in, a specific location." [GOC:BHF, GOC:dph, GOC:tb] -synonym: "lipid localisation" EXACT [GOC:mah] -is_a: GO:0033036 ! macromolecule localization -intersection_of: GO:0033036 ! macromolecule localization -intersection_of: has_primary_input CHEBI:18059 ! lipid -relationship: has_primary_input CHEBI:18059 ! lipid +def: "Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048468 ! cell development +relationship: positively_regulates GO:0048468 ! cell development + +[Term] +id: GO:0010721 +name: negative regulation of cell development +namespace: biological_process +def: "Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048468 ! cell development +relationship: negatively_regulates GO:0048468 ! cell development [Term] id: GO:0010927 @@ -38353,17 +38307,6 @@ relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane relationship: part_of CL:0000000 ! cell -[Term] -id: GO:0012506 -name: vesicle membrane -namespace: cellular_component -def: "The lipid bilayer surrounding any membrane-bounded vesicle in the cell." [GOC:mah, GOC:vesicle] -xref: NIF_Subcellular:sao1153182838 -is_a: GO:0031090 ! organelle membrane -intersection_of: GO:0016020 ! membrane -intersection_of: part_of GO:0031982 ! vesicle -relationship: part_of GO:0031982 ! vesicle - [Term] id: GO:0015031 name: protein transport @@ -38504,9 +38447,6 @@ synonym: "multicellular organismal lipid catabolic process" NARROW [] xref: Wikipedia:Lipid_catabolism is_a: GO:0006629 ! lipid metabolic process is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:18059 ! lipid -relationship: has_primary_input CHEBI:18059 ! lipid [Term] id: GO:0016043 @@ -38540,9 +38480,6 @@ subset: goslim_yeast synonym: "vesicle organisation" EXACT [] synonym: "vesicle organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0031982 ! vesicle -relationship: results_in_organization_of GO:0031982 ! vesicle [Term] id: GO:0016053 @@ -38561,22 +38498,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:64709 ! organic acid relationship: has_primary_output CHEBI:64709 ! organic acid -[Term] -id: GO:0016054 -name: organic acid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] -synonym: "organic acid breakdown" EXACT [] -synonym: "organic acid catabolism" EXACT [] -synonym: "organic acid degradation" EXACT [] -is_a: GO:0006082 ! organic acid metabolic process -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:0044282 ! small molecule catabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:64709 ! organic acid -relationship: has_primary_input CHEBI:64709 ! organic acid - [Term] id: GO:0016070 name: RNA metabolic process @@ -38586,7 +38507,7 @@ subset: goslim_agr subset: goslim_candida subset: goslim_metagenomics subset: goslim_pir -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "RNA metabolism" EXACT [] is_a: GO:0090304 ! nucleic acid metabolic process intersection_of: GO:0008152 ! metabolic process @@ -38637,9 +38558,6 @@ synonym: "vesicle transport" EXACT [] synonym: "vesicular transport" EXACT [GOC:mah] is_a: GO:0006810 ! transport is_a: GO:0009987 ! cellular process -intersection_of: GO:0006810 ! transport -intersection_of: process_has_causal_agent GO:0031982 ! vesicle -relationship: process_has_causal_agent GO:0031982 ! vesicle property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25421" xsd:anyURI [Term] @@ -38702,7 +38620,6 @@ subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset xref: EC:2.-.-.- xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" @@ -38926,26 +38843,13 @@ synonym: "negative regulation of protein synthesis" EXACT [] synonym: "protein biosynthesis inhibitor activity" RELATED [] synonym: "protein biosynthetic process inhibitor activity" RELATED [] is_a: GO:0006417 ! regulation of translation -is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process is_a: GO:0010629 ! negative regulation of gene expression -is_a: GO:0031327 ! negative regulation of cellular biosynthetic process is_a: GO:0034249 ! negative regulation of amide metabolic process is_a: GO:0051248 ! negative regulation of protein metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006412 ! translation relationship: negatively_regulates GO:0006412 ! translation -[Term] -id: GO:0017157 -name: regulation of exocytosis -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of exocytosis." [GOC:go_curators] -is_a: GO:0060627 ! regulation of vesicle-mediated transport -is_a: GO:1903530 ! regulation of secretion by cell -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006887 ! exocytosis -relationship: regulates GO:0006887 ! exocytosis - [Term] id: GO:0018130 name: heterocycle biosynthetic process @@ -38982,17 +38886,6 @@ synonym: "host organism" EXACT [] xref: Wikipedia:Host_(biology) is_a: GO:0110165 ! cellular anatomical entity -[Term] -id: GO:0019216 -name: regulation of lipid metabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] -synonym: "regulation of lipid metabolism" EXACT [] -is_a: GO:0080090 ! regulation of primary metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006629 ! lipid metabolic process -relationship: regulates GO:0006629 ! lipid metabolic process - [Term] id: GO:0019219 name: regulation of nucleobase-containing compound metabolic process @@ -39050,22 +38943,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33655 ! aromatic compound relationship: has_primary_output CHEBI:33655 ! aromatic compound -[Term] -id: GO:0019439 -name: aromatic compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] -synonym: "aromatic compound breakdown" EXACT [] -synonym: "aromatic compound catabolism" EXACT [] -synonym: "aromatic compound degradation" EXACT [] -synonym: "aromatic hydrocarbon catabolic process" NARROW [] -synonym: "aromatic hydrocarbon catabolism" NARROW [] -is_a: GO:0006725 ! cellular aromatic compound metabolic process -is_a: GO:0044248 ! cellular catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33655 ! aromatic compound -relationship: has_primary_input CHEBI:33655 ! aromatic compound - [Term] id: GO:0019538 name: protein metabolic process @@ -39276,8 +39153,8 @@ alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: goslim_generic synonym: "single organism reproductive process" RELATED [] -is_a: GO:0008150 ! biological_process -intersection_of: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process +intersection_of: GO:0008150 ! biological process intersection_of: part_of GO:0000003 ! reproduction disjoint_from: GO:0044848 ! biological phase relationship: part_of GO:0000003 ! reproduction @@ -39326,61 +39203,22 @@ relationship: part_of GO:0022613 ! ribonucleoprotein complex biogenesis relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex [Term] -id: GO:0030100 -name: regulation of endocytosis +id: GO:0030154 +name: cell differentiation namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of endocytosis." [GOC:go_curators] -is_a: GO:0051128 ! regulation of cellular component organization -is_a: GO:0060627 ! regulation of vesicle-mediated transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006897 ! endocytosis -relationship: regulates GO:0006897 ! endocytosis - -[Term] -id: GO:0030133 -name: transport vesicle -namespace: cellular_component -def: "Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell." [GOC:mah, PMID:22160157] -comment: Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'. -synonym: "constitutive secretory pathway transport vesicle" EXACT [] -synonym: "Golgi to vacuole transport vesicle" NARROW [] -synonym: "Golgi-vacuole transport vesicle" NARROW [] -synonym: "secretory vesicle" RELATED [] -xref: NIF_Subcellular:sao885490876 -is_a: GO:0031410 ! cytoplasmic vesicle -relationship: part_of GO:0012505 ! endomembrane system - -[Term] -id: GO:0030163 -name: protein catabolic process -namespace: biological_process -alt_id: GO:0044254 -alt_id: GO:0044257 -def: "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:mah] -comment: This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children. -subset: goslim_candida +def: "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732] +subset: goslim_agr +subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic -subset: goslim_pombe -subset: prokaryote_subset -synonym: "cellular protein breakdown" EXACT [] -synonym: "cellular protein catabolic process" EXACT [] -synonym: "cellular protein catabolism" EXACT [] -synonym: "cellular protein degradation" EXACT [] -synonym: "multicellular organismal protein catabolic process" NARROW [] -synonym: "pheromone catabolic process" RELATED [] -synonym: "pheromone catabolism" RELATED [] -synonym: "protein breakdown" EXACT [] -synonym: "protein catabolism" EXACT [] -synonym: "protein degradation" EXACT [] -xref: Wikipedia:Protein_catabolism -is_a: GO:0009057 ! macromolecule catabolic process -is_a: GO:0019538 ! protein metabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input PR:000000001 ! protein -relationship: has_primary_input PR:000000001 ! protein -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI +subset: goslim_mouse +subset: goslim_plant +xref: Wikipedia:Cellular_differentiation +is_a: GO:0048869 ! cellular developmental process +intersection_of: GO:0048869 ! cellular developmental process +intersection_of: results_in_acquisition_of_features_of CL:0000000 ! cell +relationship: results_in_acquisition_of_features_of CL:0000000 ! cell +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24390" xsd:anyURI [Term] id: GO:0030246 @@ -39483,16 +39321,6 @@ synonym: "symbiont invasive hypha formation within host" EXACT [] is_a: GO:0030447 ! filamentous growth property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/19013" xsd:anyURI -[Term] -id: GO:0030659 -name: cytoplasmic vesicle membrane -namespace: cellular_component -def: "The lipid bilayer surrounding a cytoplasmic vesicle." [GOC:mah] -is_a: GO:0012506 ! vesicle membrane -intersection_of: GO:0016020 ! membrane -intersection_of: part_of GO:0031410 ! cytoplasmic vesicle -relationship: part_of GO:0031410 ! cytoplasmic vesicle - [Term] id: GO:0031090 name: organelle membrane @@ -39611,59 +39439,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0044249 ! cellular biosynthetic process relationship: positively_regulates GO:0044249 ! cellular biosynthetic process -[Term] -id: GO:0031329 -name: regulation of cellular catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -synonym: "regulation of cellular breakdown" EXACT [] -synonym: "regulation of cellular catabolism" EXACT [] -synonym: "regulation of cellular degradation" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0044248 ! cellular catabolic process -relationship: regulates GO:0044248 ! cellular catabolic process - -[Term] -id: GO:0031330 -name: negative regulation of cellular catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -synonym: "down regulation of cellular catabolic process" EXACT [] -synonym: "down-regulation of cellular catabolic process" EXACT [] -synonym: "downregulation of cellular catabolic process" EXACT [] -synonym: "inhibition of cellular catabolic process" NARROW [] -synonym: "negative regulation of cellular breakdown" EXACT [] -synonym: "negative regulation of cellular catabolism" EXACT [] -synonym: "negative regulation of cellular degradation" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0044248 ! cellular catabolic process -relationship: negatively_regulates GO:0044248 ! cellular catabolic process - -[Term] -id: GO:0031331 -name: positive regulation of cellular catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -synonym: "activation of cellular catabolic process" NARROW [] -synonym: "positive regulation of cellular breakdown" EXACT [] -synonym: "positive regulation of cellular catabolism" EXACT [] -synonym: "positive regulation of cellular degradation" EXACT [] -synonym: "stimulation of cellular catabolic process" NARROW [] -synonym: "up regulation of cellular catabolic process" EXACT [] -synonym: "up-regulation of cellular catabolic process" EXACT [] -synonym: "upregulation of cellular catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0044248 ! cellular catabolic process -relationship: positively_regulates GO:0044248 ! cellular catabolic process - [Term] id: GO:0031333 name: negative regulation of protein-containing complex assembly @@ -39698,71 +39473,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0065003 ! protein-containing complex assembly relationship: positively_regulates GO:0065003 ! protein-containing complex assembly -[Term] -id: GO:0031338 -name: regulation of vesicle fusion -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of vesicle fusion." [GOC:mah] -is_a: GO:0033043 ! regulation of organelle organization -is_a: GO:0060627 ! regulation of vesicle-mediated transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006906 ! vesicle fusion -relationship: regulates GO:0006906 ! vesicle fusion - -[Term] -id: GO:0031339 -name: negative regulation of vesicle fusion -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion." [GOC:mah] -synonym: "down regulation of vesicle fusion" EXACT [] -synonym: "down-regulation of vesicle fusion" EXACT [] -synonym: "downregulation of vesicle fusion" EXACT [] -synonym: "inhibition of vesicle fusion" NARROW [] -is_a: GO:0010639 ! negative regulation of organelle organization -is_a: GO:0031338 ! regulation of vesicle fusion -is_a: GO:0051051 ! negative regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006906 ! vesicle fusion -relationship: negatively_regulates GO:0006906 ! vesicle fusion - -[Term] -id: GO:0031340 -name: positive regulation of vesicle fusion -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of vesicle fusion." [GOC:mah] -synonym: "activation of vesicle fusion" NARROW [] -synonym: "stimulation of vesicle fusion" NARROW [] -synonym: "up regulation of vesicle fusion" EXACT [] -synonym: "up-regulation of vesicle fusion" EXACT [] -synonym: "upregulation of vesicle fusion" EXACT [] -is_a: GO:0010638 ! positive regulation of organelle organization -is_a: GO:0031338 ! regulation of vesicle fusion -is_a: GO:0051050 ! positive regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006906 ! vesicle fusion -relationship: positively_regulates GO:0006906 ! vesicle fusion - -[Term] -id: GO:0031410 -name: cytoplasmic vesicle -namespace: cellular_component -alt_id: GO:0016023 -def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_generic -subset: goslim_mouse -subset: goslim_yeast -synonym: "cytoplasmic membrane bounded vesicle" RELATED [] -synonym: "cytoplasmic membrane-enclosed vesicle" RELATED [] -synonym: "cytoplasmic, membrane-bounded vesicle" RELATED [] -xref: NIF_Subcellular:sao180601769 -is_a: GO:0097708 ! intracellular vesicle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0005737 ! cytoplasm - [Term] id: GO:0031503 name: protein-containing complex localization @@ -39790,7 +39500,7 @@ def: "Either of the lipid bilayers that surround the nucleus and form the nuclea xref: NIF_Subcellular:sao1687101204 is_a: GO:0031090 ! organelle membrane intersection_of: GO:0016020 ! membrane -intersection_of: part_of GO:0005634 ! nucleus +intersection_of: part_of GO:0005634 ! cell nucleus relationship: part_of GO:0005635 ! nuclear envelope [Term] @@ -39811,19 +39521,6 @@ def: "A multilayered structure surrounding all or part of a cell; encompasses on is_a: GO:0110165 ! cellular anatomical entity relationship: part_of CL:0000000 ! cell -[Term] -id: GO:0031982 -name: vesicle -namespace: cellular_component -alt_id: GO:0031988 -def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] -subset: goslim_pir -synonym: "membrane-bounded vesicle" RELATED [] -synonym: "membrane-enclosed vesicle" RELATED [] -xref: NIF_Subcellular:sao221389602 -xref: Wikipedia:Vesicle_(biology) -is_a: GO:0043227 ! membrane-bounded organelle - [Term] id: GO:0032179 name: germ tube @@ -39877,105 +39574,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0015931 ! nucleobase-containing compound transport relationship: positively_regulates GO:0015931 ! nucleobase-containing compound transport -[Term] -id: GO:0032365 -name: intracellular lipid transport -namespace: biological_process -def: "The directed movement of lipids within cells." [GOC:mah] -is_a: GO:0006869 ! lipid transport -is_a: GO:0046907 ! intracellular transport -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:18059 ! lipid -intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure - -[Term] -id: GO:0032368 -name: regulation of lipid transport -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] -is_a: GO:0051049 ! regulation of transport -is_a: GO:1905952 ! regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006869 ! lipid transport -relationship: regulates GO:0006869 ! lipid transport - -[Term] -id: GO:0032369 -name: negative regulation of lipid transport -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] -synonym: "down regulation of lipid transport" EXACT [] -synonym: "down-regulation of lipid transport" EXACT [] -synonym: "downregulation of lipid transport" EXACT [] -synonym: "inhibition of lipid transport" NARROW [] -is_a: GO:0032368 ! regulation of lipid transport -is_a: GO:0051051 ! negative regulation of transport -is_a: GO:1905953 ! negative regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006869 ! lipid transport -relationship: negatively_regulates GO:0006869 ! lipid transport - -[Term] -id: GO:0032370 -name: positive regulation of lipid transport -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] -synonym: "activation of lipid transport" NARROW [] -synonym: "stimulation of lipid transport" NARROW [] -synonym: "up regulation of lipid transport" EXACT [] -synonym: "up-regulation of lipid transport" EXACT [] -synonym: "upregulation of lipid transport" EXACT [] -is_a: GO:0032368 ! regulation of lipid transport -is_a: GO:0051050 ! positive regulation of transport -is_a: GO:1905954 ! positive regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006869 ! lipid transport -relationship: positively_regulates GO:0006869 ! lipid transport - -[Term] -id: GO:0032377 -name: regulation of intracellular lipid transport -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells." [GOC:mah] -is_a: GO:0032368 ! regulation of lipid transport -is_a: GO:0032386 ! regulation of intracellular transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0032365 ! intracellular lipid transport -relationship: regulates GO:0032365 ! intracellular lipid transport - -[Term] -id: GO:0032378 -name: negative regulation of intracellular lipid transport -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells." [GOC:mah] -synonym: "down regulation of intracellular lipid transport" EXACT [] -synonym: "down-regulation of intracellular lipid transport" EXACT [] -synonym: "downregulation of intracellular lipid transport" EXACT [] -synonym: "inhibition of intracellular lipid transport" NARROW [] -is_a: GO:0032369 ! negative regulation of lipid transport -is_a: GO:0032377 ! regulation of intracellular lipid transport -is_a: GO:0032387 ! negative regulation of intracellular transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0032365 ! intracellular lipid transport -relationship: negatively_regulates GO:0032365 ! intracellular lipid transport - -[Term] -id: GO:0032379 -name: positive regulation of intracellular lipid transport -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells." [GOC:mah] -synonym: "activation of intracellular lipid transport" NARROW [] -synonym: "stimulation of intracellular lipid transport" NARROW [] -synonym: "up regulation of intracellular lipid transport" EXACT [] -synonym: "up-regulation of intracellular lipid transport" EXACT [] -synonym: "upregulation of intracellular lipid transport" EXACT [] -is_a: GO:0032370 ! positive regulation of lipid transport -is_a: GO:0032377 ! regulation of intracellular lipid transport -is_a: GO:0032388 ! positive regulation of intracellular transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0032365 ! intracellular lipid transport -relationship: positively_regulates GO:0032365 ! intracellular lipid transport - [Term] id: GO:0032386 name: regulation of intracellular transport @@ -40021,50 +39619,23 @@ intersection_of: positively_regulates GO:0046907 ! intracellular transport relationship: positively_regulates GO:0046907 ! intracellular transport [Term] -id: GO:0032409 -name: regulation of transporter activity -namespace: biological_process -def: "Any process that modulates the activity of a transporter." [GOC:mah] -subset: term_scheduled_for_obsoletion -is_a: GO:0065009 ! regulation of molecular function -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0005215 ! transporter activity -relationship: regulates GO:0005215 ! transporter activity - -[Term] -id: GO:0032410 -name: negative regulation of transporter activity -namespace: biological_process -def: "Any process that stops or reduces the activity of a transporter." [GOC:mah] -subset: term_scheduled_for_obsoletion -synonym: "down regulation of transporter activity" EXACT [] -synonym: "down-regulation of transporter activity" EXACT [] -synonym: "downregulation of transporter activity" EXACT [] -synonym: "inhibition of transporter activity" NARROW [] -is_a: GO:0032409 ! regulation of transporter activity -is_a: GO:0044092 ! negative regulation of molecular function -is_a: GO:0051051 ! negative regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0005215 ! transporter activity -relationship: negatively_regulates GO:0005215 ! transporter activity - -[Term] -id: GO:0032411 -name: positive regulation of transporter activity +id: GO:0032501 +name: multicellular organismal process namespace: biological_process -def: "Any process that activates or increases the activity of a transporter." [GOC:mah] -subset: term_scheduled_for_obsoletion -synonym: "activation of transporter activity" NARROW [] -synonym: "stimulation of transporter activity" NARROW [] -synonym: "up regulation of transporter activity" EXACT [] -synonym: "up-regulation of transporter activity" EXACT [] -synonym: "upregulation of transporter activity" EXACT [] -is_a: GO:0032409 ! regulation of transporter activity -is_a: GO:0044093 ! positive regulation of molecular function -is_a: GO:0051050 ! positive regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0005215 ! transporter activity -relationship: positively_regulates GO:0005215 ! transporter activity +alt_id: GO:0044707 +alt_id: GO:0050874 +def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "organismal physiological process" EXACT [] +synonym: "single-multicellular organism process" RELATED [] +is_a: GO:0008150 ! biological process +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 +created_by: jl +creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 @@ -40077,7 +39648,7 @@ subset: goslim_flybase_ribbon subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase created_by: jl creation_date: 2012-12-19T12:21:31Z @@ -40115,20 +39686,10 @@ synonym: "RNA synthesis" EXACT [] is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0016070 ! RNA metabolic process is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process -intersection_of: GO:0009058 ! biosynthetic process +intersection_of: GO:0009059 ! macromolecule biosynthetic process intersection_of: has_primary_output CHEBI:33697 ! ribonucleic acid relationship: has_primary_output CHEBI:33697 ! ribonucleic acid -[Term] -id: GO:0032871 -name: regulation of karyogamy -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion." [GOC:mah] -is_a: GO:1903353 ! regulation of nucleus organization -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0000741 ! karyogamy -relationship: regulates GO:0000741 ! karyogamy - [Term] id: GO:0032879 name: regulation of localization @@ -40363,52 +39924,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009308 ! amine metabolic process relationship: positively_regulates GO:0009308 ! amine metabolic process -[Term] -id: GO:0033241 -name: regulation of amine catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah] -synonym: "regulation of amine breakdown" EXACT [] -synonym: "regulation of amine catabolism" EXACT [] -synonym: "regulation of amine degradation" EXACT [] -synonym: "regulation of cellular amine catabolic process" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0033238 ! regulation of amine metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0009310 ! amine catabolic process -relationship: regulates GO:0009310 ! amine catabolic process - -[Term] -id: GO:0033242 -name: negative regulation of amine catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah] -synonym: "negative regulation of amine breakdown" EXACT [] -synonym: "negative regulation of amine catabolism" EXACT [] -synonym: "negative regulation of amine degradation" EXACT [] -synonym: "negative regulation of cellular amine catabolic process" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0033239 ! negative regulation of amine metabolic process -is_a: GO:0033241 ! regulation of amine catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0009310 ! amine catabolic process -relationship: negatively_regulates GO:0009310 ! amine catabolic process - -[Term] -id: GO:0033243 -name: positive regulation of amine catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah] -synonym: "positive regulation of amine breakdown" EXACT [] -synonym: "positive regulation of amine catabolism" EXACT [] -synonym: "positive regulation of amine degradation" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0033240 ! positive regulation of amine metabolic process -is_a: GO:0033241 ! regulation of amine catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0009310 ! amine catabolic process -relationship: positively_regulates GO:0009310 ! amine catabolic process - [Term] id: GO:0033365 name: protein localization to organelle @@ -40436,7 +39951,7 @@ id: GO:0033673 name: negative regulation of kinase activity namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate synonym: "down regulation of kinase activity" EXACT [] synonym: "down-regulation of kinase activity" EXACT [] synonym: "downregulation of kinase activity" EXACT [] @@ -40454,7 +39969,7 @@ id: GO:0033674 name: positive regulation of kinase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate synonym: "kinase activator" NARROW [] synonym: "stimulation of kinase activity" NARROW [] synonym: "up regulation of kinase activity" EXACT [] @@ -40517,53 +40032,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0043603 ! amide metabolic process relationship: positively_regulates GO:0043603 ! amide metabolic process -[Term] -id: GO:0034251 -name: regulation of amide catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah] -synonym: "regulation of amide breakdown" EXACT [] -synonym: "regulation of amide catabolism" EXACT [] -synonym: "regulation of amide degradation" EXACT [] -synonym: "regulation of cellular amide catabolic process" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0034248 ! regulation of amide metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0043605 ! amide catabolic process -relationship: regulates GO:0043605 ! amide catabolic process - -[Term] -id: GO:0034252 -name: negative regulation of amide catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah] -synonym: "negative regulation of amide breakdown" EXACT [] -synonym: "negative regulation of amide catabolism" EXACT [] -synonym: "negative regulation of amide degradation" RELATED [] -synonym: "negative regulation of cellular amide catabolic process" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0034249 ! negative regulation of amide metabolic process -is_a: GO:0034251 ! regulation of amide catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0043605 ! amide catabolic process -relationship: negatively_regulates GO:0043605 ! amide catabolic process - -[Term] -id: GO:0034253 -name: positive regulation of amide catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah] -synonym: "positive regulation of amide breakdown" EXACT [] -synonym: "positive regulation of amide catabolism" EXACT [] -synonym: "positive regulation of amide degradation" RELATED [] -synonym: "positive regulation of cellular amide catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0034250 ! positive regulation of amide metabolic process -is_a: GO:0034251 ! regulation of amide catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0043605 ! amide catabolic process -relationship: positively_regulates GO:0043605 ! amide catabolic process - [Term] id: GO:0034293 name: sexual sporulation @@ -40620,8 +40088,8 @@ synonym: "protein localization in nucleus" EXACT [GOC:mah] synonym: "protein targeting to nucleus" RELATED [] is_a: GO:0033365 ! protein localization to organelle intersection_of: GO:0008104 ! protein localization -intersection_of: has_target_end_location GO:0005634 ! nucleus -relationship: has_target_end_location GO:0005634 ! nucleus +intersection_of: has_target_end_location GO:0005634 ! cell nucleus +relationship: has_target_end_location GO:0005634 ! cell nucleus creation_date: 2012-11-07T15:45:54Z [Term] @@ -40629,10 +40097,12 @@ id: GO:0034641 name: cellular nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_chembl synonym: "cellular nitrogen compound metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044237 ! cellular metabolic process +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [Term] id: GO:0034654 @@ -40653,23 +40123,15 @@ intersection_of: has_primary_output CHEBI:61120 ! nucleobase-containing molecula relationship: has_primary_output CHEBI:61120 ! nucleobase-containing molecular entity [Term] -id: GO:0034655 -name: nucleobase-containing compound catabolic process +id: GO:0035190 +name: syncytial nuclear migration namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] -subset: goslim_chembl -synonym: "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" EXACT [] -synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process" RELATED [GOC:dph, GOC:tb] -synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" EXACT [] -synonym: "nucleobase, nucleoside, nucleotide and nucleic acid degradation" EXACT [] -is_a: GO:0006139 ! nucleobase-containing compound metabolic process -is_a: GO:0019439 ! aromatic compound catabolic process -is_a: GO:0044270 ! cellular nitrogen compound catabolic process -is_a: GO:0046700 ! heterocycle catabolic process -is_a: GO:1901361 ! organic cyclic compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:61120 ! nucleobase-containing molecular entity -relationship: has_primary_input CHEBI:61120 ! nucleobase-containing molecular entity +def: "The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex." [GOC:bf, ISBN:0879694238, PMID:8314839] +is_a: GO:0007097 ! nuclear migration +intersection_of: GO:0007097 ! nuclear migration +intersection_of: occurs_in CL:0000228 ! multinucleate cell +relationship: occurs_in CL:0000228 ! multinucleate cell +relationship: part_of GO:0001700 ! embryonic development via the syncytial blastoderm [Term] id: GO:0035592 @@ -40730,9 +40192,26 @@ subset: goslim_pir subset: goslim_plant synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0044848 ! biological phase +[Term] +id: GO:0040019 +name: positive regulation of embryonic development +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of embryonic development." [GOC:go_curators] +synonym: "activation of embryonic development" NARROW [] +synonym: "stimulation of embryonic development" NARROW [] +synonym: "up regulation of embryonic development" EXACT [] +synonym: "up-regulation of embryonic development" EXACT [] +synonym: "upregulation of embryonic development" EXACT [] +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009790 ! embryo development +relationship: positively_regulates GO:0009790 ! embryo development + [Term] id: GO:0040020 name: regulation of meiotic nuclear division @@ -40758,76 +40237,6 @@ intersection_of: regulates GO:0008283 ! cell population proliferation relationship: regulates GO:0008283 ! cell population proliferation property_value: RO:0002161 NCBITaxon:4751 -[Term] -id: GO:0042176 -name: regulation of protein catabolic process -namespace: biological_process -alt_id: GO:1903362 -alt_id: GO:2000598 -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators, GOC:jl] -synonym: "regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "regulation of cellular protein catabolic process" EXACT [] -synonym: "regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "regulation of cyclin breakdown" NARROW [GOC:obol] -synonym: "regulation of cyclin catabolic process" NARROW [] -synonym: "regulation of cyclin catabolism" NARROW [GOC:obol] -synonym: "regulation of cyclin degradation" NARROW [GOC:obol] -synonym: "regulation of degradation of cyclin" NARROW [GOC:obol] -synonym: "regulation of protein breakdown" EXACT [] -synonym: "regulation of protein catabolism" EXACT [] -synonym: "regulation of protein degradation" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0051246 ! regulation of protein metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0030163 ! protein catabolic process -relationship: regulates GO:0030163 ! protein catabolic process -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI -created_by: kmv -creation_date: 2014-08-21T15:05:45Z - -[Term] -id: GO:0042177 -name: negative regulation of protein catabolic process -namespace: biological_process -alt_id: GO:1903363 -alt_id: GO:2000599 -def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process." [GO_REF:0000058, GOC:kmv, GOC:obol, GOC:TermGenie, PMID:24785082] -synonym: "down regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "down regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "down regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "down regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "down regulation of protein catabolic process" EXACT [] -synonym: "down-regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "down-regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "down-regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "down-regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "down-regulation of protein catabolic process" EXACT [] -synonym: "downregulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "downregulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "downregulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "downregulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "downregulation of protein catabolic process" EXACT [] -synonym: "inhibition of cellular protein breakdown" NARROW [GOC:TermGenie] -synonym: "inhibition of cellular protein catabolic process" NARROW [GOC:TermGenie] -synonym: "inhibition of cellular protein catabolism" NARROW [GOC:TermGenie] -synonym: "inhibition of cellular protein degradation" NARROW [GOC:TermGenie] -synonym: "inhibition of protein catabolic process" NARROW [] -synonym: "negative regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "negative regulation of cellular protein catabolic process" EXACT [] -synonym: "negative regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "negative regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "negative regulation of protein breakdown" EXACT [] -synonym: "negative regulation of protein catabolism" EXACT [] -synonym: "negative regulation of protein degradation" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0042176 ! regulation of protein catabolic process -is_a: GO:0051248 ! negative regulation of protein metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0030163 ! protein catabolic process -relationship: negatively_regulates GO:0030163 ! protein catabolic process -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI - [Term] id: GO:0042180 name: cellular ketone metabolic process @@ -40859,22 +40268,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:17087 ! ketone relationship: has_primary_output CHEBI:17087 ! ketone -[Term] -id: GO:0042182 -name: ketone catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:go_curators] -synonym: "ketone breakdown" EXACT [] -synonym: "ketone catabolism" EXACT [] -synonym: "ketone degradation" EXACT [] -is_a: GO:0042180 ! cellular ketone metabolic process -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:0044282 ! small molecule catabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:17087 ! ketone -relationship: has_primary_input CHEBI:17087 ! ketone - [Term] id: GO:0042325 name: regulation of phosphorylation @@ -40949,7 +40342,7 @@ name: extracellular structure organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "extracellular structure organisation" EXACT [] synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization @@ -40963,8 +40356,8 @@ name: positive regulation of catalytic activity namespace: biological_process alt_id: GO:0048554 def: "Any process that activates or increases the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] +subset: gocheck_do_not_annotate subset: goslim_chembl -subset: term_scheduled_for_obsoletion synonym: "activation of enzyme activity" NARROW [] synonym: "activation of metalloenzyme activity" NARROW [] synonym: "positive regulation of enzyme activity" EXACT [GOC:tb] @@ -40989,7 +40382,7 @@ name: negative regulation of catalytic activity namespace: biological_process alt_id: GO:0048553 def: "Any process that stops or reduces the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate synonym: "down regulation of enzyme activity" EXACT [] synonym: "down regulation of metalloenzyme activity" NARROW [] synonym: "down-regulation of enzyme activity" EXACT [] @@ -41042,21 +40435,6 @@ intersection_of: has_primary_input_or_output CHEBI:33694 ! biomacromolecule relationship: has_primary_input_or_output CHEBI:33694 ! biomacromolecule property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0043171 -name: peptide catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [GOC:jl] -synonym: "peptide breakdown" EXACT [] -synonym: "peptide catabolism" EXACT [] -synonym: "peptide degradation" EXACT [] -is_a: GO:0006518 ! peptide metabolic process -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:16670 ! peptide -relationship: has_primary_input CHEBI:16670 ! peptide - [Term] id: GO:0043207 name: response to external biotic stimulus @@ -41074,7 +40452,6 @@ subset: goslim_chembl subset: goslim_generic subset: goslim_pir subset: goslim_prokaryote -subset: prokaryote_subset xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle is_a: GO:0110165 ! cellular anatomical entity @@ -41258,7 +40635,7 @@ namespace: biological_process def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl] subset: goslim_chembl subset: goslim_pir -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process [Term] id: GO:0043476 @@ -41283,7 +40660,7 @@ id: GO:0043549 name: regulation of kinase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:bf] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate is_a: GO:0042325 ! regulation of phosphorylation is_a: GO:0051338 ! regulation of transferase activity intersection_of: GO:0065007 ! biological regulation @@ -41314,18 +40691,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:32988 ! amide relationship: has_primary_output CHEBI:32988 ! amide -[Term] -id: GO:0043605 -name: amide catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [GOC:curators] -synonym: "cellular amide catabolic process" EXACT [] -is_a: GO:0009056 ! catabolic process -is_a: GO:0043603 ! amide metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_output CHEBI:32988 ! amide -relationship: has_primary_output CHEBI:32988 ! amide - [Term] id: GO:0043933 name: protein-containing complex organization @@ -41452,15 +40817,15 @@ namespace: biological_process def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane." [GOC:jl] is_a: GO:0044085 ! cellular component biogenesis intersection_of: GO:0044085 ! cellular component biogenesis -intersection_of: has_output GO:0016020 ! membrane -relationship: has_output GO:0016020 ! membrane +intersection_of: has_primary_output GO:0016020 ! membrane +relationship: has_primary_output GO:0016020 ! membrane [Term] id: GO:0044092 name: negative regulation of molecular function namespace: biological_process def: "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003674 ! molecular_function @@ -41473,7 +40838,7 @@ id: GO:0044093 name: positive regulation of molecular function namespace: biological_process def: "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] -subset: term_scheduled_for_obsoletion +subset: gocheck_do_not_annotate is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003674 ! molecular_function @@ -41581,17 +40946,6 @@ synonym: "cellular lipid metabolism" EXACT [] is_a: GO:0006629 ! lipid metabolic process is_a: GO:0044237 ! cellular metabolic process -[Term] -id: GO:0044270 -name: cellular nitrogen compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] -synonym: "nitrogen compound breakdown" BROAD [] -synonym: "nitrogen compound catabolism" BROAD [] -synonym: "nitrogen compound degradation" BROAD [] -is_a: GO:0034641 ! cellular nitrogen compound metabolic process -is_a: GO:0044248 ! cellular catabolic process - [Term] id: GO:0044271 name: cellular nitrogen compound biosynthetic process @@ -41618,18 +40972,6 @@ is_a: GO:0008152 ! metabolic process created_by: jl creation_date: 2010-01-26T12:05:20Z -[Term] -id: GO:0044282 -name: small molecule catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:vw] -comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. -synonym: "small molecule catabolism" EXACT [] -is_a: GO:0009056 ! catabolic process -is_a: GO:0044281 ! small molecule metabolic process -created_by: jl -creation_date: 2010-01-26T12:06:10Z - [Term] id: GO:0044283 name: small molecule biosynthetic process @@ -41637,7 +40979,6 @@ namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. subset: goslim_prokaryote -subset: prokaryote_subset synonym: "small molecule biosynthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0044281 ! small molecule metabolic process @@ -41724,7 +41065,7 @@ synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI property_value: RO:0002161 NCBITaxon:4895 @@ -41757,7 +41098,7 @@ namespace: biological_process def: "A distinct period or stage in a biological process or cycle." [GOC:jl] comment: Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase. subset: gocheck_do_not_manually_annotate -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process disjoint_from: GO:0050896 ! response to stimulus disjoint_from: GO:0051179 ! localization disjoint_from: GO:0071840 ! cellular component organization or biogenesis @@ -41777,20 +41118,6 @@ is_a: GO:0005488 ! binding created_by: jl creation_date: 2014-12-16T11:38:58Z -[Term] -id: GO:0045026 -name: plasma membrane fusion -namespace: biological_process -alt_id: GO:0006947 -def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] -synonym: "cell fusion" BROAD [] -synonym: "cell-cell fusion" BROAD [] -is_a: GO:0007009 ! plasma membrane organization -is_a: GO:0061025 ! membrane fusion -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0005886 ! plasma membrane -relationship: results_in_fusion_of GO:0005886 ! plasma membrane - [Term] id: GO:0045087 name: innate immune response @@ -41827,6 +41154,50 @@ synonym: "external encapsulating structure organisation" EXACT [] synonym: "external encapsulating structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization +[Term] +id: GO:0045595 +name: regulation of cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features." [GOC:go_curators] +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030154 ! cell differentiation +relationship: regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045596 +name: negative regulation of cell differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation." [GOC:go_curators] +synonym: "down regulation of cell differentiation" EXACT [] +synonym: "down-regulation of cell differentiation" EXACT [] +synonym: "downregulation of cell differentiation" EXACT [] +synonym: "inhibition of cell differentiation" NARROW [] +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051093 ! negative regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030154 ! cell differentiation +relationship: negatively_regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045597 +name: positive regulation of cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell differentiation." [GOC:go_curators] +synonym: "activation of cell differentiation" NARROW [] +synonym: "stimulation of cell differentiation" NARROW [] +synonym: "up regulation of cell differentiation" EXACT [] +synonym: "up-regulation of cell differentiation" EXACT [] +synonym: "upregulation of cell differentiation" EXACT [] +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030154 ! cell differentiation +relationship: positively_regulates GO:0030154 ! cell differentiation + [Term] id: GO:0045727 name: positive regulation of translation @@ -41844,9 +41215,7 @@ synonym: "up regulation of protein biosynthetic process" EXACT [] synonym: "up-regulation of protein biosynthetic process" EXACT [] synonym: "upregulation of protein biosynthetic process" EXACT [] is_a: GO:0006417 ! regulation of translation -is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process is_a: GO:0010628 ! positive regulation of gene expression -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0034250 ! positive regulation of amide metabolic process is_a: GO:0051247 ! positive regulation of protein metabolic process intersection_of: GO:0065007 ! biological regulation @@ -41863,54 +41232,6 @@ synonym: "oxidative burst" EXACT [] xref: Wikipedia:Respiratory_burst is_a: GO:0008152 ! metabolic process -[Term] -id: GO:0045732 -name: positive regulation of protein catabolic process -namespace: biological_process -alt_id: GO:1903364 -alt_id: GO:2000600 -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators] -synonym: "activation of cellular protein breakdown" NARROW [GOC:TermGenie] -synonym: "activation of cellular protein catabolic process" NARROW [GOC:TermGenie] -synonym: "activation of cellular protein catabolism" NARROW [GOC:TermGenie] -synonym: "activation of cellular protein degradation" NARROW [GOC:TermGenie] -synonym: "activation of protein catabolic process" NARROW [] -synonym: "positive regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "positive regulation of cellular protein catabolic process" EXACT [] -synonym: "positive regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "positive regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "positive regulation of cyclin breakdown" NARROW [GOC:obol] -synonym: "positive regulation of cyclin catabolic process" NARROW [] -synonym: "positive regulation of cyclin catabolism" NARROW [GOC:obol] -synonym: "positive regulation of cyclin degradation" NARROW [GOC:obol] -synonym: "positive regulation of degradation of cyclin" NARROW [GOC:obol] -synonym: "positive regulation of protein breakdown" EXACT [] -synonym: "positive regulation of protein catabolism" EXACT [] -synonym: "positive regulation of protein degradation" EXACT [] -synonym: "stimulation of protein catabolic process" NARROW [] -synonym: "up regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "up regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "up regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "up regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "up regulation of protein catabolic process" EXACT [] -synonym: "up-regulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "up-regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "up-regulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "up-regulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "up-regulation of protein catabolic process" EXACT [] -synonym: "upregulation of cellular protein breakdown" EXACT [GOC:TermGenie] -synonym: "upregulation of cellular protein catabolic process" EXACT [GOC:TermGenie] -synonym: "upregulation of cellular protein catabolism" EXACT [GOC:TermGenie] -synonym: "upregulation of cellular protein degradation" EXACT [GOC:TermGenie] -synonym: "upregulation of protein catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0042176 ! regulation of protein catabolic process -is_a: GO:0051247 ! positive regulation of protein metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0030163 ! protein catabolic process -relationship: positively_regulates GO:0030163 ! protein catabolic process -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI - [Term] id: GO:0045763 name: negative regulation of cellular amino acid metabolic process @@ -41922,9 +41243,7 @@ synonym: "downregulation of amino acid metabolic process" EXACT [] synonym: "inhibition of amino acid metabolic process" NARROW [] synonym: "negative regulation of amino acid metabolism" EXACT [] is_a: GO:0006521 ! regulation of cellular amino acid metabolic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0033239 ! negative regulation of amine metabolic process -is_a: GO:0062014 ! negative regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006520 ! amino acid metabolic process relationship: negatively_regulates GO:0006520 ! amino acid metabolic process @@ -41942,9 +41261,7 @@ synonym: "up regulation of amino acid metabolic process" EXACT [] synonym: "up-regulation of amino acid metabolic process" EXACT [] synonym: "upregulation of amino acid metabolic process" EXACT [] is_a: GO:0006521 ! regulation of cellular amino acid metabolic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0033240 ! positive regulation of amine metabolic process -is_a: GO:0062013 ! positive regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006520 ! amino acid metabolic process relationship: positively_regulates GO:0006520 ! amino acid metabolic process @@ -41984,72 +41301,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007049 ! cell cycle relationship: positively_regulates GO:0007049 ! cell cycle -[Term] -id: GO:0045806 -name: negative regulation of endocytosis -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis." [GOC:go_curators] -synonym: "down regulation of endocytosis" EXACT [] -synonym: "down-regulation of endocytosis" EXACT [] -synonym: "downregulation of endocytosis" EXACT [] -synonym: "inhibition of endocytosis" NARROW [] -is_a: GO:0030100 ! regulation of endocytosis -is_a: GO:0051051 ! negative regulation of transport -is_a: GO:0051129 ! negative regulation of cellular component organization -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006897 ! endocytosis -relationship: negatively_regulates GO:0006897 ! endocytosis - -[Term] -id: GO:0045807 -name: positive regulation of endocytosis -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of endocytosis." [GOC:go_curators] -synonym: "activation of endocytosis" NARROW [] -synonym: "stimulation of endocytosis" NARROW [] -synonym: "up regulation of endocytosis" EXACT [] -synonym: "up-regulation of endocytosis" EXACT [] -synonym: "upregulation of endocytosis" EXACT [] -is_a: GO:0030100 ! regulation of endocytosis -is_a: GO:0051050 ! positive regulation of transport -is_a: GO:0051130 ! positive regulation of cellular component organization -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006897 ! endocytosis -relationship: positively_regulates GO:0006897 ! endocytosis - -[Term] -id: GO:0045833 -name: negative regulation of lipid metabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] -synonym: "down regulation of lipid metabolic process" EXACT [] -synonym: "down-regulation of lipid metabolic process" EXACT [] -synonym: "downregulation of lipid metabolic process" EXACT [] -synonym: "inhibition of lipid metabolic process" NARROW [] -synonym: "negative regulation of lipid metabolism" EXACT [] -is_a: GO:0009892 ! negative regulation of metabolic process -is_a: GO:0019216 ! regulation of lipid metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006629 ! lipid metabolic process -relationship: negatively_regulates GO:0006629 ! lipid metabolic process - -[Term] -id: GO:0045834 -name: positive regulation of lipid metabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] -synonym: "activation of lipid metabolic process" NARROW [] -synonym: "positive regulation of lipid metabolism" EXACT [] -synonym: "stimulation of lipid metabolic process" NARROW [] -synonym: "up regulation of lipid metabolic process" EXACT [] -synonym: "up-regulation of lipid metabolic process" EXACT [] -synonym: "upregulation of lipid metabolic process" EXACT [] -is_a: GO:0009893 ! positive regulation of metabolic process -is_a: GO:0019216 ! regulation of lipid metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006629 ! lipid metabolic process -relationship: positively_regulates GO:0006629 ! lipid metabolic process - [Term] id: GO:0045835 name: negative regulation of meiotic nuclear division @@ -42151,37 +41402,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006415 ! translational termination relationship: positively_regulates GO:0006415 ! translational termination -[Term] -id: GO:0045920 -name: negative regulation of exocytosis -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis." [GOC:go_curators] -synonym: "down regulation of exocytosis" EXACT [] -synonym: "down-regulation of exocytosis" EXACT [] -synonym: "downregulation of exocytosis" EXACT [] -synonym: "inhibition of exocytosis" NARROW [] -is_a: GO:0017157 ! regulation of exocytosis -is_a: GO:1903531 ! negative regulation of secretion by cell -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006887 ! exocytosis -relationship: negatively_regulates GO:0006887 ! exocytosis - -[Term] -id: GO:0045921 -name: positive regulation of exocytosis -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of exocytosis." [GOC:go_curators] -synonym: "activation of exocytosis" NARROW [] -synonym: "stimulation of exocytosis" NARROW [] -synonym: "up regulation of exocytosis" EXACT [] -synonym: "up-regulation of exocytosis" EXACT [] -synonym: "upregulation of exocytosis" EXACT [] -is_a: GO:0017157 ! regulation of exocytosis -is_a: GO:1903532 ! positive regulation of secretion by cell -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006887 ! exocytosis -relationship: positively_regulates GO:0006887 ! exocytosis - [Term] id: GO:0045934 name: negative regulation of nucleobase-containing compound metabolic process @@ -42283,6 +41503,32 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006413 ! translational initiation relationship: positively_regulates GO:0006413 ! translational initiation +[Term] +id: GO:0045992 +name: negative regulation of embryonic development +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development." [GOC:go_curators] +synonym: "down regulation of embryonic development" EXACT [] +synonym: "down-regulation of embryonic development" EXACT [] +synonym: "downregulation of embryonic development" EXACT [] +synonym: "inhibition of embryonic development" NARROW [] +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009790 ! embryo development +relationship: negatively_regulates GO:0009790 ! embryo development + +[Term] +id: GO:0045995 +name: regulation of embryonic development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of embryonic development." [GOC:go_curators] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009790 ! embryo development +relationship: regulates GO:0009790 ! embryo development + [Term] id: GO:0046112 name: nucleobase biosynthetic process @@ -42300,22 +41546,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:18282 ! nucleobase relationship: has_primary_output CHEBI:18282 ! nucleobase -[Term] -id: GO:0046113 -name: nucleobase catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid." [GOC:ai] -synonym: "nucleobase breakdown" EXACT [] -synonym: "nucleobase catabolism" EXACT [] -synonym: "nucleobase degradation" EXACT [] -is_a: GO:0009112 ! nucleobase metabolic process -is_a: GO:0046700 ! heterocycle catabolic process -is_a: GO:1901361 ! organic cyclic compound catabolic process -is_a: GO:1901565 ! organonitrogen compound catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:18282 ! nucleobase -relationship: has_primary_input CHEBI:18282 ! nucleobase - [Term] id: GO:0046165 name: alcohol biosynthetic process @@ -42357,20 +41587,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:29067 ! carboxylic acid anion relationship: has_primary_output CHEBI:29067 ! carboxylic acid anion -[Term] -id: GO:0046395 -name: carboxylic acid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." [ISBN:0198506732] -synonym: "carboxylic acid breakdown" EXACT [] -synonym: "carboxylic acid catabolism" EXACT [] -synonym: "carboxylic acid degradation" EXACT [] -is_a: GO:0016054 ! organic acid catabolic process -is_a: GO:0019752 ! carboxylic acid metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:29067 ! carboxylic acid anion -relationship: has_primary_input CHEBI:29067 ! carboxylic acid anion - [Term] id: GO:0046483 name: heterocycle metabolic process @@ -42383,58 +41599,6 @@ intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:5686 ! heterocyclic compound relationship: has_primary_input_or_output CHEBI:5686 ! heterocyclic compound -[Term] -id: GO:0046700 -name: heterocycle catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [GOC:ai] -synonym: "heterocycle breakdown" EXACT [] -synonym: "heterocycle catabolism" EXACT [] -synonym: "heterocycle degradation" EXACT [] -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:0046483 ! heterocycle metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:5686 ! heterocyclic compound -relationship: has_primary_input CHEBI:5686 ! heterocyclic compound - -[Term] -id: GO:0046889 -name: positive regulation of lipid biosynthetic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] -synonym: "activation of lipid biosynthetic process" NARROW [] -synonym: "positive regulation of lipid anabolism" EXACT [] -synonym: "positive regulation of lipid biosynthesis" EXACT [] -synonym: "positive regulation of lipid formation" EXACT [] -synonym: "positive regulation of lipid synthesis" EXACT [] -synonym: "positive regulation of lipogenesis" EXACT [GOC:sl] -synonym: "stimulation of lipid biosynthetic process" NARROW [] -synonym: "up regulation of lipid biosynthetic process" EXACT [] -synonym: "up-regulation of lipid biosynthetic process" EXACT [] -synonym: "upregulation of lipid biosynthetic process" EXACT [] -is_a: GO:0009891 ! positive regulation of biosynthetic process -is_a: GO:0045834 ! positive regulation of lipid metabolic process -is_a: GO:0046890 ! regulation of lipid biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0008610 ! lipid biosynthetic process -relationship: positively_regulates GO:0008610 ! lipid biosynthetic process - -[Term] -id: GO:0046890 -name: regulation of lipid biosynthetic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] -synonym: "regulation of lipid anabolism" EXACT [] -synonym: "regulation of lipid biosynthesis" EXACT [] -synonym: "regulation of lipid formation" EXACT [] -synonym: "regulation of lipid synthesis" EXACT [] -synonym: "regulation of lipogenesis" EXACT [GOC:sl] -is_a: GO:0009889 ! regulation of biosynthetic process -is_a: GO:0019216 ! regulation of lipid metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0008610 ! lipid biosynthetic process -relationship: regulates GO:0008610 ! lipid biosynthetic process - [Term] id: GO:0046903 name: secretion @@ -42494,18 +41658,6 @@ intersection_of: GO:0012501 ! programmed cell death intersection_of: has_part GO:0016236 ! macroautophagy relationship: has_part GO:0016236 ! macroautophagy -[Term] -id: GO:0048284 -name: organelle fusion -namespace: biological_process -def: "The creation of a single organelle from two or more organelles." [GOC:jid] -subset: goslim_pir -subset: goslim_yeast -is_a: GO:0006996 ! organelle organization -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0043226 ! organelle -relationship: results_in_fusion_of GO:0043226 ! organelle - [Term] id: GO:0048285 name: organelle fission @@ -42519,15 +41671,30 @@ intersection_of: results_in_fission_of GO:0043226 ! organelle relationship: results_in_fission_of GO:0043226 ! organelle [Term] -id: GO:0048288 -name: nuclear membrane fusion involved in karyogamy +id: GO:0048468 +name: cell development +namespace: biological_process +def: "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place." [GOC:go_curators] +subset: goslim_candida +synonym: "terminal differentiation" RELATED [GOC:dph, GOC:tb] +is_a: GO:0048856 ! anatomical structure development +is_a: GO:0048869 ! cellular developmental process +intersection_of: GO:0008150 ! biological process +intersection_of: results_in_development_of CL:0000000 ! cell +relationship: part_of GO:0030154 ! cell differentiation +relationship: results_in_development_of CL:0000000 ! cell +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24390" xsd:anyURI + +[Term] +id: GO:0048513 +name: animal organ development namespace: biological_process -def: "The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei." [GOC:jid] -synonym: "nuclear membrane fusion during karyogamy" RELATED [GOC:dph, GOC:tb] -is_a: GO:0000740 ! nuclear membrane fusion -intersection_of: GO:0000740 ! nuclear membrane fusion -intersection_of: part_of GO:0000741 ! karyogamy -relationship: part_of GO:0000741 ! karyogamy +def: "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dph, GOC:jid] +synonym: "development of an organ" EXACT [] +synonym: "organogenesis" EXACT [] +xref: Wikipedia:Organogenesis +is_a: GO:0048856 ! anatomical structure development +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/25943" xsd:anyURI [Term] id: GO:0048518 @@ -42544,8 +41711,8 @@ synonym: "up-regulation of biological process" EXACT [] synonym: "upregulation of biological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0008150 ! biological_process -relationship: positively_regulates GO:0008150 ! biological_process +intersection_of: positively_regulates GO:0008150 ! biological process +relationship: positively_regulates GO:0008150 ! biological process [Term] id: GO:0048519 @@ -42561,8 +41728,8 @@ synonym: "inhibition of biological process" NARROW [] synonym: "negative regulation of physiological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0008150 ! biological_process -relationship: negatively_regulates GO:0008150 ! biological_process +intersection_of: negatively_regulates GO:0008150 ! biological process +relationship: negatively_regulates GO:0008150 ! biological process [Term] id: GO:0048522 @@ -42601,6 +41768,49 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009987 ! cellular process relationship: negatively_regulates GO:0009987 ! cellular process +[Term] +id: GO:0048580 +name: regulation of post-embryonic development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." [GOC:jid] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009791 ! post-embryonic development +relationship: regulates GO:0009791 ! post-embryonic development + +[Term] +id: GO:0048581 +name: negative regulation of post-embryonic development +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." [GOC:jid] +synonym: "down regulation of post-embryonic development" EXACT [] +synonym: "down-regulation of post-embryonic development" EXACT [] +synonym: "downregulation of post-embryonic development" EXACT [] +synonym: "inhibition of post-embryonic development" NARROW [] +is_a: GO:0048580 ! regulation of post-embryonic development +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009791 ! post-embryonic development +relationship: negatively_regulates GO:0009791 ! post-embryonic development + +[Term] +id: GO:0048582 +name: positive regulation of post-embryonic development +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." [GOC:jid] +synonym: "activation of post-embryonic development" NARROW [] +synonym: "stimulation of post-embryonic development" NARROW [] +synonym: "up regulation of post-embryonic development" EXACT [] +synonym: "up-regulation of post-embryonic development" EXACT [] +synonym: "upregulation of post-embryonic development" EXACT [] +is_a: GO:0048580 ! regulation of post-embryonic development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009791 ! post-embryonic development +relationship: positively_regulates GO:0009791 ! post-embryonic development + [Term] id: GO:0048589 name: developmental growth @@ -42633,6 +41843,9 @@ subset: goslim_generic subset: goslim_plant synonym: "development of an anatomical structure" EXACT [] is_a: GO:0032502 ! developmental process +intersection_of: GO:0032502 ! developmental process +intersection_of: results_in_development_of UBERON:0000061 ! anatomical structure +relationship: results_in_development_of UBERON:0000061 ! anatomical structure property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [Term] @@ -42720,8 +41933,8 @@ subset: goslim_pir synonym: "regulation of physiological process" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0008150 ! biological_process -relationship: regulates GO:0008150 ! biological_process +intersection_of: regulates GO:0008150 ! biological process +relationship: regulates GO:0008150 ! biological process [Term] id: GO:0050790 @@ -42729,8 +41942,8 @@ name: regulation of catalytic activity namespace: biological_process alt_id: GO:0048552 def: "Any process that modulates the activity of an enzyme." [GOC:ai, GOC:ebc, GOC:vw] +subset: gocheck_do_not_annotate subset: goslim_chembl -subset: term_scheduled_for_obsoletion synonym: "regulation of enzyme activity" EXACT [] synonym: "regulation of metalloenzyme activity" NARROW [] is_a: GO:0065009 ! regulation of molecular function @@ -42738,6 +41951,16 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003824 ! catalytic activity relationship: regulates GO:0003824 ! catalytic activity +[Term] +id: GO:0050793 +name: regulation of developmental process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:go_curators] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032502 ! developmental process +relationship: regulates GO:0032502 ! developmental process + [Term] id: GO:0050794 name: regulation of cellular process @@ -42765,60 +41988,7 @@ subset: goslim_mouse subset: goslim_pir subset: goslim_prokaryote synonym: "physiological response to stimulus" EXACT [] -is_a: GO:0008150 ! biological_process - -[Term] -id: GO:0050994 -name: regulation of lipid catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids." [GOC:ai] -synonym: "regulation of lipid breakdown" EXACT [] -synonym: "regulation of lipid catabolism" EXACT [] -synonym: "regulation of lipid degradation" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0019216 ! regulation of lipid metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0016042 ! lipid catabolic process -relationship: regulates GO:0016042 ! lipid catabolic process - -[Term] -id: GO:0050995 -name: negative regulation of lipid catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids." [GOC:ai] -synonym: "down regulation of lipid catabolic process" EXACT [] -synonym: "down-regulation of lipid catabolic process" EXACT [] -synonym: "downregulation of lipid catabolic process" EXACT [] -synonym: "inhibition of lipid catabolic process" NARROW [] -synonym: "negative regulation of lipid breakdown" EXACT [] -synonym: "negative regulation of lipid catabolism" EXACT [] -synonym: "negative regulation of lipid degradation" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0045833 ! negative regulation of lipid metabolic process -is_a: GO:0050994 ! regulation of lipid catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0016042 ! lipid catabolic process -relationship: negatively_regulates GO:0016042 ! lipid catabolic process - -[Term] -id: GO:0050996 -name: positive regulation of lipid catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids." [GOC:ai] -synonym: "activation of lipid catabolic process" NARROW [] -synonym: "positive regulation of lipid breakdown" EXACT [] -synonym: "positive regulation of lipid catabolism" EXACT [] -synonym: "positive regulation of lipid degradation" EXACT [] -synonym: "stimulation of lipid catabolic process" NARROW [] -synonym: "up regulation of lipid catabolic process" EXACT [] -synonym: "up-regulation of lipid catabolic process" EXACT [] -synonym: "upregulation of lipid catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0045834 ! positive regulation of lipid metabolic process -is_a: GO:0050994 ! regulation of lipid catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0016042 ! lipid catabolic process -relationship: positively_regulates GO:0016042 ! lipid catabolic process +is_a: GO:0008150 ! biological process [Term] id: GO:0051046 @@ -42903,27 +42073,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006810 ! transport relationship: negatively_regulates GO:0006810 ! transport -[Term] -id: GO:0051055 -name: negative regulation of lipid biosynthetic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] -synonym: "down regulation of lipid biosynthetic process" EXACT [] -synonym: "down-regulation of lipid biosynthetic process" EXACT [] -synonym: "downregulation of lipid biosynthetic process" EXACT [] -synonym: "inhibition of lipid biosynthetic process" NARROW [] -synonym: "negative regulation of lipid anabolism" EXACT [] -synonym: "negative regulation of lipid biosynthesis" EXACT [] -synonym: "negative regulation of lipid formation" EXACT [] -synonym: "negative regulation of lipid synthesis" EXACT [] -synonym: "negative regulation of lipogenesis" EXACT [GOC:sl] -is_a: GO:0009890 ! negative regulation of biosynthetic process -is_a: GO:0045833 ! negative regulation of lipid metabolic process -is_a: GO:0046890 ! regulation of lipid biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0008610 ! lipid biosynthetic process -relationship: negatively_regulates GO:0008610 ! lipid biosynthetic process - [Term] id: GO:0051078 name: meiotic nuclear membrane disassembly @@ -42953,6 +42102,37 @@ intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0031965 ! nuclear membrane relationship: results_in_disassembly_of GO:0031965 ! nuclear membrane +[Term] +id: GO:0051093 +name: negative regulation of developmental process +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] +synonym: "down regulation of developmental process" EXACT [] +synonym: "down-regulation of developmental process" EXACT [] +synonym: "downregulation of developmental process" EXACT [] +synonym: "inhibition of developmental process" NARROW [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032502 ! developmental process +relationship: negatively_regulates GO:0032502 ! developmental process + +[Term] +id: GO:0051094 +name: positive regulation of developmental process +namespace: biological_process +def: "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] +synonym: "activation of developmental process" NARROW [] +synonym: "stimulation of developmental process" NARROW [] +synonym: "up regulation of developmental process" EXACT [] +synonym: "up-regulation of developmental process" EXACT [] +synonym: "upregulation of developmental process" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032502 ! developmental process +relationship: positively_regulates GO:0032502 ! developmental process + [Term] id: GO:0051128 name: regulation of cellular component organization @@ -43013,8 +42193,8 @@ xref: Wikipedia:Nuclear_transport is_a: GO:0046907 ! intracellular transport intersection_of: GO:0006810 ! transport intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure -intersection_of: results_in_transport_to_from_or_in GO:0005634 ! nucleus -relationship: results_in_transport_to_from_or_in GO:0005634 ! nucleus +intersection_of: results_in_transport_to_from_or_in GO:0005634 ! cell nucleus +relationship: results_in_transport_to_from_or_in GO:0005634 ! cell nucleus [Term] id: GO:0051171 @@ -43089,7 +42269,7 @@ synonym: "establishment and maintenance of substrate location" NARROW [] synonym: "localisation" EXACT [GOC:mah] synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process created_by: jl creation_date: 2013-12-18T13:51:04Z @@ -43162,6 +42342,47 @@ synonym: "RNA recruitment" EXACT [] is_a: GO:0051234 ! establishment of localization relationship: part_of GO:0006403 ! RNA localization +[Term] +id: GO:0051239 +name: regulation of multicellular organismal process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai, GOC:dph, GOC:tb] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032501 ! multicellular organismal process +relationship: regulates GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0051240 +name: positive regulation of multicellular organismal process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] +synonym: "activation of multicellular organismal process" NARROW [] +synonym: "stimulation of multicellular organismal process" NARROW [] +synonym: "up regulation of multicellular organismal process" EXACT [] +synonym: "up-regulation of multicellular organismal process" EXACT [] +synonym: "upregulation of multicellular organismal process" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032501 ! multicellular organismal process +relationship: positively_regulates GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0051241 +name: negative regulation of multicellular organismal process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] +synonym: "down regulation of multicellular organismal process" EXACT [] +synonym: "down-regulation of multicellular organismal process" EXACT [] +synonym: "downregulation of multicellular organismal process" EXACT [] +synonym: "inhibition of multicellular organismal process" NARROW [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032501 ! multicellular organismal process +relationship: negatively_regulates GO:0032501 ! multicellular organismal process + [Term] id: GO:0051246 name: regulation of protein metabolic process @@ -43294,9 +42515,9 @@ is_a: GO:0022414 ! reproductive process intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140013 ! meiotic nuclear division relationship: has_part GO:0140013 ! meiotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0019953 ! sexual reproduction +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24599" xsd:anyURI [Term] @@ -43329,8 +42550,8 @@ name: regulation of transferase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. +subset: gocheck_do_not_annotate subset: gocheck_do_not_manually_annotate -subset: term_scheduled_for_obsoletion synonym: "transferase regulator" EXACT [] is_a: GO:0050790 ! regulation of catalytic activity intersection_of: GO:0065007 ! biological regulation @@ -43343,8 +42564,8 @@ name: positive regulation of transferase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. +subset: gocheck_do_not_annotate subset: gocheck_do_not_manually_annotate -subset: term_scheduled_for_obsoletion synonym: "activation of transferase activity" NARROW [] synonym: "stimulation of transferase activity" NARROW [] synonym: "transferase activator" EXACT [] @@ -43363,8 +42584,8 @@ name: negative regulation of transferase activity namespace: biological_process def: "Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. +subset: gocheck_do_not_annotate subset: gocheck_do_not_manually_annotate -subset: term_scheduled_for_obsoletion synonym: "down regulation of transferase activity" EXACT [] synonym: "down-regulation of transferase activity" EXACT [] synonym: "downregulation of transferase activity" EXACT [] @@ -43430,21 +42651,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051321 ! meiotic cell cycle relationship: negatively_regulates GO:0051321 ! meiotic cell cycle -[Term] -id: GO:0051469 -name: vesicle fusion with vacuole -namespace: biological_process -alt_id: GO:0042146 -def: "The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole." [GOC:ai] -synonym: "heterotypic vacuole fusion (non-autophagic)" RELATED [] -synonym: "heterotypic vacuole fusion, non-autophagic" RELATED [] -is_a: GO:0006906 ! vesicle fusion -is_a: GO:0097576 ! vacuole fusion -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0005773 ! vacuole -intersection_of: results_in_fusion_of GO:0031982 ! vesicle -relationship: results_in_fusion_of GO:0031982 ! vesicle - [Term] id: GO:0051640 name: organelle localization @@ -43457,8 +42663,8 @@ is_a: GO:0051179 ! localization intersection_of: GO:0051179 ! localization intersection_of: has_primary_input GO:0043226 ! organelle relationship: has_primary_input GO:0043226 ! organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI [Term] @@ -43491,21 +42697,8 @@ synonym: "localization of nucleus" EXACT [] synonym: "nucleus localisation" EXACT [GOC:mah] is_a: GO:0051640 ! organelle localization intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0005634 ! nucleus -relationship: has_primary_input GO:0005634 ! nucleus - -[Term] -id: GO:0051648 -name: vesicle localization -namespace: biological_process -def: "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location." [GOC:ai] -synonym: "cytoplasmic vesicle localization" EXACT [] -synonym: "establishment and maintenance of vesicle localization" EXACT [] -synonym: "vesicle localisation" EXACT [GOC:mah] -is_a: GO:0051640 ! organelle localization -intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0031982 ! vesicle -relationship: has_primary_input GO:0031982 ! vesicle +intersection_of: has_primary_input GO:0005634 ! cell nucleus +relationship: has_primary_input GO:0005634 ! cell nucleus [Term] id: GO:0051649 @@ -43520,22 +42713,10 @@ synonym: "positioning within cell" NARROW [] is_a: GO:0051234 ! establishment of localization intersection_of: GO:0051234 ! establishment of localization intersection_of: occurs_in CL:0000000 ! cell -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms relationship: occurs_in CL:0000000 ! cell -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms relationship: part_of GO:0051641 ! cellular localization - -[Term] -id: GO:0051650 -name: establishment of vesicle localization -namespace: biological_process -def: "The directed movement of a vesicle to a specific location." [GOC:ai] -synonym: "establishment of vesicle localisation" EXACT [GOC:mah] -is_a: GO:0051648 ! vesicle localization -is_a: GO:0051649 ! establishment of localization in cell -is_a: GO:0051656 ! establishment of organelle localization -intersection_of: GO:0051234 ! establishment of localization -intersection_of: has_primary_input GO:0031982 ! vesicle +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0051656 @@ -43602,7 +42783,7 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ id: GO:0051704 name: multi-organism process def: "A biological process which involves another organism of the same or different species." [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] @@ -43792,8 +42973,8 @@ def: "The cellular chemical reactions and pathways involving a nucleobase-contai subset: goslim_drosophila subset: goslim_generic subset: goslim_pombe +subset: goslim_prokaryote subset: goslim_yeast -subset: prokaryote_subset synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] synonym: "nucleobase, nucleoside and nucleotide metabolism" EXACT [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process @@ -43809,6 +42990,16 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0043170 ! macromolecule metabolic process relationship: regulates GO:0043170 ! macromolecule metabolic process +[Term] +id: GO:0060284 +name: regulation of cell development +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:dph, GOC:tb] +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048468 ! cell development +relationship: regulates GO:0048468 ! cell development + [Term] id: GO:0060341 name: regulation of cellular localization @@ -43834,19 +43025,6 @@ relationship: part_of GO:0009653 ! anatomical structure morphogenesis created_by: dph creation_date: 2009-04-28T08:42:53Z -[Term] -id: GO:0060627 -name: regulation of vesicle-mediated transport -namespace: biological_process -def: "Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell." [GOC:dph, GOC:tb] -is_a: GO:0050794 ! regulation of cellular process -is_a: GO:0051049 ! regulation of transport -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0016192 ! vesicle-mediated transport -relationship: regulates GO:0016192 ! vesicle-mediated transport -created_by: dph -creation_date: 2009-05-18T02:29:43Z - [Term] id: GO:0061024 name: membrane organization @@ -43860,7 +43038,6 @@ subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote -subset: prokaryote_subset synonym: "cellular membrane organisation" EXACT [] synonym: "cellular membrane organization" EXACT [] synonym: "membrane organisation" EXACT [GOC:mah] @@ -43873,24 +43050,6 @@ relationship: results_in_organization_of GO:0016020 ! membrane created_by: jl creation_date: 2010-02-08T02:43:11Z -[Term] -id: GO:0061025 -name: membrane fusion -namespace: biological_process -alt_id: GO:0006944 -alt_id: GO:0044801 -def: "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] -subset: goslim_yeast -synonym: "cellular membrane fusion" EXACT [] -synonym: "single-organism membrane fusion" RELATED [] -xref: Wikipedia:Lipid_bilayer_fusion -is_a: GO:0061024 ! membrane organization -intersection_of: GO:0061024 ! membrane organization -intersection_of: results_in_fusion_of GO:0016020 ! membrane -relationship: results_in_fusion_of GO:0016020 ! membrane -created_by: jl -creation_date: 2010-02-08T02:48:06Z - [Term] id: GO:0061650 name: ubiquitin-like protein conjugating enzyme activity @@ -44057,7 +43216,7 @@ subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_pombe -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "cellular macromolecule complex assembly" RELATED [] synonym: "cellular protein complex assembly" EXACT [] synonym: "cellular protein-containing complex assembly" RELATED [] @@ -44081,7 +43240,7 @@ def: "Any process that modulates a measurable attribute of any biological proces subset: gocheck_do_not_annotate subset: goslim_pir synonym: "regulation" BROAD [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process [Term] id: GO:0065009 @@ -44091,7 +43250,6 @@ def: "Any process that modulates the frequency, rate or extent of a molecular fu subset: gocheck_do_not_annotate subset: goslim_pir subset: goslim_plant -subset: term_scheduled_for_obsoletion synonym: "regulation of a molecular function" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation @@ -44131,18 +43289,6 @@ synonym: "necrosis" BROAD [GOC:mah] property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24680" xsd:anyURI is_obsolete: true -[Term] -id: GO:0070382 -name: exocytic vesicle -namespace: cellular_component -def: "A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis." [GOC:kad, GOC:mah] -synonym: "exocytic constitutive secretory pathway transport vesicle" EXACT [] -synonym: "exocytotic vesicle" EXACT [GOC:kad] -is_a: GO:0030133 ! transport vesicle -is_a: GO:0099503 ! secretory vesicle -intersection_of: GO:0030133 ! transport vesicle -intersection_of: capable_of GO:0099500 ! vesicle fusion to plasma membrane - [Term] id: GO:0070727 name: cellular macromolecule localization @@ -44328,7 +43474,6 @@ creation_date: 2010-09-10T01:39:16Z id: GO:0071944 name: cell periphery namespace: cellular_component -def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon is_a: GO:0110165 ! cellular anatomical entity @@ -44364,7 +43509,7 @@ id: GO:0072657 name: protein localization to membrane namespace: biological_process def: "A process in which a protein is transported to, or maintained in, a specific location in a membrane." [GOC:mah] -subset: prokaryote_subset +subset: goslim_prokaryote synonym: "protein localisation in membrane" EXACT [GOC:mah] synonym: "protein localization in membrane" EXACT [] is_a: GO:0008104 ! protein localization @@ -44538,19 +43683,6 @@ intersection_of: has_target_end_location GO:0016020 ! membrane created_by: tb creation_date: 2009-12-08T03:18:51Z -[Term] -id: GO:0090174 -name: organelle membrane fusion -namespace: biological_process -def: "The joining of two lipid bilayers to form a single organelle membrane." [GOC:ascb_2009, GOC:dph, GOC:tb] -is_a: GO:0048284 ! organelle fusion -is_a: GO:0061025 ! membrane fusion -intersection_of: GO:0061025 ! membrane fusion -intersection_of: results_in_fusion_of GO:0031090 ! organelle membrane -relationship: results_in_fusion_of GO:0031090 ! organelle membrane -created_by: tb -creation_date: 2009-12-11T11:44:58Z - [Term] id: GO:0090304 name: nucleic acid metabolic process @@ -44561,6 +43693,7 @@ is_a: GO:0043170 ! macromolecule metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33696 ! nucleic acid relationship: has_primary_input_or_output CHEBI:33696 ! nucleic acid +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26133" xsd:anyURI created_by: tb creation_date: 2010-04-07T10:18:47Z @@ -44613,8 +43746,8 @@ def: "A macromolecular localization process in which RNA is transported to and m synonym: "RNA localisation to nucleus" EXACT [GOC:mah] is_a: GO:0006403 ! RNA localization intersection_of: GO:0006403 ! RNA localization -intersection_of: has_target_end_location GO:0005634 ! nucleus -relationship: has_target_end_location GO:0005634 ! nucleus +intersection_of: has_target_end_location GO:0005634 ! cell nucleus +relationship: has_target_end_location GO:0005634 ! cell nucleus created_by: tb creation_date: 2016-07-19T17:00:49Z @@ -44664,31 +43797,6 @@ is_a: GO:0005488 ! binding created_by: pr creation_date: 2012-08-02T13:03:39Z -[Term] -id: GO:0097576 -name: vacuole fusion -namespace: biological_process -def: "Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole." [GOC:pr, GOC:vw, Wikipedia:Vacuole] -is_a: GO:0007033 ! vacuole organization -is_a: GO:0048284 ! organelle fusion -intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_fusion_of GO:0005773 ! vacuole -relationship: results_in_fusion_of GO:0005773 ! vacuole -created_by: pr -creation_date: 2014-02-28T09:49:31Z - -[Term] -id: GO:0097708 -name: intracellular vesicle -namespace: cellular_component -def: "Any vesicle that is part of the intracellular region." [GOC:vesicles] -is_a: GO:0031982 ! vesicle -is_a: GO:0043231 ! intracellular membrane-bounded organelle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr -creation_date: 2016-03-29T17:39:45Z - [Term] id: GO:0098542 name: defense response to other organism @@ -44779,43 +43887,6 @@ intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -[Term] -id: GO:0098876 -name: vesicle-mediated transport to the plasma membrane -namespace: biological_process -def: "The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis." [GOC:dos] -is_a: GO:0016192 ! vesicle-mediated transport -is_a: GO:0051668 ! localization within membrane -intersection_of: GO:0006810 ! transport -intersection_of: has_target_end_location GO:0005886 ! plasma membrane -intersection_of: process_has_causal_agent GO:0031982 ! vesicle -relationship: ends_with GO:0006887 ! exocytosis -relationship: has_target_end_location GO:0005886 ! plasma membrane - -[Term] -id: GO:0099500 -name: vesicle fusion to plasma membrane -namespace: biological_process -def: "Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space." [GOC:aruk, GOC:bc, ISBN:0071120009, PMID:18618940] -is_a: GO:0006906 ! vesicle fusion -is_a: GO:0140029 ! exocytic process -intersection_of: GO:0061025 ! membrane fusion -intersection_of: part_of GO:0006887 ! exocytosis -intersection_of: results_in_fusion_of GO:0012506 ! vesicle membrane -intersection_of: results_in_fusion_of GO:0098590 ! plasma membrane region -relationship: results_in_fusion_of GO:0098590 ! plasma membrane region - -[Term] -id: GO:0099503 -name: secretory vesicle -namespace: cellular_component -def: "A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space." [GOC:dos] -subset: goslim_drosophila -is_a: GO:0031410 ! cytoplasmic vesicle -intersection_of: GO:0031982 ! vesicle -intersection_of: capable_of GO:0099500 ! vesicle fusion to plasma membrane -relationship: capable_of GO:0099500 ! vesicle fusion to plasma membrane - [Term] id: GO:0099568 name: cytoplasmic region @@ -44858,8 +43929,8 @@ namespace: biological_process def: "The process in which a nuclear membrane is synthesized, aggregates, and bonds together." [GOC:vw] is_a: GO:0044091 ! membrane biogenesis intersection_of: GO:0044085 ! cellular component biogenesis -intersection_of: has_output GO:0031965 ! nuclear membrane -relationship: has_output GO:0031965 ! nuclear membrane +intersection_of: has_primary_output GO:0031965 ! nuclear membrane +relationship: has_primary_output GO:0031965 ! nuclear membrane relationship: part_of GO:0071763 ! nuclear membrane organization [Term] @@ -44896,50 +43967,6 @@ is_a: GO:0044001 ! migration in host created_by: hjd creation_date: 2020-05-01T14:09:35Z -[Term] -id: GO:0110112 -name: regulation of lipid transporter activity -namespace: biological_process -def: "Any process that modulates the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: term_scheduled_for_obsoletion -is_a: GO:0032368 ! regulation of lipid transport -is_a: GO:0032409 ! regulation of transporter activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0005319 ! lipid transporter activity -relationship: regulates GO:0005319 ! lipid transporter activity -created_by: kmv -creation_date: 2018-07-06T18:53:55Z - -[Term] -id: GO:0110113 -name: positive regulation of lipid transporter activity -namespace: biological_process -def: "Any process that increases the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: term_scheduled_for_obsoletion -is_a: GO:0032370 ! positive regulation of lipid transport -is_a: GO:0032411 ! positive regulation of transporter activity -is_a: GO:0110112 ! regulation of lipid transporter activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0005319 ! lipid transporter activity -relationship: positively_regulates GO:0005319 ! lipid transporter activity -created_by: kmv -creation_date: 2018-07-06T19:14:13Z - -[Term] -id: GO:0110114 -name: negative regulation of lipid transporter activity -namespace: biological_process -def: "Any process that decreases the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: term_scheduled_for_obsoletion -is_a: GO:0032369 ! negative regulation of lipid transport -is_a: GO:0032410 ! negative regulation of transporter activity -is_a: GO:0110112 ! regulation of lipid transporter activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0005319 ! lipid transporter activity -relationship: negatively_regulates GO:0005319 ! lipid transporter activity -created_by: kmv -creation_date: 2018-07-06T19:21:44Z - [Term] id: GO:0110165 name: cellular anatomical entity @@ -44948,6 +43975,7 @@ def: "A part of a cellular organism that is either an immaterial entity or a mat subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0005575 ! cellular_component +is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI created_by: kmv @@ -44996,19 +44024,6 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ created_by: pg creation_date: 2017-03-23T09:40:00Z -[Term] -id: GO:0140029 -name: exocytic process -namespace: biological_process -def: "The cellular processes that contribute to exocytosis." [Wikipedia:Exocytosis] -subset: gocheck_do_not_annotate -is_a: GO:0009987 ! cellular process -intersection_of: GO:0009987 ! cellular process -intersection_of: part_of GO:0006887 ! exocytosis -relationship: part_of GO:0006887 ! exocytosis -created_by: pg -creation_date: 2017-05-15T13:20:45Z - [Term] id: GO:0140096 name: catalytic activity, acting on a protein @@ -45016,11 +44031,10 @@ namespace: molecular_function def: "Catalytic activity that acts to modify a protein." [GOC:molecular_function_refactoring, GOC:pdt] subset: goslim_generic subset: goslim_prokaryote -subset: prokaryote_subset is_a: GO:0003824 ! catalytic activity intersection_of: GO:0003824 ! catalytic activity -intersection_of: has_input PR:000000001 ! protein -relationship: has_input PR:000000001 ! protein +intersection_of: has_primary_input PR:000000001 ! protein +relationship: has_primary_input PR:000000001 ! protein property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI created_by: pg creation_date: 2017-09-14T10:32:59Z @@ -45031,11 +44045,11 @@ name: catalytic activity, acting on RNA namespace: molecular_function def: "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis." [GOC:molecular_function_refactoring, GOC:pdt] subset: goslim_generic -subset: prokaryote_subset +subset: goslim_prokaryote is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid intersection_of: GO:0003824 ! catalytic activity -intersection_of: has_input CHEBI:33697 ! ribonucleic acid -relationship: has_input CHEBI:33697 ! ribonucleic acid +intersection_of: has_primary_input CHEBI:33697 ! ribonucleic acid +relationship: has_primary_input CHEBI:33697 ! ribonucleic acid property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21612" xsd:anyURI created_by: pg @@ -45051,24 +44065,6 @@ is_a: GO:0005515 ! protein binding created_by: pg creation_date: 2018-10-01T10:03:21Z -[Term] -id: GO:0140318 -name: protein transporter activity -namespace: molecular_function -def: "Directly binding to a specific protein and delivering it to a specific cellular location." [PMID:18706423] -comment: Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation. -synonym: "protein carrier activity" RELATED [] -synonym: "protein transport chaperone" RELATED [] -xref: Reactome:R-HSA-9662747 "iRHOM2 transports ADAM17 from ER to the Golgi-network" -xref: Reactome:R-HSA-9662818 "iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane" -is_a: GO:0005215 ! transporter activity -intersection_of: GO:0005215 ! transporter activity -intersection_of: has_primary_input PR:000000001 ! protein -relationship: has_primary_input PR:000000001 ! protein -property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17073" xsd:anyURI -created_by: pg -creation_date: 2019-04-01T10:41:38Z - [Term] id: GO:0140352 name: export from cell @@ -45085,37 +44081,6 @@ relationship: has_target_start_location GO:0005622 ! intracellular anatomical st created_by: pg creation_date: 2019-05-22T11:20:45Z -[Term] -id: GO:0140353 -name: lipid export from cell -namespace: biological_process -def: "The directed movement of a lipid from a cell, into the extracellular region." [GOC:pg] -synonym: "lipid efflux" BROAD [] -is_a: GO:0006869 ! lipid transport -is_a: GO:0140352 ! export from cell -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:18059 ! lipid -intersection_of: has_target_end_location GO:0005576 ! extracellular region -intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg -creation_date: 2019-05-22T11:33:07Z - -[Term] -id: GO:0140354 -name: lipid import into cell -namespace: biological_process -def: "The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis." [GOC:pg] -synonym: "lipid uptake" BROAD [] -is_a: GO:0006869 ! lipid transport -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:18059 ! lipid -intersection_of: has_target_end_location GO:0005622 ! intracellular anatomical structure -intersection_of: has_target_start_location GO:0005576 ! extracellular region -relationship: has_target_end_location GO:0005622 ! intracellular anatomical structure -relationship: has_target_start_location GO:0005576 ! extracellular region -created_by: pg -creation_date: 2019-05-22T11:38:15Z - [Term] id: GO:0140513 name: nuclear protein-containing complex @@ -45125,8 +44090,8 @@ subset: gocheck_do_not_annotate synonym: "nuclear complex" EXACT [] is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex -intersection_of: part_of GO:0005634 ! nucleus -relationship: part_of GO:0005634 ! nucleus +intersection_of: part_of GO:0005634 ! cell nucleus +relationship: part_of GO:0005634 ! cell nucleus created_by: pg creation_date: 2020-09-09T05:12:38Z @@ -45160,8 +44125,8 @@ namespace: molecular_function def: "Catalytic activity that acts to modify a nucleic acid." [GOC:pg] is_a: GO:0003824 ! catalytic activity intersection_of: GO:0003824 ! catalytic activity -intersection_of: has_input CHEBI:33696 ! nucleic acid -relationship: has_input CHEBI:33696 ! nucleic acid +intersection_of: has_primary_input CHEBI:33696 ! nucleic acid +relationship: has_primary_input CHEBI:33696 ! nucleic acid property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21402" xsd:anyURI created_by: pg creation_date: 2021-05-11T06:31:07Z @@ -45212,6 +44177,7 @@ synonym: "L-amino acid anabolism" EXACT [] synonym: "L-amino acid biosynthesis" EXACT [] synonym: "L-amino acid formation" EXACT [] synonym: "L-amino acid synthesis" EXACT [] +is_a: GO:0008652 ! amino acid biosynthetic process is_a: GO:0170033 ! L-amino acid metabolic process is_a: GO:1901607 ! alpha-amino acid biosynthetic process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23268" xsd:anyURI @@ -45241,6 +44207,8 @@ namespace: biological_process def: "The chemical reactions and pathways involving any amino acid that is incorporated into protein naturally by ribosomal translation of mRNA, and that has a specific codon for translation from mRNA to protein." [GOC:ew] synonym: "proteinogenic amino acid metabolism" EXACT [] is_a: GO:0006520 ! amino acid metabolic process +is_a: GO:0019752 ! carboxylic acid metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23268" xsd:anyURI created_by: ew creation_date: 2023-12-18T17:31:08Z @@ -45395,22 +44363,6 @@ relationship: has_primary_input_or_output CHEBI:33832 ! organic cyclic compound created_by: bf creation_date: 2012-09-14T09:03:51Z -[Term] -id: GO:1901361 -name: organic cyclic compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound." [GOC:TermGenie] -synonym: "organic cyclic compound breakdown" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound catabolism" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound degradation" EXACT [GOC:TermGenie] -is_a: GO:1901360 ! organic cyclic compound metabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33832 ! organic cyclic compound -relationship: has_primary_input CHEBI:33832 ! organic cyclic compound -created_by: bf -creation_date: 2012-09-14T09:05:04Z - [Term] id: GO:1901362 name: organic cyclic compound biosynthetic process @@ -45458,22 +44410,6 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ created_by: pr creation_date: 2012-11-04T15:17:52Z -[Term] -id: GO:1901565 -name: organonitrogen compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound." [GOC:pr, GOC:TermGenie] -synonym: "organonitrogen compound breakdown" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound catabolism" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound degradation" EXACT [GOC:TermGenie] -is_a: GO:1901564 ! organonitrogen compound metabolic process -is_a: GO:1901575 ! organic substance catabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:35352 ! organonitrogen compound -relationship: has_primary_input CHEBI:35352 ! organonitrogen compound -created_by: pr -creation_date: 2012-11-04T15:17:56Z - [Term] id: GO:1901566 name: organonitrogen compound biosynthetic process @@ -45505,9 +44441,6 @@ synonym: "organic substance catabolism" EXACT [] synonym: "organic substance degradation" EXACT [] is_a: GO:0009056 ! catabolic process is_a: GO:0071704 ! organic substance metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:50860 ! organic molecular entity -relationship: has_primary_input CHEBI:50860 ! organic molecular entity created_by: pr creation_date: 2012-11-05T11:04:36Z @@ -45540,28 +44473,14 @@ namespace: biological_process def: "The chemical reactions and pathways involving an alpha-amino acid." [GOC:TermGenie] synonym: "alpha-amino acid metabolism" EXACT [GOC:TermGenie] is_a: GO:0006520 ! amino acid metabolic process +is_a: GO:0019752 ! carboxylic acid metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:78608 ! alpha-amino acid zwitterion relationship: has_primary_input_or_output CHEBI:78608 ! alpha-amino acid zwitterion created_by: tb creation_date: 2012-11-08T17:39:50Z -[Term] -id: GO:1901606 -name: alpha-amino acid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid." [GOC:TermGenie] -synonym: "alpha-amino acid breakdown" EXACT [GOC:TermGenie] -synonym: "alpha-amino acid catabolism" EXACT [GOC:TermGenie] -synonym: "alpha-amino acid degradation" EXACT [GOC:TermGenie] -is_a: GO:1901575 ! organic substance catabolic process -is_a: GO:1901605 ! alpha-amino acid metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:78608 ! alpha-amino acid zwitterion -relationship: has_primary_input CHEBI:78608 ! alpha-amino acid zwitterion -created_by: tb -creation_date: 2012-11-08T17:39:54Z - [Term] id: GO:1901607 name: alpha-amino acid biosynthetic process @@ -45571,7 +44490,8 @@ synonym: "alpha-amino acid anabolism" EXACT [GOC:TermGenie] synonym: "alpha-amino acid biosynthesis" EXACT [GOC:TermGenie] synonym: "alpha-amino acid formation" EXACT [GOC:TermGenie] synonym: "alpha-amino acid synthesis" EXACT [GOC:TermGenie] -is_a: GO:0008652 ! amino acid biosynthetic process +is_a: GO:0046394 ! carboxylic acid biosynthetic process +is_a: GO:1901566 ! organonitrogen compound biosynthetic process is_a: GO:1901605 ! alpha-amino acid metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:78608 ! alpha-amino acid zwitterion @@ -45651,38 +44571,6 @@ relationship: positively_regulates GO:0070925 ! organelle assembly created_by: pr creation_date: 2013-05-14T09:43:36Z -[Term] -id: GO:1902369 -name: negative regulation of RNA catabolic process -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process." [GOC:bf, GOC:TermGenie, PMID:16640457] -synonym: "down regulation of RNA breakdown" EXACT [GOC:TermGenie] -synonym: "down regulation of RNA catabolic process" EXACT [GOC:TermGenie] -synonym: "down regulation of RNA catabolism" EXACT [GOC:TermGenie] -synonym: "down regulation of RNA degradation" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA breakdown" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA catabolic process" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA catabolism" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA degradation" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA breakdown" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA catabolic process" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA catabolism" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA degradation" EXACT [GOC:TermGenie] -synonym: "inhibition of RNA breakdown" NARROW [GOC:TermGenie] -synonym: "inhibition of RNA catabolic process" NARROW [GOC:TermGenie] -synonym: "inhibition of RNA catabolism" NARROW [GOC:TermGenie] -synonym: "inhibition of RNA degradation" NARROW [GOC:TermGenie] -synonym: "negative regulation of RNA breakdown" EXACT [GOC:TermGenie] -synonym: "negative regulation of RNA catabolism" EXACT [GOC:TermGenie] -synonym: "negative regulation of RNA degradation" EXACT [GOC:TermGenie] -is_a: GO:0031330 ! negative regulation of cellular catabolic process -is_a: GO:0051253 ! negative regulation of RNA metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006401 ! RNA catabolic process -relationship: negatively_regulates GO:0006401 ! RNA catabolic process -created_by: bf -creation_date: 2013-08-22T14:59:39Z - [Term] id: GO:1902494 name: catalytic complex @@ -45752,7 +44640,6 @@ synonym: "negative regulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA formation" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA synthesis" EXACT [GOC:TermGenie] is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process -is_a: GO:0031327 ! negative regulation of cellular biosynthetic process is_a: GO:0051253 ! negative regulation of RNA metabolic process is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0065007 ! biological regulation @@ -45791,7 +44678,6 @@ synonym: "upregulation of RNA biosynthetic process" EXACT [GOC:TermGenie] synonym: "upregulation of RNA formation" EXACT [GOC:TermGenie] synonym: "upregulation of RNA synthesis" EXACT [GOC:TermGenie] is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0051254 ! positive regulation of RNA metabolic process is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0065007 ! biological regulation @@ -46076,19 +44962,6 @@ relationship: positively_regulates GO:0032940 ! secretion by cell created_by: pm creation_date: 2014-10-08T13:25:17Z -[Term] -id: GO:1903561 -name: extracellular vesicle -namespace: cellular_component -def: "Any vesicle that is part of the extracellular region." [GO_REF:0000064, GOC:pm, GOC:TermGenie, PMID:24769233] -synonym: "microparticle" RELATED [GOC:vesicles] -is_a: GO:0031982 ! vesicle -is_a: GO:0065010 ! extracellular membrane-bounded organelle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl -creation_date: 2014-10-22T14:26:11Z - [Term] id: GO:1903729 name: regulation of plasma membrane organization @@ -46149,96 +45022,6 @@ property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/ created_by: jl creation_date: 2015-01-20T14:32:33Z -[Term] -id: GO:1904350 -name: regulation of protein catabolic process in the vacuole -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:25635054] -synonym: "regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -is_a: GO:0042176 ! regulation of protein catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0007039 ! protein catabolic process in the vacuole -relationship: regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl -creation_date: 2015-06-12T09:10:36Z - -[Term] -id: GO:1904351 -name: negative regulation of protein catabolic process in the vacuole -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:25635054] -synonym: "down regulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "down regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "down regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "down regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "down regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "down-regulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "down-regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "down-regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "down-regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "down-regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "downregulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "downregulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "downregulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "downregulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "downregulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "inhibition of protein catabolic process in the vacuole" NARROW [GOC:TermGenie] -synonym: "inhibition of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "inhibition of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "inhibition of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "inhibition of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "negative regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "negative regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "negative regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "negative regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -is_a: GO:0042177 ! negative regulation of protein catabolic process -is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0007039 ! protein catabolic process in the vacuole -relationship: negatively_regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl -creation_date: 2015-06-12T09:10:42Z - -[Term] -id: GO:1904352 -name: positive regulation of protein catabolic process in the vacuole -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:25635054] -synonym: "activation of protein catabolic process in the vacuole" NARROW [GOC:TermGenie] -synonym: "activation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "activation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "activation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "activation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "positive regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "positive regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "positive regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "positive regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "up regulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "up regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "up regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "up regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "up regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "up-regulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "up-regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "up-regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "up-regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "up-regulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -synonym: "upregulation of protein catabolic process in the vacuole" EXACT [GOC:TermGenie] -synonym: "upregulation of vacuolar protein breakdown" RELATED [GOC:TermGenie] -synonym: "upregulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie] -synonym: "upregulation of vacuolar protein catabolism" RELATED [GOC:TermGenie] -synonym: "upregulation of vacuolar protein degradation" RELATED [GOC:TermGenie] -is_a: GO:0045732 ! positive regulation of protein catabolic process -is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0007039 ! protein catabolic process in the vacuole -relationship: positively_regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl -creation_date: 2015-06-12T09:10:49Z - [Term] id: GO:1904375 name: regulation of protein localization to cell periphery @@ -46421,52 +45204,6 @@ relationship: part_of GO:0016236 ! macroautophagy created_by: bf creation_date: 2016-03-08T14:18:10Z -[Term] -id: GO:1905153 -name: regulation of membrane invagination -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of membrane invagination." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353] -is_a: GO:0051128 ! regulation of cellular component organization -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0010324 ! membrane invagination -relationship: regulates GO:0010324 ! membrane invagination -created_by: bf -creation_date: 2016-04-18T15:43:54Z - -[Term] -id: GO:1905154 -name: negative regulation of membrane invagination -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353] -synonym: "down regulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "down-regulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "downregulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "inhibition of membrane invagination" NARROW [GOC:TermGenie] -is_a: GO:0051129 ! negative regulation of cellular component organization -is_a: GO:1905153 ! regulation of membrane invagination -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0010324 ! membrane invagination -relationship: negatively_regulates GO:0010324 ! membrane invagination -created_by: bf -creation_date: 2016-04-18T15:44:04Z - -[Term] -id: GO:1905155 -name: positive regulation of membrane invagination -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of membrane invagination." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie] -synonym: "activation of membrane invagination" NARROW [GOC:TermGenie] -synonym: "up regulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "up-regulation of membrane invagination" EXACT [GOC:TermGenie] -synonym: "upregulation of membrane invagination" EXACT [GOC:TermGenie] -is_a: GO:0051130 ! positive regulation of cellular component organization -is_a: GO:1905153 ! regulation of membrane invagination -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0010324 ! membrane invagination -relationship: positively_regulates GO:0010324 ! membrane invagination -created_by: bf -creation_date: 2016-04-18T15:44:12Z - [Term] id: GO:1905475 name: regulation of protein localization to membrane @@ -46544,68 +45281,11 @@ synonym: "cell nucleus disassembly" EXACT [GOC:TermGenie] is_a: GO:0006997 ! nucleus organization is_a: GO:1903008 ! organelle disassembly intersection_of: GO:0022411 ! cellular component disassembly -intersection_of: results_in_disassembly_of GO:0005634 ! nucleus -relationship: results_in_disassembly_of GO:0005634 ! nucleus +intersection_of: results_in_disassembly_of GO:0005634 ! cell nucleus +relationship: results_in_disassembly_of GO:0005634 ! cell nucleus created_by: pr creation_date: 2016-11-14T13:38:57Z -[Term] -id: GO:1905952 -name: regulation of lipid localization -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] -synonym: "regulation of lipid localisation" EXACT [GOC:TermGenie] -is_a: GO:0032879 ! regulation of localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0010876 ! lipid localization -relationship: regulates GO:0010876 ! lipid localization -created_by: rz -creation_date: 2017-02-21T12:12:22Z - -[Term] -id: GO:1905953 -name: negative regulation of lipid localization -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] -synonym: "down regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "down regulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "down-regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "down-regulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "downregulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "downregulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "inhibition of lipid localisation" NARROW [GOC:TermGenie] -synonym: "inhibition of lipid localization" NARROW [GOC:TermGenie] -synonym: "negative regulation of lipid localisation" EXACT [GOC:TermGenie] -is_a: GO:0048519 ! negative regulation of biological process -is_a: GO:1905952 ! regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0010876 ! lipid localization -relationship: negatively_regulates GO:0010876 ! lipid localization -created_by: rz -creation_date: 2017-02-21T12:12:41Z - -[Term] -id: GO:1905954 -name: positive regulation of lipid localization -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] -synonym: "activation of lipid localisation" NARROW [GOC:TermGenie] -synonym: "activation of lipid localization" NARROW [GOC:TermGenie] -synonym: "positive regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "up regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "up regulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "up-regulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "up-regulation of lipid localization" EXACT [GOC:TermGenie] -synonym: "upregulation of lipid localisation" EXACT [GOC:TermGenie] -synonym: "upregulation of lipid localization" EXACT [GOC:TermGenie] -is_a: GO:0048518 ! positive regulation of biological process -is_a: GO:1905952 ! regulation of lipid localization -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0010876 ! lipid localization -relationship: positively_regulates GO:0010876 ! lipid localization -created_by: rz -creation_date: 2017-02-21T12:12:49Z - [Term] id: GO:1990234 name: transferase complex @@ -46618,19 +45298,6 @@ relationship: capable_of GO:0016740 ! transferase activity created_by: bhm creation_date: 2013-11-12T13:20:12Z -[Term] -id: GO:1990351 -name: transporter complex -namespace: cellular_component -def: "A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells." [GOC:bhm, PMID:15449578] -comment: An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay). -is_a: GO:0032991 ! protein-containing complex -intersection_of: GO:0032991 ! protein-containing complex -intersection_of: capable_of GO:0005215 ! transporter activity -relationship: capable_of GO:0005215 ! transporter activity -created_by: bhm -creation_date: 2014-03-26T14:23:27Z - [Term] id: GO:1990778 name: protein localization to cell periphery @@ -46678,6 +45345,19 @@ relationship: has_part CHEBI:33697 ! ribonucleic acid created_by: pr creation_date: 2015-11-19T12:26:37Z +[Term] +id: GO:2000026 +name: regulation of multicellular organismal development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of multicellular organismal development." [GOC:obol] +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007275 ! multicellular organism development +relationship: regulates GO:0007275 ! multicellular organism development +created_by: tb +creation_date: 2010-08-05T11:25:59Z + [Term] id: GO:2000241 name: regulation of reproductive process @@ -46726,8 +45406,9 @@ synonym: "regulation of cellular amino acid anabolism" EXACT [GOC:obol] synonym: "regulation of cellular amino acid biosynthesis" EXACT [GOC:obol] synonym: "regulation of cellular amino acid formation" EXACT [GOC:obol] synonym: "regulation of cellular amino acid synthesis" EXACT [GOC:obol] -is_a: GO:0006521 ! regulation of cellular amino acid metabolic process is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0051171 ! regulation of nitrogen compound metabolic process +is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008652 ! amino acid biosynthetic process relationship: regulates GO:0008652 ! amino acid biosynthetic process @@ -46745,7 +45426,8 @@ synonym: "negative regulation of amino acid formation" EXACT [GOC:obol] synonym: "negative regulation of amino acid synthesis" EXACT [GOC:obol] synonym: "negative regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol] is_a: GO:0031327 ! negative regulation of cellular biosynthetic process -is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process +is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process +is_a: GO:0062014 ! negative regulation of small molecule metabolic process is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008652 ! amino acid biosynthetic process @@ -46764,7 +45446,8 @@ synonym: "positive regulation of amino acid formation" EXACT [GOC:obol] synonym: "positive regulation of amino acid synthesis" EXACT [GOC:obol] synonym: "positive regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol] is_a: GO:0031328 ! positive regulation of cellular biosynthetic process -is_a: GO:0045764 ! positive regulation of amino acid metabolic process +is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process +is_a: GO:0062013 ! positive regulation of small molecule metabolic process is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008652 ! amino acid biosynthetic process @@ -46782,7 +45465,6 @@ synonym: "regulation of RNA biosynthesis" EXACT [GOC:obol] synonym: "regulation of RNA formation" EXACT [GOC:obol] synonym: "regulation of RNA synthesis" EXACT [GOC:obol] is_a: GO:0010556 ! regulation of macromolecule biosynthetic process -is_a: GO:0031326 ! regulation of cellular biosynthetic process is_a: GO:0051252 ! regulation of RNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032774 ! RNA biosynthetic process @@ -46867,7 +45549,7 @@ property_value: IAO:0000117 "Lindsay Cowell" xsd:string id: IDO:0000626 name: appearance of disorder def: "A process by which a disorder comes into existence." [] -is_a: GO:0008150 ! biological_process +is_a: GO:0008150 ! biological process relationship: results_in_formation_of OGMS:0000045 ! disorder property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000117 "Alexander Diehl" xsd:string @@ -46879,8 +45561,18 @@ name: root namespace: ncbi_taxonomy synonym: "all" RELATED synonym [] xref: GC_ID:1 +xref: PMID:30365038 +xref: PMID:32761142 is_a: OBI:0100026 +[Term] +id: NCBITaxon:1206794 +name: Ecdysozoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33317 ! Protostomia +property_value: has_rank NCBITaxon:clade + [Term] id: NCBITaxon:131567 name: cellular organisms @@ -46889,6 +45581,133 @@ synonym: "biota" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:1 ! root +[Term] +id: NCBITaxon:147537 +name: Saccharomycotina +namespace: ncbi_taxonomy +synonym: "true yeasts" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:716545 ! saccharomyceta +property_value: has_rank NCBITaxon:subphylum + +[Term] +id: NCBITaxon:147554 +name: Schizosaccharomycetes +namespace: ncbi_taxonomy +synonym: "Archiascomycota" RELATED in_part [] +xref: GC_ID:1 +is_a: NCBITaxon:451866 ! Taphrinomycotina +property_value: has_rank NCBITaxon:class + +[Term] +id: NCBITaxon:197562 +name: Pancrustacea +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:10874751 +xref: PMID:11557979 +is_a: NCBITaxon:197563 ! Mandibulata +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:197563 +name: Mandibulata +namespace: ncbi_taxonomy +synonym: "mandibulates" EXACT OMO:0003003 [] +xref: GC_ID:1 +xref: PMID:11557979 +xref: PMID:9727836 +is_a: NCBITaxon:6656 ! Arthropoda +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:2 +name: Bacteria +namespace: ncbi_taxonomy +synonym: "bacteria" RELATED blast_name [] +synonym: "eubacteria" EXACT genbank_common_name [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11542017 +xref: PMID:11542087 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:270744 +xref: PMID:32628106 +xref: PMID:36748408 +xref: PMID:7520741 +xref: PMID:8123559 +xref: PMID:8186100 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom + +[Term] +id: NCBITaxon:2157 +name: Archaea +namespace: ncbi_taxonomy +synonym: "archaea" RELATED blast_name [] +synonym: "Archaebacteria" RELATED synonym [] +synonym: "Mendosicutes" RELATED synonym [] +synonym: "Metabacteria" RELATED synonym [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11541975 +xref: PMID:11542064 +xref: PMID:11542149 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:25527841 +xref: PMID:270744 +xref: PMID:32628106 +xref: PMID:36748408 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom + [Term] id: NCBITaxon:2759 name: Eukaryota @@ -46898,7 +45717,7 @@ synonym: "Eucaryotae" RELATED synonym [] synonym: "eucaryotes" EXACT genbank_common_name [] synonym: "Eukarya" RELATED synonym [] synonym: "Eukaryotae" RELATED synonym [] -synonym: "eukaryotes" EXACT common_name [] +synonym: "eukaryotes" EXACT OMO:0003003 [] synonym: "eukaryotes" RELATED blast_name [] xref: GC_ID:1 xref: PMID:23020233 @@ -46916,6 +45735,63 @@ xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:clade +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT OMO:0003003 [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:33317 +name: Protostomia +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:34346 +name: Schizosaccharomycetales +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:147554 ! Schizosaccharomycetes +property_value: has_rank NCBITaxon:order + +[Term] +id: NCBITaxon:451864 +name: Dikarya +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:15689432 +xref: PMID:16151185 +xref: PMID:17010206 +xref: PMID:17051209 +xref: PMID:17572334 +is_a: NCBITaxon:4751 ! Fungi +property_value: has_rank NCBITaxon:subkingdom + +[Term] +id: NCBITaxon:451866 +name: Taphrinomycotina +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:4890 ! Ascomycota +property_value: has_rank NCBITaxon:subphylum + [Term] id: NCBITaxon:4751 name: Fungi @@ -46928,6 +45804,162 @@ xref: PMID:12684019 is_a: NCBITaxon:33154 ! Opisthokonta property_value: has_rank NCBITaxon:kingdom +[Term] +id: NCBITaxon:4890 +name: Ascomycota +namespace: ncbi_taxonomy +synonym: "ascomycete fungi" RELATED blast_name [] +synonym: "ascomycetes" EXACT genbank_common_name [] +synonym: "sac fungi" EXACT OMO:0003003 [] +xref: GC_ID:1 +xref: PMID:17572334 +is_a: NCBITaxon:451864 ! Dikarya +property_value: has_rank NCBITaxon:phylum + +[Term] +id: NCBITaxon:4891 +name: Saccharomycetes +namespace: ncbi_taxonomy +synonym: "Hemiascomycetes" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:147537 ! Saccharomycotina +property_value: has_rank NCBITaxon:class + +[Term] +id: NCBITaxon:4892 +name: Saccharomycetales +namespace: ncbi_taxonomy +synonym: "budding yeasts" RELATED blast_name [] +synonym: "Endomycetales" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:4891 ! Saccharomycetes +property_value: has_rank NCBITaxon:order + +[Term] +id: NCBITaxon:4893 +name: Saccharomycetaceae +namespace: ncbi_taxonomy +alt_id: NCBITaxon:221665 +alt_id: NCBITaxon:44280 +xref: GC_ID:1 +is_a: NCBITaxon:4892 ! Saccharomycetales +property_value: has_rank NCBITaxon:family + +[Term] +id: NCBITaxon:4894 +name: Schizosaccharomycetaceae +namespace: ncbi_taxonomy +synonym: "fission yeasts" EXACT genbank_common_name [] +synonym: "Schizosaccharomycetoideae" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:34346 ! Schizosaccharomycetales +property_value: has_rank NCBITaxon:family + +[Term] +id: NCBITaxon:4895 +name: Schizosaccharomyces +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:4894 ! Schizosaccharomycetaceae +property_value: has_rank NCBITaxon:genus + +[Term] +id: NCBITaxon:4896 +name: Schizosaccharomyces pombe +namespace: ncbi_taxonomy +alt_id: NCBITaxon:45042 +synonym: "fission yeast" EXACT genbank_common_name [] +synonym: "Schizosaccharomyces malidevorans" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:4895 ! Schizosaccharomyces +property_value: has_rank NCBITaxon:species + +[Term] +id: NCBITaxon:4930 +name: Saccharomyces +namespace: ncbi_taxonomy +alt_id: NCBITaxon:36915 +synonym: "Pachytichospora" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:4893 ! Saccharomycetaceae +property_value: has_rank NCBITaxon:genus + +[Term] +id: NCBITaxon:4932 +name: Saccharomyces cerevisiae +namespace: ncbi_taxonomy +alt_id: NCBITaxon:41870 +synonym: "baker's yeast" EXACT OMO:0003003 [] +synonym: "brewer's yeast" EXACT genbank_common_name [] +synonym: "Candida robusta" RELATED synonym [] +synonym: "Mycoderma cerevisiae" RELATED synonym [] +synonym: "Saccharomyces capensis" RELATED synonym [] +synonym: "Saccharomyces cerevisiae 'var. diastaticus'" EXACT equivalent_name [] +synonym: "Saccharomyces diastaticus" RELATED synonym [] +synonym: "Saccharomyces italicus" RELATED synonym [] +synonym: "Saccharomyces oviformis" RELATED synonym [] +synonym: "Saccharomyces uvarum var. melibiosus" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:4930 ! Saccharomyces +property_value: has_rank NCBITaxon:species + +[Term] +id: NCBITaxon:50557 +name: Insecta +namespace: ncbi_taxonomy +synonym: "insects" RELATED blast_name [] +synonym: "true insects" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:6960 ! Hexapoda +property_value: has_rank NCBITaxon:class + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:6656 +name: Arthropoda +namespace: ncbi_taxonomy +synonym: "arthropods" EXACT genbank_common_name [] +synonym: "arthropods" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:88770 ! Panarthropoda +property_value: has_rank NCBITaxon:phylum + +[Term] +id: NCBITaxon:6960 +name: Hexapoda +namespace: ncbi_taxonomy +synonym: "Atelocerata" RELATED in_part [] +synonym: "hexapods" RELATED blast_name [] +synonym: "insects" EXACT genbank_common_name [] +synonym: "Tracheata" RELATED in_part [] +synonym: "Uniramia" RELATED in_part [] +xref: GC_ID:1 +is_a: NCBITaxon:197562 ! Pancrustacea +property_value: has_rank NCBITaxon:subphylum + +[Term] +id: NCBITaxon:716545 +name: saccharomyceta +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:4890 ! Ascomycota +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:88770 +name: Panarthropoda +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:1206794 ! Ecdysozoa +property_value: has_rank NCBITaxon:clade + [Term] id: OGMS:0000045 name: disorder @@ -46941,7 +45973,7 @@ name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic [Term] id: PATO:0000033 @@ -47650,6 +46682,23 @@ subset: mpath_slim subset: value_slim is_a: PATO:0002505 ! nucleated +[Term] +id: PATO:0001992 +name: cellularity +namespace: quality +def: "An organismal quality inhering in a bearer by virtue of the bearer's consisting cells." [PATOC:GVG] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0001995 ! organismal quality + +[Term] +id: PATO:0001993 +name: multicellular +namespace: quality +def: "A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell." [PATOC:GVG] +subset: value_slim +is_a: PATO:0001992 ! cellularity + [Term] id: PATO:0001995 name: organismal quality @@ -58312,7 +57361,7 @@ namespace: single_species_phenotype def: "A single species cell morphology phenotype in which fungal hyphae form an increased number of branches." [] synonym: "increased branching of hyphae" EXACT [] synonym: "increased hyphal branching" EXACT [] -is_a: PHIPO:0001205 ! abnormal filament morphology +is_a: PHIPO:0001427 ! abnormal hyphal branching created_by: alaynecuzick creation_date: 2020-03-04T14:33:49Z @@ -60751,6 +59800,258 @@ is_a: PHIPO:0001308 ! normal growth on chemical created_by: alaynecuzick creation_date: 2024-01-30T14:16:53Z +[Term] +id: PHIPO:0001411 +name: resistance to dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001412 +name: sensitive to dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001413 +name: normal growth on dalfopristin +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-05T09:44:00Z + +[Term] +id: PHIPO:0001414 +name: resistance to thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001415 +name: sensitive to thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001416 +name: normal growth on thifluzamide +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001417 +name: resistance to penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001418 +name: sensitive to penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001419 +name: normal growth on penflufen +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001420 +name: resistance to flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001421 +name: sensitive to flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001422 +name: normal growth on flutolanil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-07T11:32:37Z + +[Term] +id: PHIPO:0001423 +name: resistance to imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001424 +name: sensitive to imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001425 +name: normal growth on imazalil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-12T10:06:39Z + +[Term] +id: PHIPO:0001426 +name: normal growth on fludioxonil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-02-28T09:44:54Z + +[Term] +id: PHIPO:0001427 +name: abnormal hyphal branching +namespace: single_species_phenotype +def: "A single species cell morphology phenotype in which fungal hyphae branching is abnormal." [] +is_a: PHIPO:0001205 ! abnormal filament morphology +created_by: alaynecuzick +creation_date: 2024-03-04T15:00:58Z + +[Term] +id: PHIPO:0001428 +name: normal growth on brefeldin A +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-12T15:12:17Z + +[Term] +id: PHIPO:0001429 +name: normal growth on fluconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-12T15:14:22Z + +[Term] +id: PHIPO:0001430 +name: resistance to ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001431 +name: sensitive to ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001432 +name: normal growth on ipconazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001433 +name: resistance to cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." [] +is_a: PHIPO:0000022 ! increased resistance to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001434 +name: sensitive to cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow." [] +is_a: PHIPO:0000021 ! increased sensitivity to chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001435 +name: normal growth on cyprodinil +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-18T13:26:33Z + +[Term] +id: PHIPO:0001436 +name: normal growth on caspofungin +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + +[Term] +id: PHIPO:0001437 +name: normal growth on terbinafine +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + +[Term] +id: PHIPO:0001438 +name: normal growth on bifonazole +namespace: single_species_phenotype +def: "A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type)." [] +is_a: PHIPO:0001308 ! normal growth on chemical +created_by: alaynecuzick +creation_date: 2024-03-27T11:45:23Z + [Term] id: PR:000000001 name: protein @@ -60784,8 +60085,8 @@ synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: CHEBI:36080 ! protein is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000050567 @@ -60813,6 +60114,7 @@ namespace: uberon def: "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." [span:ProcessualEntity] subset: common_anatomy subset: upper_level +xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 @@ -60833,7 +60135,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 +xref: FBbt:00007001 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -60848,11 +60150,61 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage +relationship: RO:0002496 UBERON:0000106 {gci_filler="NCBITaxon:33208", gci_relation="RO:0002162"} ! existence starts during or after zygote stage +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0000066 +name: fully formed stage +namespace: uberon +def: "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "adult stage" BROAD [] +synonym: "fully formed animal stage" EXACT [] +synonym: "juvenile-adult stage" EXACT [] +xref: BilaDO:0000004 +xref: BTO:0001043 +xref: EFO:0001272 +xref: FBdv:00005369 +xref: WBls:0000041 +xref: XtroDO:0000084 +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000092 ! post-embryonic stage +relationship: preceded_by UBERON:0000111 ! organogenesis stage +relationship: precedes UBERON:0000071 ! death stage +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/566" xsd:anyURI + +[Term] +id: UBERON:0000068 +name: embryo stage +namespace: uberon +def: "A life cycle stage that starts with fertilization and ends with the fully formed embryo." [http://orcid.org/0000-0002-6601-2165] +synonym: "embryogenesis" RELATED [] +synonym: "embryonic stage" EXACT [] +xref: BilaDO:0000002 +xref: EV:0300001 +xref: FBdv:00005289 +xref: FMA:72652 +xref: HsapDv:0000002 +xref: MmusDv:0000002 +xref: OGES:000000 +xref: OGES:000022 +xref: SCTID:296280003 +xref: WBls:0000003 +xref: WBls:0000092 +xref: WBls:0000102 +xref: XAO:1000012 +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +disjoint_from: UBERON:0000092 ! post-embryonic stage +relationship: precedes UBERON:0000066 ! fully formed stage +relationship: precedes UBERON:0000092 ! post-embryonic stage +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development + [Term] id: UBERON:0000071 name: death stage @@ -60864,12 +60216,34 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle +relationship: RO:0002229 UBERON:0000104 ! ends life cycle property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +[Term] +id: UBERON:0000092 +name: post-embryonic stage +namespace: uberon +def: "Stage succeeding embryo, including mature structure." [https://orcid.org/0000-0002-6601-2165] +synonym: "post-hatching stage" NARROW [] +synonym: "postembryonic" RELATED [] +synonym: "postembryonic stage" EXACT [] +xref: BilaDO:0000003 +xref: OGES:000010 +xref: OGES:000014 +xref: OGES:000024 +xref: WBls:0000022 +xref: WBls:0000093 +xref: WBls:0000103 +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +relationship: preceded_by UBERON:0000068 ! embryo stage +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI +property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string + [Term] id: UBERON:0000104 name: life cycle @@ -60890,6 +60264,7 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage +relationship: starts_with UBERON:0000106 {gci_filler="NCBITaxon:33208", gci_relation="RO:0002162"} ! zygote stage property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 @@ -60928,6 +60303,59 @@ property_value: RO:0002175 NCBITaxon:4751 property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +[Term] +id: UBERON:0000106 +name: zygote stage +namespace: uberon +def: "A stage at which the organism is a single cell produced by means of sexual reproduction." [Wikipedia:Zygote] +subset: efo_slim +synonym: "1-cell stage" EXACT [] +synonym: "fertilized egg stage" EXACT [BTO:0000854] +synonym: "fertilized egg stage" RELATED [] +synonym: "one cell stage" EXACT [] +synonym: "one-cell stage" RELATED [VHOG:0000745] +synonym: "zygote" RELATED [VHOG:0000745] +synonym: "zygotum" RELATED OMO:0003011 [Wikipedia:Zygote] +xref: BilaDO:0000005 +xref: BILS:0000106 +xref: EFO:0001322 +xref: EHDAA:27 +xref: FBdv:00005288 +xref: IDOMAL:0000302 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration", https://w3id.org/sssom/author_id="https://orcid.org/0000-0003-4423-4370", https://w3id.org/sssom/mapping_provider="https://github.com/biopragmatics/biomappings"} +xref: NCIT:C12601 +xref: PdumDv:0000100 +xref: VHOG:0000745 +xref: Wikipedia:Zygote +xref: XAO:1000001 +xref: ZFS:0000001 +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 +property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} + +[Term] +id: UBERON:0000111 +name: organogenesis stage +namespace: uberon +def: "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism." [Wikipedia:Organogenesis] +synonym: "segmentation stage" RELATED [] +xref: BilaDO:0000010 +xref: BILS:0000111 +xref: HsapDv:0000015 +xref: MmusDv:0000018 +xref: OGES:000005 +xref: OGES:000032 +xref: Wikipedia:Organogenesis +is_a: BFO:0000003 ! occurrent +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI + [Term] id: UBERON:0000465 name: material anatomical entity @@ -60940,7 +60368,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 +xref: FBbt:00007016 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -60952,6 +60380,107 @@ property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0000468 +name: multicellular organism +namespace: uberon +def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, http://orcid.org/0000-0001-9114-8737, Wikipedia:Multi-cellular_organism] +subset: common_anatomy +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "body" RELATED [AEO:0000103, BIRNLEX:18, FMA:256135, NCIT:C13041] +synonym: "Koerper" RELATED [BTO:0001489] +synonym: "multi-cellular organism" EXACT [CARO:0000012] +synonym: "organism" BROAD [FBbt:00000001, VHOG:0000671, WBbt:0007833] +synonym: "whole body" RELATED [BTO:0001489] +synonym: "whole organism" RELATED [FBbt:00000001] +xref: AAO:0010026 +xref: AEO:0000191 +xref: BILA:0000012 +xref: BIRNLEX:18 +xref: BSA:0000038 +xref: BTO:0000042 +xref: CARO:0000012 +xref: EFO:0002906 +xref: EHDAA2:0003103 +xref: EHDAA2:0003191 +xref: EHDAA:1 +xref: EMAPA:25765 +xref: EV:0100016 +xref: FBbt:00000001 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FMA:256135 +xref: galen:Organism +xref: HAO:0000012 +xref: NCIT:C13041 +xref: ncithesaurus:Whole_Organism +xref: SCTID:243928005 +xref: TADS:0000001 +xref: TAO:0001094 +xref: TGMA:0001832 +xref: VHOG:0000671 +xref: WBbt:0007833 +xref: Wikipedia:Multi-cellular_organism +xref: XAO:0003004 +xref: ZFA:0001094 +is_a: UBERON:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: UBPROP:0000007 "organismal" xsd:string + +[Term] +id: UBERON:0000922 +name: embryo +namespace: uberon +def: "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, Wikipedia:Embryo] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "developing organism" RELATED [BILA:0000056] +synonym: "developmental tissue" RELATED [] +synonym: "embryonic organism" EXACT [BILA:0000056] +xref: AAO:0011035 +xref: AEO:0000169 +xref: BILA:0000056 +xref: BSA:0000039 +xref: BTO:0000379 +xref: CALOHA:TS-0229 +xref: EFO:0001367 +xref: EHDAA2:0000002 +xref: EHDAA2_RETIRED:0003236 +xref: EHDAA:38 +xref: EMAPA:16039 +xref: FBbt:00000052 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FMA:69068 +xref: GAID:963 +xref: http://neurolex.org/wiki/Category\:Embryonic_organism +xref: IDOMAL:0000646 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration", https://w3id.org/sssom/author_id="https://orcid.org/0000-0003-4423-4370", https://w3id.org/sssom/mapping_provider="https://github.com/biopragmatics/biomappings"} +xref: MAT:0000226 +xref: MESH:D004622 +xref: MIAA:0000019 +xref: NCIT:C28147 +xref: OGEM:000001 +xref: SCTID:57991002 +xref: UMLS:C0013935 {source="ncithesaurus:Embryo"} +xref: VHOG:0001766 +xref: Wikipedia:Embryo +xref: XAO:0000113 +xref: ZFA:0000103 +is_a: UBERON:0000468 ! multicellular organism +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI +property_value: UBPROP:0000007 "embryonic" xsd:string +property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} + [Term] id: UBERON:0001062 name: anatomical entity @@ -60961,11 +60490,12 @@ subset: common_anatomy subset: upper_level xref: AAO:0010841 xref: AEO:0000000 +xref: BFO:0000004 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 +xref: FBbt:10000000 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -60981,6 +60511,42 @@ property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0009953 +name: post-embryonic organism +namespace: uberon +def: "A multicellular organism that existence_starts_with a post-embryonic stage." [OBOL:automatic] +synonym: "post-hatching organism" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "post-natal organism" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "postnatal mouse" NARROW [MA:0002405] +synonym: "postnatal organism" EXACT [] +synonym: "TS28 mouse" NARROW [MA:0002405] +xref: MA:0002405 +is_a: UBERON:0000468 ! multicellular organism +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: RO:0002489 UBERON:0000092 ! existence starts with post-embryonic stage +relationship: RO:0002489 UBERON:0000092 ! existence starts with post-embryonic stage +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/667" xsd:anyURI + +[Term] +id: UBERON:0010000 +name: multicellular anatomical structure +namespace: uberon +def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] +subset: common_anatomy +subset: upper_level +synonym: "multicellular structure" EXACT [FBbt:00100313] +xref: CARO:0010000 +xref: FBbt:00100313 {https://w3id.org/sssom/mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular +relationship: has_part CL:0000000 ! cell +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 + [Typedef] id: BFO:0000054 name: realized in @@ -61010,6 +60576,14 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + [Typedef] id: IDO:0000660 name: results_in @@ -61063,7 +60637,7 @@ property_value: IAO:0000116 "A quality inheres in its bearer at all times for wh property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! inheres in -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 @@ -61088,6 +60662,16 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role @@ -61123,7 +60707,6 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z @@ -61132,7 +60715,6 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z @@ -61143,55 +60725,67 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: has_component ! has component -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z +[Typedef] +id: RO:0002081 +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after @@ -61201,6 +60795,38 @@ property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +range: OBI:0100026 +holds_over_chain: capable_of RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002222 name: temporally related to @@ -61214,6 +60840,31 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part_of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: part_of ! part_of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + [Typedef] id: RO:0002263 name: acts upstream of @@ -61231,7 +60882,6 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process @@ -61291,6 +60941,13 @@ inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string + [Typedef] id: RO:0002329 name: part of structure that is capable of @@ -61298,7 +60955,7 @@ def: "this relation holds between c and p when c is part of some c', and c' is c property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002331 @@ -61308,7 +60965,6 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI -property_value: seeAlso Involved:in holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -61321,8 +60977,8 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 @@ -61333,6 +60989,16 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping domain: BFO:0000015 ! process range: BFO:0000002 ! continuant +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to + [Typedef] id: RO:0002354 name: formed as result of @@ -61415,14 +61081,13 @@ def: "c involved in or regulates p if and only if either (i) c is involved in p property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string @@ -61430,8 +61095,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI holds_over_chain: RO:0002327 occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002434 @@ -61535,6 +61200,72 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002488 ! existence starts during + +[Typedef] +id: RO:0002490 +name: existence overlaps +def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002487 ! relation between physical entity and a process or stage + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: part_of RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part_of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: part_of RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part_of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process @@ -61623,8 +61354,8 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string -domain: BFO:0000020 ! specifically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic +range: BFO:0000020 ! characteristic [Typedef] id: RO:0002584 @@ -61633,7 +61364,7 @@ def: "s 'has part structure that is capable of' p if and only if there exists so property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -61684,7 +61415,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -61693,7 +61424,6 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -61717,7 +61447,6 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -61731,7 +61460,6 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_negative_effect is_a: RO:0002263 ! acts upstream of @@ -61772,7 +61500,6 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: causally_upstream_of ! causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 -created_by: pg creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -61782,7 +61509,6 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p is_a: regulates ! regulates is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 -created_by: pg creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -61848,14 +61574,14 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string +range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 @@ -61874,14 +61600,13 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -61964,44 +61689,6 @@ is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - [Typedef] id: decreased_in_magnitude_relative_to name: obsolete decreased_in_magnitude_relative_to @@ -62062,20 +61749,6 @@ property_value: RO:0002575 RO:0002211 is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: regulates ! regulates -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with - [Typedef] id: ends_during name: ends during @@ -62086,7 +61759,6 @@ xref: RO:0002093 id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 @@ -62098,28 +61770,6 @@ is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes - -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - [Typedef] id: happens_during name: happens during @@ -62132,7 +61782,6 @@ is_a: ends_during ! ends during id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 @@ -62175,7 +61824,7 @@ property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_negative_regulatory_component_activity @@ -62186,7 +61835,6 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z @@ -62203,6 +61851,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -62214,7 +61863,6 @@ name: has_part namespace: external namespace: quality namespace: sequence -namespace: uberon def: "a core relation that holds between a whole and its part" [] def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1] comment: Example: operon has_part gene. @@ -62241,7 +61889,6 @@ name: has participant namespace: external def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string @@ -62250,6 +61897,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: has_part has_participant @@ -62257,7 +61905,7 @@ holds_over_chain: has_part has_participant id: has_primary_input name: has primary input namespace: external -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -62280,7 +61928,7 @@ creation_date: 2018-12-13T11:26:17Z id: has_primary_output name: has primary output namespace: external -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -62288,18 +61936,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -range: BFO:0000019 ! quality -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -62308,7 +61944,6 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: regulated_by ! regulated by is_a: RO:0002017 ! has component activity -created_by: dos created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z @@ -62387,7 +62022,6 @@ is_a: immediately_precedes ! immediately precedes id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string @@ -62411,29 +62045,6 @@ property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: capable_of in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: increased_in_magnitude_relative_to name: obsolete increased_in_magnitude_relative_to @@ -62446,18 +62057,6 @@ is_transitive: true is_obsolete: true replaced_by: RO:0015007 -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - [Typedef] id: negatively_regulated_by name: negatively regulated by @@ -62514,44 +62113,28 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process +inverse_of: BFO:0000067 ! contains process transitive_over: part_of ! part_of -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon - [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -62573,7 +62156,6 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term @@ -62609,7 +62191,6 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 property_value: IAO:0000111 "participates in" xsd:string @@ -62665,11 +62246,9 @@ is_a: regulates_characteristic ! regulates characteristic id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string @@ -62686,7 +62265,6 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 @@ -62710,7 +62288,6 @@ is_a: RO:0002410 ! causally related to id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 @@ -62723,7 +62300,6 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco @@ -62786,6 +62362,22 @@ range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic is_a: RO:0002410 ! causally related to +[Typedef] +id: results_in_acquisition_of_features_of +name: results in acquisition of features of +namespace: external +def: "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002315 +property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string +range: UBERON:0000061 ! anatomical structure +is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure +is_a: results_in_developmental_progression_of ! results in developmental progression of + [Typedef] id: results_in_assembly_of name: results in assembly of @@ -62794,7 +62386,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -62807,6 +62399,22 @@ is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z +[Typedef] +id: results_in_development_of +name: results in development of +namespace: external +def: "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002296 +property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI +is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure +is_a: results_in_developmental_progression_of ! results in developmental progression of + [Typedef] id: results_in_developmental_progression_of name: results in developmental progression of @@ -62817,7 +62425,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions -domain: GO:0008150 ! biological_process +domain: GO:0008150 ! biological process +range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -62839,6 +62448,7 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -62855,18 +62465,6 @@ is_a: IDO:0000660 ! results_in is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of -[Typedef] -id: results_in_fusion_of -name: results in fusion of -namespace: external -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0012008 -is_a: results_in_organization_of ! results in organization of -created_by: pg -creation_date: 2021-02-26T07:28:29Z - [Typedef] id: results_in_organization_of name: results in organization of @@ -62885,26 +62483,10 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 diff --git a/phipo.owl b/phipo.owl index 499582e..3241c77 100644 --- a/phipo.owl +++ b/phipo.owl @@ -1,6 +1,7 @@ - + alaynecuzick 2018-07-09T13:43:00Z Ontology of species-neutral phenotypes observed in pathogen-host interactions. Pathogen Host Interactions Phenotype Ontology https://creativecommons.org/licenses/by/3.0/ - 2024-01-31 + 2024-04-04 @@ -220,6 +221,22 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + @@ -300,6 +317,24 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + + + @@ -452,6 +487,14 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + @@ -572,22 +615,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - @@ -596,9 +623,9 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + @@ -618,6 +645,14 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + @@ -736,6 +771,22 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + @@ -744,6 +795,14 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + @@ -760,14 +819,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -779,14 +831,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -804,14 +849,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + @@ -841,14 +879,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - + @@ -890,13 +921,17 @@ We also have the outstanding issue of how to aim different definitions to differ - + + created by + - + + creation date + @@ -906,12 +941,24 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + @@ -1008,7 +1055,9 @@ We also have the outstanding issue of how to aim different definitions to differ - + + id + @@ -1020,9 +1069,9 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + @@ -1044,12 +1093,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -1068,12 +1111,36 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + + + + + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + @@ -1778,7 +1828,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -1866,7 +1915,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0002131 external - uberon overlaps @@ -1900,10 +1948,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -1914,6 +1958,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -1922,10 +1967,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - @@ -1934,25 +1975,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -1971,7 +2000,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0002180 external - uberon has_component has_component @@ -2101,7 +2129,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -2125,7 +2152,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of @@ -2172,12 +2198,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -2197,7 +2218,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. started by RO:0002224 external - uberon starts_with starts_with @@ -2217,12 +2237,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of ends with Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -2241,7 +2256,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. finished by RO:0002230 external - uberon ends_with ends_with @@ -2353,6 +2367,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_output has output has output + https://wiki.geneontology.org/Has_output @@ -2387,7 +2402,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. affects acts upstream of or within - https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2398,6 +2412,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -2413,6 +2428,29 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + every flower development (GO:0009908) results in development of some flower (PO:0009046) + + p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + + http://www.geneontology.org/GO.doc.development.shtml + RO:0002296 + external + results_in_development_of + + + + results_in_development_of + results in development of + results in development of + + + + @@ -2435,6 +2473,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. results_in_formation_of results in formation of results in formation of + results in formation of anatomical entity @@ -2513,6 +2552,29 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + + GOC:mtg_berkeley_2013 + RO:0002315 + external + results_in_acquisition_of_features_of + + + + results_in_acquisition_of_features_of + results in acquisition of features of + results in acquisition of features of + + + + @@ -2582,11 +2644,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -2635,7 +2692,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. actively involved in enables part of involved in - https://wiki.geneontology.org/Involved_in @@ -2649,6 +2705,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -2792,13 +2849,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of has input - RO:0002352 - uberon - input_of - input_of - input of input of @@ -2813,7 +2865,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0002353 external - uberon output_of @@ -3148,13 +3199,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - @@ -3331,6 +3375,102 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + + existence starts during + + + + + + + + + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + + existence starts with + + + + + + + + + x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence overlaps + + + + + + + + + + + + + + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during + + + + + + + + + x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends with + + + + + + + + + + + + + + + + + + + + + + + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts during or after + + + + @@ -3347,12 +3487,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -3733,7 +3873,6 @@ For example, A and B may be gene products and binding of B by A positively regul RO:0003000 external - uberon produces produces @@ -3754,7 +3893,6 @@ For example, A and B may be gene products and binding of B by A positively regul RO:0003001 external - uberon produced_by produced_by @@ -3800,7 +3938,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -3828,7 +3966,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -3866,7 +4004,6 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -3905,7 +4042,6 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -3926,7 +4062,6 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -3971,32 +4106,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - pg - 2021-02-26T07:28:29Z - RO:0012008 - external - results_in_fusion_of - - - - results_in_fusion_of - results in fusion of - results in fusion of - - - - p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg 2022-09-26T06:07:17Z indirectly causally upstream of @@ -4010,7 +4125,6 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg 2022-09-26T06:08:01Z indirectly regulates @@ -4109,7 +4223,6 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z 2021-11-08T12:00:00Z utilizes device utilizes material @@ -4634,6 +4747,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + process Process a process of cell-division, \ a beating of the heart @@ -4736,6 +4855,7 @@ For example, A and B may be gene products and binding of B by A positively regul (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + realizable realizable entity @@ -4790,6 +4910,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + sdc SpecificallyDependentContinuant @@ -4812,7 +4938,10 @@ For example, A and B may be gene products and binding of B by A positively regul (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + characteristic specifically dependent continuant + https://github.com/OBOFoundry/COB/issues/65 + https://github.com/oborel/obo-relations/pull/284 @@ -4851,8 +4980,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role @@ -11666,6 +11794,36 @@ For example, A and B may be gene products and binding of B by A positively regul cytosine + + + + CAS:71-30-7 + ChemIDplus + + + + + CAS:71-30-7 + KEGG COMPOUND + + + + + CAS:71-30-7 + NIST Chemistry WebBook + + + + + Gmelin:82472 + Gmelin + + + + + PMID:14253484 + Europe PMC + @@ -11745,36 +11903,6 @@ For example, A and B may be gene products and binding of B by A positively regul Beilstein:2637 Beilstein - - - - CAS:71-30-7 - ChemIDplus - - - - - CAS:71-30-7 - KEGG COMPOUND - - - - - CAS:71-30-7 - NIST Chemistry WebBook - - - - - Gmelin:82472 - Gmelin - - - - - PMID:14253484 - Europe PMC - @@ -11863,6 +11991,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -26830,6 +26964,69 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Any compound that produces a peak used to reference an NMR spectrum during data pre-processing. + chebi_ontology + NMR chemical shift reference compounds + NMR chemical shift standard + NMR chemical shift standards + NMR internal standard + NMR internal standards + NMR reference standard + NMR reference standards + CHEBI:228364 + + NMR chemical shift reference compound + + + + + NMR chemical shift reference compounds + ChEBI + + + + + NMR chemical shift standard + ChEBI + + + + + NMR chemical shift standards + ChEBI + + + + + NMR internal standard + ChEBI + + + + + NMR internal standards + ChEBI + + + + + NMR reference standard + ChEBI + + + + + NMR reference standards + ChEBI + + + + @@ -29071,7 +29268,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A role played by the molecular entity or part thereof within a biological context. chebi_ontology @@ -32860,6 +33056,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -52822,7 +53024,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Intended use of the molecular entity or part thereof by humans. chebi_ontology @@ -57210,8 +57411,15 @@ For example, A and B may be gene products and binding of B by A positively regul + An amino-acid residue derived from an alpha-amino acid. + 0 + C2H2NOR + 56.043 + 56.01364 + *-NC([*])C(-*)=O chebi_ontology alpha-amino-acid residues + an alpha-amino acid residue CHEBI:33710 alpha-amino-acid residue @@ -57222,6 +57430,12 @@ For example, A and B may be gene products and binding of B by A positively regul alpha-amino-acid residues ChEBI + + + + an alpha-amino acid residue + UniProt + @@ -90142,7 +90356,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A role is particular behaviour which a material entity may exhibit. chebi_ontology CHEBI:50906 @@ -90647,7 +90861,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A role played by the molecular entity or part thereof within a chemical context. chebi_ontology @@ -95418,13 +95631,6 @@ For example, A and B may be gene products and binding of B by A positively regul hygromycin B(3+) - - - - (1R,2S,3R,5S,6R)-3-azaniumyl-2,6-dihydroxy-5-(methylazaniumyl)cyclohexyl O-6-azaniumyl-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1->2-3)-beta-D-talopyranoside - IUPAC - - @@ -95437,6 +95643,13 @@ For example, A and B may be gene products and binding of B by A positively regul hygromycin B trication ChEBI + + + + (1R,2S,3R,5S,6R)-3-azaniumyl-2,6-dihydroxy-5-(methylazaniumyl)cyclohexyl O-6-azaniumyl-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1->2-3)-beta-D-talopyranoside + IUPAC + + @@ -95532,24 +95745,6 @@ For example, A and B may be gene products and binding of B by A positively regul 3',5'-cyclic AMP(1-) - - - - adenosine 3',5'-cyclic monophosphate - ChEBI - - - - - adenosine 3',5'-cyclic monophosphate anion - ChEBI - - - - - adenosine 3',5'-cyclic monophosphate(1-) - ChEBI - @@ -95587,6 +95782,24 @@ For example, A and B may be gene products and binding of B by A positively regul 3',5'-cyclic AMP anion ChEBI + + + + adenosine 3',5'-cyclic monophosphate + ChEBI + + + + + adenosine 3',5'-cyclic monophosphate anion + ChEBI + + + + + adenosine 3',5'-cyclic monophosphate(1-) + ChEBI + @@ -129893,6 +130106,7 @@ For example, A and B may be gene products and binding of B by A positively regul A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity that has a plasma membrane and results from cellular division. CALOHA:TS-2035 FBbt:00007002 @@ -129903,8 +130117,11 @@ For example, A and B may be gene products and binding of B by A positively regul VHOG:0001533 WBbt:0004017 XAO:0003012 + + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell cell @@ -129917,6 +130134,257 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + A cell that specializes in controlled release of one or more substances. + BTO:0003659 + FMA:86916 + + secretory cell + + + + + A cell that specializes in controlled release of one or more substances. + GOC:tfm + ISBN:0721662544 + + + + + + + + + + + + + + + + + + + + + + + + + + protein secreting cell + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell that lacks a nucleus. + FMA:68647 + non-nucleated cell + anucleate cell + + + + + A cell that lacks a nucleus. + FB:ma + + + + + + + + + + + + + + + + + + + + + + + + + + A cell with a single nucleus. + single nucleate cell + + + + + A cell with a single nucleus. + FB:ma + GOC:tfm + + + + + + + + + + + + + + + + + + + + + + + + + + binucleate cell + + + + + + + + + + + + + + + + + + + + + + + + + + A cell with more than one nucleus. + AEO:0000203 + WBbt:0008074 + syncitium + syncytial cell + syncytium + multinucleate cell + + + + + A cell with more than one nucleus. + FB:ma + + + + + + + + + + + + + + + + + + + + + + + + + + MESH:D005057 + + eukaryotic cell + + + + + + + + + + + + + + + + + + + + + + + + + + fungal cell + + + + @@ -129954,6 +130422,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2017-01-30T18:53:32Z https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 + https://github.com/obophenotype/cell-ontology/issues/448 abnormal cell @@ -129968,41 +130437,77 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - + - + - + - A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. + A cell containing at least one nucleus. - 2009-12-23T10:53:24Z - increased nucleus size + 2010-09-07T03:32:33Z + FMA:67513 + nucleate cell - + - A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. + A cell containing at least one nucleus. GOC:tfm + + + + + + + + + + + + + + + + + + + + + + A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. + precursor cell + + + + + A cell that, by division or terminal differentiation, can give rise to other cell types. + GOC:dos + + + + @@ -130155,126 +130660,75 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The joining of 2 or more lipid bilayer membranes that surround the nucleus. - biological_process - GO:0000740 - nuclear membrane fusion - - - - - The joining of 2 or more lipid bilayer membranes that surround the nucleus. - GOC:elh - - - - - + - + - + - - + + - - + - + - - + + - The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. - GO:0007335 - Wikipedia:Karyogamy - nuclear fusion - nuclear fusion during karyogamy + Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + translation initiation ternary complex assembly biological_process - GO:0000741 - karyogamy + GO:0001677 + formation of translation initiation ternary complex - + - The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. - GOC:elh + Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + GOC:hjd - + - - - - - - - - - - - - - + + - - + + - - + + - Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - translation initiation ternary complex assembly + The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster. biological_process - GO:0001677 - formation of translation initiation ternary complex + GO:0001700 + embryonic development via the syncytial blastoderm - + - Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - GOC:hjd + The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster. + GOC:go_curators + GOC:mtg_sensu @@ -130579,6 +131033,8 @@ For example, A and B may be gene products and binding of B by A positively regul Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -130903,7 +131359,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. transporter activity @@ -130929,131 +131384,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Enables the directed movement of lipids into, out of or within a cell, or between cells. - Reactome:R-HSA-1369028 - Reactome:R-HSA-1369052 - Reactome:R-HSA-174786 - Reactome:R-HSA-5682285 - Reactome:R-HSA-5682311 - Reactome:R-HSA-5683672 - Reactome:R-HSA-5683714 - Reactome:R-HSA-5688397 - Reactome:R-HSA-6801250 - Reactome:R-HSA-8848053 - Reactome:R-HSA-8866329 - lipophorin - molecular_function - apolipoprotein - GO:0005319 - lipid transporter activity - - - - - - - - - - GO_REF:0000090 - - - - - Enables the directed movement of lipids into, out of or within a cell, or between cells. - GOC:ai - - - - - Reactome:R-HSA-1369028 - ABCAs mediate lipid efflux - - - - - Reactome:R-HSA-1369052 - ABCAs mediate lipid influx - - - - - Reactome:R-HSA-174786 - ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex - - - - - Reactome:R-HSA-5682285 - ABCA12 transports lipids from cytosol to extracellular region - - - - - Reactome:R-HSA-5682311 - Defective ABCA12 does not transport lipids from cytosol to extracellular region - - - - - Reactome:R-HSA-5683672 - Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body - - - - - Reactome:R-HSA-5683714 - ABCA3 transports PC, PG from ER membrane to lamellar body - - - - - Reactome:R-HSA-5688397 - Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body - - - - - Reactome:R-HSA-6801250 - TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane - - - - - Reactome:R-HSA-8848053 - ABCA5 transports CHOL from lysosomal lumen to cytosol - - - - - Reactome:R-HSA-8866329 - MTTP lipidates APOB-100, forming a pre-VLDL - - - - @@ -131112,7 +131442,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 GO:0008372 @@ -131129,16 +131458,8 @@ For example, A and B may be gene products and binding of B by A positively regul Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. - Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component - - - - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - GOC:pdt - NIF_Subcellular:sao1337158144 - @@ -131172,8 +131493,8 @@ For example, A and B may be gene products and binding of B by A positively regul + - Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. extracellular region @@ -131274,6 +131595,7 @@ For example, A and B may be gene products and binding of B by A positively regul + cell nucleus nucleus @@ -131351,7 +131673,6 @@ For example, A and B may be gene products and binding of B by A positively regul - cytoplasm @@ -131497,7 +131818,6 @@ For example, A and B may be gene products and binding of B by A positively regul - plasma membrane @@ -131705,47 +132025,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. - RNA breakdown - RNA catabolism - RNA degradation - biological_process - GO:0006401 - - RNA catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. - ISBN:0198506732 - - - - @@ -131843,7 +132122,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + translation @@ -131965,9 +132244,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -132177,18 +132454,17 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + - + The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. @@ -132207,7 +132483,6 @@ For example, A and B may be gene products and binding of B by A positively regul - amino acid metabolic process @@ -132280,25 +132555,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. Wikipedia:Lipid_metabolism lipid metabolism @@ -132316,7 +132574,6 @@ For example, A and B may be gene products and binding of B by A positively regul - lipid metabolic process @@ -132566,7 +132823,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport @@ -132722,50 +132978,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. - biological_process - GO:0006869 - - - - lipid transport - - - - - The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. - ISBN:0198506732 - - - - @@ -132799,7 +133011,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0006886 - intracellular protein transport @@ -132817,56 +133028,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. - GO:0016194 - GO:0016195 - Wikipedia:Exocytosis - vesicle exocytosis - biological_process - nonselective vesicle exocytosis - GO:0006887 - - exocytosis - - - - - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. - GOC:mah - ISBN:0716731363 - PMID:22323285 - - - - @@ -132884,12 +133045,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/go-ontology/issues/24907 https://github.com/geneontology/go-ontology/issues/25268 @@ -132961,48 +133116,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Fusion of the membrane of a transport vesicle with its target membrane. - biological_process - GO:0006906 - vesicle fusion - - - - - Fusion of the membrane of a transport vesicle with its target membrane. - GOC:jid - - - - @@ -133484,46 +133597,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases. - biological_process - vacuolar protein breakdown - vacuolar protein catabolic process - vacuolar protein catabolism - vacuolar protein degradation - GO:0007039 - protein catabolic process in the vacuole - - - - - The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases. - GOC:mah - GOC:vw - - - - @@ -133674,6 +133747,50 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + https://github.com/geneontology/go-ontology/issues/21234 + biological_process + GO:0007275 + + + + Note that this term was 'developmental process'. + multicellular organism development + + + + + The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:dph + GOC:ems + GOC:isa_complete + GOC:tb + + + + @@ -133770,7 +133887,14 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. https://github.com/geneontology/go-ontology/issues/24968 @@ -133793,8 +133917,10 @@ For example, A and B may be gene products and binding of B by A positively regul + A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological process biological_process @@ -134181,25 +134307,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. lipid anabolism lipid biosynthesis @@ -134264,7 +134373,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -134325,59 +134433,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - GO:0043285 - GO:0044266 - biopolymer catabolic process - macromolecule breakdown - macromolecule catabolism - macromolecule degradation - multicellular organismal macromolecule catabolic process - biological_process - cellular macromolecule catabolic process - cellular macromolecule catabolism - cellular macromolecule degradation - GO:0009057 - - macromolecule catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - GOC:mah - - - - - biopolymer catabolic process - GOC:mtg_chebi_dec09 - - - - @@ -134426,6 +134481,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -134434,7 +134490,8 @@ For example, A and B may be gene products and binding of B by A positively regul The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - http://amigo.geneontology.org/amigo/term/GO:0070589 + https://github.com/geneontology/go-ontology/issues/15249 + https://github.com/geneontology/go-ontology/issues/25418 GO:0043284 biopolymer biosynthetic process macromolecule anabolism @@ -134461,48 +134518,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. - https://github.com/geneontology/go-ontology/issues/17904 - amino acid breakdown - amino acid catabolism - amino acid degradation - cellular amino acid catabolic process - biological_process - GO:0009063 - amino acid catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. - GOC:ai - - - - @@ -134729,46 +134744,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. - amine breakdown - amine catabolism - amine degradation - biological_process - GO:0009310 - amine catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. - GOC:jl - ISBN:0198506732 - - - - @@ -134914,6 +134889,109 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + GO:0009795 + embryogenesis and morphogenesis + Wikipedia:Embryogenesis + embryogenesis + embryonal development + biological_process + GO:0009790 + + + + embryo development + + + + + The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + GOC:go_curators + GOC:isa_complete + GOC:mtg_sensu + + + + + + + + + + + + + + + The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. + biological_process + GO:0009791 + + post-embryonic development + + + + + The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. + embryogenesis + biological_process + GO:0009792 + embryo development ending in birth or egg hatching + + + + + The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. + GOC:go_curators + GOC:isa_complete + GOC:mtg_sensu + + + + @@ -135155,131 +135233,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. - regulation of breakdown - regulation of catabolism - regulation of degradation - biological_process - GO:0009894 - regulation of catabolic process - - - - - Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. - down regulation of catabolic process - down-regulation of catabolic process - downregulation of catabolic process - negative regulation of breakdown - negative regulation of catabolism - negative regulation of degradation - inhibition of catabolic process - biological_process - GO:0009895 - negative regulation of catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. - positive regulation of breakdown - positive regulation of catabolism - positive regulation of degradation - up regulation of catabolic process - up-regulation of catabolic process - upregulation of catabolic process - activation of catabolic process - stimulation of catabolic process - biological_process - GO:0009896 - positive regulation of catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. - GOC:go_curators - - - - @@ -135383,9 +135336,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. + + The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. https://github.com/geneontology/go-ontology/issues/22557 + https://github.com/geneontology/go-ontology/issues/25419 Wikipedia:Gene_expression biological_process GO:0010467 @@ -135395,7 +135349,7 @@ For example, A and B may be gene products and binding of B by A positively regul - The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. + The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. GOC:txnOH-2018 PMID:25934543 PMID:31580950 @@ -135417,7 +135371,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135500,7 +135454,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135537,9 +135491,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135575,9 +135529,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135783,43 +135737,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells. - biological_process - GO:0010567 - regulation of ketone catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells. - GOC:dph - GOC:tb - - - - @@ -135929,7 +135846,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -135966,7 +135883,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -136092,46 +136009,78 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - + + - - + + - Any process in which a lipid is transported to, or maintained in, a specific location. - lipid localisation + Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process - GO:0010876 - lipid localization + GO:0010720 + positive regulation of cell development - + - Any process in which a lipid is transported to, or maintained in, a specific location. + Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. + biological_process + GO:0010721 + negative regulation of cell development + - - - lipid localisation - GOC:mah + + + Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. + GOC:BHF + GOC:dph + GOC:tb @@ -136327,43 +136276,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The lipid bilayer surrounding any membrane-bounded vesicle in the cell. - NIF_Subcellular:sao1153182838 - cellular_component - GO:0012506 - vesicle membrane - - - - - The lipid bilayer surrounding any membrane-bounded vesicle in the cell. - GOC:mah - GOC:vesicle - - - - @@ -136720,25 +136632,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GO:0006724 GO:0044240 @@ -136832,24 +136727,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. vesicle organisation biological_process @@ -136916,47 +136794,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage. - organic acid breakdown - organic acid catabolism - organic acid degradation - biological_process - GO:0016054 - organic acid catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage. - ISBN:0198506732 - - - - @@ -136986,7 +136823,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + RNA metabolic process @@ -137048,25 +136885,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. https://github.com/geneontology/go-ontology/issues/25421 GO:0006899 @@ -137238,7 +137058,6 @@ For example, A and B may be gene products and binding of B by A positively regul - transferase activity @@ -137892,9 +137711,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -137929,42 +137746,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of exocytosis. - biological_process - GO:0017157 - regulation of exocytosis - - - - - Any process that modulates the frequency, rate or extent of exocytosis. - GOC:go_curators - - - - @@ -138049,42 +137830,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. - regulation of lipid metabolism - biological_process - GO:0019216 - regulation of lipid metabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. - GOC:go_curators - - - - @@ -138255,47 +138000,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. - aromatic compound breakdown - aromatic compound catabolism - aromatic compound degradation - aromatic hydrocarbon catabolic process - aromatic hydrocarbon catabolism - biological_process - GO:0019439 - aromatic compound catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. - GOC:ai - - - - @@ -138966,126 +138670,45 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - - + - - + + - Any process that modulates the frequency, rate or extent of endocytosis. + The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. + https://github.com/geneontology/go-ontology/issues/24390 + Wikipedia:Cellular_differentiation biological_process - GO:0030100 - regulation of endocytosis - - - - - Any process that modulates the frequency, rate or extent of endocytosis. - GOC:go_curators - - - - - - - - - - - - - - - Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. - NIF_Subcellular:sao885490876 - constitutive secretory pathway transport vesicle - Golgi to vacuole transport vesicle - Golgi-vacuole transport vesicle - cellular_component - secretory vesicle - GO:0030133 - Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'. - transport vesicle - - - - - Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. - GOC:mah - PMID:22160157 - - - - - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - https://github.com/geneontology/go-ontology/issues/23112 - GO:0044254 - GO:0044257 - Wikipedia:Protein_catabolism - cellular protein breakdown - cellular protein catabolic process - cellular protein catabolism - cellular protein degradation - protein breakdown - protein catabolism - protein degradation - multicellular organismal protein catabolic process - biological_process - pheromone catabolic process - pheromone catabolism - GO:0030163 - + GO:0030154 + + - - - This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children. - protein catabolic process + + + cell differentiation - + - The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - GOC:mah + The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. + ISBN:0198506732 @@ -139306,41 +138929,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The lipid bilayer surrounding a cytoplasmic vesicle. - cellular_component - GO:0030659 - cytoplasmic vesicle membrane - - - - - The lipid bilayer surrounding a cytoplasmic vesicle. - GOC:mah - - - - @@ -139641,134 +139229,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - regulation of cellular breakdown - regulation of cellular catabolism - regulation of cellular degradation - biological_process - GO:0031329 - regulation of cellular catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - down regulation of cellular catabolic process - down-regulation of cellular catabolic process - downregulation of cellular catabolic process - negative regulation of cellular breakdown - negative regulation of cellular catabolism - negative regulation of cellular degradation - inhibition of cellular catabolic process - biological_process - GO:0031330 - negative regulation of cellular catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - positive regulation of cellular breakdown - positive regulation of cellular catabolism - positive regulation of cellular degradation - up regulation of cellular catabolic process - up-regulation of cellular catabolic process - upregulation of cellular catabolic process - activation of cellular catabolic process - stimulation of cellular catabolic process - biological_process - GO:0031331 - positive regulation of cellular catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. - GOC:mah - - - - @@ -139853,173 +139313,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of vesicle fusion. - biological_process - GO:0031338 - regulation of vesicle fusion - - - - - Any process that modulates the frequency, rate or extent of vesicle fusion. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion. - down regulation of vesicle fusion - down-regulation of vesicle fusion - downregulation of vesicle fusion - inhibition of vesicle fusion - biological_process - GO:0031339 - negative regulation of vesicle fusion - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of vesicle fusion. - up regulation of vesicle fusion - up-regulation of vesicle fusion - upregulation of vesicle fusion - activation of vesicle fusion - stimulation of vesicle fusion - biological_process - GO:0031340 - positive regulation of vesicle fusion - - - - - Any process that activates or increases the frequency, rate or extent of vesicle fusion. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - A vesicle found in the cytoplasm of a cell. - GO:0016023 - NIF_Subcellular:sao180601769 - cellular_component - cytoplasmic membrane bounded vesicle - cytoplasmic membrane-enclosed vesicle - cytoplasmic, membrane-bounded vesicle - GO:0031410 - - - - - - - cytoplasmic vesicle - - - - - A vesicle found in the cytoplasm of a cell. - GOC:ai - GOC:mah - GOC:vesicles - - - - @@ -140170,32 +139463,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 - NIF_Subcellular:sao221389602 - Wikipedia:Vesicle_(biology) - cellular_component - membrane-bounded vesicle - membrane-enclosed vesicle - GO:0031982 - - vesicle - - - - - Any small, fluid-filled, spherical organelle enclosed by membrane. - GOC:mah - GOC:pz - GOC:vesicles - - - - @@ -140356,278 +139623,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - The directed movement of lipids within cells. - biological_process - GO:0032365 - intracellular lipid transport - - - - - The directed movement of lipids within cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - biological_process - GO:0032368 - regulation of lipid transport - - - - - Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - down regulation of lipid transport - down-regulation of lipid transport - downregulation of lipid transport - inhibition of lipid transport - biological_process - GO:0032369 - negative regulation of lipid transport - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - up regulation of lipid transport - up-regulation of lipid transport - upregulation of lipid transport - activation of lipid transport - stimulation of lipid transport - biological_process - GO:0032370 - positive regulation of lipid transport - - - - - Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells. - biological_process - GO:0032377 - regulation of intracellular lipid transport - - - - - Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells. - down regulation of intracellular lipid transport - down-regulation of intracellular lipid transport - downregulation of intracellular lipid transport - inhibition of intracellular lipid transport - biological_process - GO:0032378 - negative regulation of intracellular lipid transport - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells. - up regulation of intracellular lipid transport - up-regulation of intracellular lipid transport - upregulation of intracellular lipid transport - activation of intracellular lipid transport - stimulation of intracellular lipid transport - biological_process - GO:0032379 - positive regulation of intracellular lipid transport - - - - - Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells. - GOC:mah - - - - @@ -140747,123 +139742,139 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + + - - + - - + + - + - - - - - - - - Any process that modulates the activity of a transporter. - biological_process - GO:0032409 - - regulation of transporter activity - - - - - Any process that modulates the activity of a transporter. - GOC:mah - - - - - - - - + - - + - - + + - + - - - - + - - - - + + + + + + + + - Any process that stops or reduces the activity of a transporter. - down regulation of transporter activity - down-regulation of transporter activity - downregulation of transporter activity - inhibition of transporter activity - biological_process - GO:0032410 - - negative regulation of transporter activity - - - - - Any process that stops or reduces the activity of a transporter. - GOC:mah - - - - - - - - + - - + - - + + - + - - - - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Any process that activates or increases the activity of a transporter. - up regulation of transporter activity - up-regulation of transporter activity - upregulation of transporter activity - activation of transporter activity - stimulation of transporter activity + + + + + + + + + + + + + + + + + + + + + + + + + Any biological process, occurring at the level of a multicellular organism, pertinent to its function. + + + + + jl + 2012-09-19T16:07:47Z + GO:0044707 + GO:0050874 + organismal physiological process biological_process - GO:0032411 - - positive regulation of transporter activity + single-multicellular organism process + GO:0032501 + + + multicellular organismal process - + - Any process that activates or increases the activity of a transporter. - GOC:mah + Any biological process, occurring at the level of a multicellular organism, pertinent to its function. + GOC:curators + GOC:dph + GOC:isa_complete + GOC:tb @@ -140940,7 +139951,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -140992,41 +140003,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion. - biological_process - GO:0032871 - regulation of karyogamy - - - - - Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion. - GOC:mah - - - - @@ -141681,127 +140657,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - regulation of amine breakdown - regulation of amine catabolism - regulation of amine degradation - regulation of cellular amine catabolic process - biological_process - GO:0033241 - regulation of amine catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - negative regulation of amine breakdown - negative regulation of amine catabolism - negative regulation of amine degradation - negative regulation of cellular amine catabolic process - biological_process - GO:0033242 - negative regulation of amine catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - positive regulation of amine breakdown - positive regulation of amine catabolism - positive regulation of amine degradation - biological_process - GO:0033243 - positive regulation of amine catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. - GOC:mah - - - - @@ -141903,7 +140758,7 @@ For example, A and B may be gene products and binding of B by A positively regul kinase inhibitor biological_process GO:0033673 - + negative regulation of kinase activity @@ -141946,7 +140801,7 @@ For example, A and B may be gene products and binding of B by A positively regul stimulation of kinase activity biological_process GO:0033674 - + positive regulation of kinase activity @@ -142094,128 +140949,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - regulation of amide breakdown - regulation of amide catabolism - regulation of amide degradation - regulation of cellular amide catabolic process - biological_process - GO:0034251 - regulation of amide catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - negative regulation of amide breakdown - negative regulation of amide catabolism - negative regulation of cellular amide catabolic process - biological_process - negative regulation of amide degradation - GO:0034252 - negative regulation of amide catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - positive regulation of amide breakdown - positive regulation of amide catabolism - positive regulation of cellular amide catabolic process - biological_process - positive regulation of amide degradation - GO:0034253 - positive regulation of amide catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. - GOC:mah - - - - @@ -142429,9 +141162,11 @@ For example, A and B may be gene products and binding of B by A positively regul The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. + https://github.com/geneontology/go-ontology/issues/26424 cellular nitrogen compound metabolism biological_process GO:0034641 + cellular nitrogen compound metabolic process @@ -142487,53 +141222,45 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - - - - - + - - + + + + + + + + - The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. - nucleobase, nucleoside, nucleotide and nucleic acid breakdown - nucleobase, nucleoside, nucleotide and nucleic acid catabolism - nucleobase, nucleoside, nucleotide and nucleic acid degradation + The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex. biological_process - nucleobase, nucleoside, nucleotide and nucleic acid catabolic process - GO:0034655 - - nucleobase-containing compound catabolic process + GO:0035190 + syncytial nuclear migration - + - The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. - GOC:mah - - - - - nucleobase, nucleoside, nucleotide and nucleic acid catabolic process - GOC:dph - GOC:tb + The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex. + GOC:bf + ISBN:0879694238 + PMID:8314839 @@ -142676,6 +141403,48 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of embryonic development. + up regulation of embryonic development + up-regulation of embryonic development + upregulation of embryonic development + activation of embryonic development + stimulation of embryonic development + biological_process + GO:0040019 + positive regulation of embryonic development + + + + + Any process that activates or increases the frequency, rate or extent of embryonic development. + GOC:go_curators + + + + @@ -142784,287 +141553,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - https://github.com/geneontology/go-ontology/issues/23112 - kmv - 2014-08-21T15:05:45Z - GO:1903362 - GO:2000598 - regulation of cellular protein breakdown - regulation of cellular protein catabolic process - regulation of cellular protein catabolism - regulation of cellular protein degradation - regulation of protein breakdown - regulation of protein catabolism - regulation of protein degradation - regulation of cyclin breakdown - regulation of cyclin catabolic process - regulation of cyclin catabolism - regulation of cyclin degradation - regulation of degradation of cyclin - biological_process - GO:0042176 - regulation of protein catabolic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - GOC:go_curators - GOC:jl - - - - - regulation of cellular protein breakdown - GOC:TermGenie - - - - - regulation of cellular protein catabolism - GOC:TermGenie - - - - - regulation of cellular protein degradation - GOC:TermGenie - - - - - regulation of cyclin breakdown - GOC:obol - - - - - regulation of cyclin catabolism - GOC:obol - - - - - regulation of cyclin degradation - GOC:obol - - - - - regulation of degradation of cyclin - GOC:obol - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process. - https://github.com/geneontology/go-ontology/issues/23112 - GO:1903363 - GO:2000599 - down regulation of cellular protein breakdown - down regulation of cellular protein catabolic process - down regulation of cellular protein catabolism - down regulation of cellular protein degradation - down regulation of protein catabolic process - down-regulation of cellular protein breakdown - down-regulation of cellular protein catabolic process - down-regulation of cellular protein catabolism - down-regulation of cellular protein degradation - down-regulation of protein catabolic process - downregulation of cellular protein breakdown - downregulation of cellular protein catabolic process - downregulation of cellular protein catabolism - downregulation of cellular protein degradation - downregulation of protein catabolic process - negative regulation of cellular protein breakdown - negative regulation of cellular protein catabolic process - negative regulation of cellular protein catabolism - negative regulation of cellular protein degradation - negative regulation of protein breakdown - negative regulation of protein catabolism - negative regulation of protein degradation - inhibition of cellular protein breakdown - inhibition of cellular protein catabolic process - inhibition of cellular protein catabolism - inhibition of cellular protein degradation - inhibition of protein catabolic process - biological_process - GO:0042177 - negative regulation of protein catabolic process - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process. - GOC:TermGenie - GOC:kmv - GOC:obol - GO_REF:0000058 - PMID:24785082 - - - - - down regulation of cellular protein breakdown - GOC:TermGenie - - - - - down regulation of cellular protein catabolic process - GOC:TermGenie - - - - - down regulation of cellular protein catabolism - GOC:TermGenie - - - - - down regulation of cellular protein degradation - GOC:TermGenie - - - - - down-regulation of cellular protein breakdown - GOC:TermGenie - - - - - down-regulation of cellular protein catabolic process - GOC:TermGenie - - - - - down-regulation of cellular protein catabolism - GOC:TermGenie - - - - - down-regulation of cellular protein degradation - GOC:TermGenie - - - - - downregulation of cellular protein breakdown - GOC:TermGenie - - - - - downregulation of cellular protein catabolic process - GOC:TermGenie - - - - - downregulation of cellular protein catabolism - GOC:TermGenie - - - - - downregulation of cellular protein degradation - GOC:TermGenie - - - - - negative regulation of cellular protein breakdown - GOC:TermGenie - - - - - negative regulation of cellular protein catabolism - GOC:TermGenie - - - - - negative regulation of cellular protein degradation - GOC:TermGenie - - - - - inhibition of cellular protein breakdown - GOC:TermGenie - - - - - inhibition of cellular protein catabolic process - GOC:TermGenie - - - - - inhibition of cellular protein catabolism - GOC:TermGenie - - - - - inhibition of cellular protein degradation - GOC:TermGenie - - - - @@ -143147,47 +141635,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. - ketone breakdown - ketone catabolism - ketone degradation - biological_process - GO:0042182 - ketone catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. - GOC:go_curators - - - - @@ -143410,7 +141857,7 @@ For example, A and B may be gene products and binding of B by A positively regul biological_process GO:0043062 - + extracellular structure organization @@ -143471,8 +141918,8 @@ For example, A and B may be gene products and binding of B by A positively regul upregulation of metalloenzyme activity biological_process GO:0043085 + - positive regulation of catalytic activity @@ -143529,7 +141976,7 @@ For example, A and B may be gene products and binding of B by A positively regul negative regulation of metalloenzyme activity biological_process GO:0043086 - + negative regulation of catalytic activity @@ -143655,46 +142102,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. - peptide breakdown - peptide catabolism - peptide degradation - biological_process - GO:0043171 - peptide catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. - GOC:jl - - - - @@ -143727,7 +142134,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organelle @@ -144281,7 +142687,7 @@ For example, A and B may be gene products and binding of B by A positively regul Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. biological_process GO:0043549 - + regulation of kinase activity @@ -144367,43 +142773,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. - cellular amide catabolic process - biological_process - GO:0043605 - amide catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. - GOC:curators - - - - @@ -144765,7 +143134,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -144774,7 +143143,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -144818,7 +143187,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2009-04-21T04:07:27Z biological_process GO:0044092 - + negative regulation of molecular function @@ -144856,7 +143225,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2009-04-21T04:11:06Z biological_process GO:0044093 - + positive regulation of molecular function @@ -145088,29 +143457,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. - nitrogen compound breakdown - nitrogen compound catabolism - nitrogen compound degradation - biological_process - GO:0044270 - cellular nitrogen compound catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. - GOC:jl - ISBN:0198506732 - - - - @@ -145162,30 +143508,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. - jl - 2010-01-26T12:06:10Z - small molecule catabolism - biological_process - GO:0044282 - Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. - small molecule catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. - GOC:curators - GOC:vw - - - - @@ -145198,7 +143520,6 @@ For example, A and B may be gene products and binding of B by A positively regul biological_process GO:0044283 - Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule biosynthetic process @@ -145472,46 +143793,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. - GO:0006947 - cell fusion - cell-cell fusion - biological_process - GO:0045026 - plasma membrane fusion - - - - - The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. - GOC:elh - GOC:mtg_muscle - - - - @@ -145616,6 +143897,125 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. + biological_process + GO:0045595 + regulation of cell differentiation + + + + + Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. + down regulation of cell differentiation + down-regulation of cell differentiation + downregulation of cell differentiation + inhibition of cell differentiation + biological_process + GO:0045596 + negative regulation of cell differentiation + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of cell differentiation. + up regulation of cell differentiation + up-regulation of cell differentiation + upregulation of cell differentiation + activation of cell differentiation + stimulation of cell differentiation + biological_process + GO:0045597 + positive regulation of cell differentiation + + + + + Any process that activates or increases the frequency, rate or extent of cell differentiation. + GOC:go_curators + + + + @@ -145631,9 +144031,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -145696,217 +144094,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - https://github.com/geneontology/go-ontology/issues/23112 - GO:1903364 - GO:2000600 - positive regulation of cellular protein breakdown - positive regulation of cellular protein catabolic process - positive regulation of cellular protein catabolism - positive regulation of cellular protein degradation - positive regulation of protein breakdown - positive regulation of protein catabolism - positive regulation of protein degradation - up regulation of cellular protein breakdown - up regulation of cellular protein catabolic process - up regulation of cellular protein catabolism - up regulation of cellular protein degradation - up regulation of protein catabolic process - up-regulation of cellular protein breakdown - up-regulation of cellular protein catabolic process - up-regulation of cellular protein catabolism - up-regulation of cellular protein degradation - up-regulation of protein catabolic process - upregulation of cellular protein breakdown - upregulation of cellular protein catabolic process - upregulation of cellular protein catabolism - upregulation of cellular protein degradation - upregulation of protein catabolic process - activation of cellular protein breakdown - activation of cellular protein catabolic process - activation of cellular protein catabolism - activation of cellular protein degradation - activation of protein catabolic process - positive regulation of cyclin breakdown - positive regulation of cyclin catabolic process - positive regulation of cyclin catabolism - positive regulation of cyclin degradation - positive regulation of degradation of cyclin - stimulation of protein catabolic process - biological_process - GO:0045732 - positive regulation of protein catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. - GOC:go_curators - - - - - positive regulation of cellular protein breakdown - GOC:TermGenie - - - - - positive regulation of cellular protein catabolism - GOC:TermGenie - - - - - positive regulation of cellular protein degradation - GOC:TermGenie - - - - - up regulation of cellular protein breakdown - GOC:TermGenie - - - - - up regulation of cellular protein catabolic process - GOC:TermGenie - - - - - up regulation of cellular protein catabolism - GOC:TermGenie - - - - - up regulation of cellular protein degradation - GOC:TermGenie - - - - - up-regulation of cellular protein breakdown - GOC:TermGenie - - - - - up-regulation of cellular protein catabolic process - GOC:TermGenie - - - - - up-regulation of cellular protein catabolism - GOC:TermGenie - - - - - up-regulation of cellular protein degradation - GOC:TermGenie - - - - - upregulation of cellular protein breakdown - GOC:TermGenie - - - - - upregulation of cellular protein catabolic process - GOC:TermGenie - - - - - upregulation of cellular protein catabolism - GOC:TermGenie - - - - - upregulation of cellular protein degradation - GOC:TermGenie - - - - - activation of cellular protein breakdown - GOC:TermGenie - - - - - activation of cellular protein catabolic process - GOC:TermGenie - - - - - activation of cellular protein catabolism - GOC:TermGenie - - - - - activation of cellular protein degradation - GOC:TermGenie - - - - - positive regulation of cyclin breakdown - GOC:obol - - - - - positive regulation of cyclin catabolism - GOC:obol - - - - - positive regulation of cyclin degradation - GOC:obol - - - - - positive regulation of degradation of cyclin - GOC:obol - - - - @@ -145922,9 +144109,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -145965,9 +144150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - @@ -146089,172 +144272,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. - down regulation of endocytosis - down-regulation of endocytosis - downregulation of endocytosis - inhibition of endocytosis - biological_process - GO:0045806 - negative regulation of endocytosis - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of endocytosis. - up regulation of endocytosis - up-regulation of endocytosis - upregulation of endocytosis - activation of endocytosis - stimulation of endocytosis - biological_process - GO:0045807 - positive regulation of endocytosis - - - - - Any process that activates or increases the frequency, rate or extent of endocytosis. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. - down regulation of lipid metabolic process - down-regulation of lipid metabolic process - downregulation of lipid metabolic process - negative regulation of lipid metabolism - inhibition of lipid metabolic process - biological_process - GO:0045833 - negative regulation of lipid metabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. - positive regulation of lipid metabolism - up regulation of lipid metabolic process - up-regulation of lipid metabolic process - upregulation of lipid metabolic process - activation of lipid metabolic process - stimulation of lipid metabolic process - biological_process - GO:0045834 - positive regulation of lipid metabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. - GOC:go_curators - - - - @@ -146506,87 +144523,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. - down regulation of exocytosis - down-regulation of exocytosis - downregulation of exocytosis - inhibition of exocytosis - biological_process - GO:0045920 - negative regulation of exocytosis - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of exocytosis. - up regulation of exocytosis - up-regulation of exocytosis - upregulation of exocytosis - activation of exocytosis - stimulation of exocytosis - biological_process - GO:0045921 - positive regulation of exocytosis - - - - - Any process that activates or increases the frequency, rate or extent of exocytosis. - GOC:go_curators - - - - @@ -146852,84 +144788,119 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - - - - + + + - - + + - The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. - nucleobase anabolism - nucleobase biosynthesis - nucleobase formation - nucleobase synthesis + Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. + down regulation of embryonic development + down-regulation of embryonic development + downregulation of embryonic development + inhibition of embryonic development biological_process - GO:0046112 - nucleobase biosynthetic process + GO:0045992 + negative regulation of embryonic development - + - The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. - GOC:ai + Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. + GOC:go_curators - + - + - + - + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of embryonic development. + biological_process + GO:0045995 + regulation of embryonic development + + + + + Any process that modulates the frequency, rate or extent of embryonic development. + GOC:go_curators + + + + + + + + + + + + + - - - + + + - + - The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. - nucleobase breakdown - nucleobase catabolism - nucleobase degradation + The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. + nucleobase anabolism + nucleobase biosynthesis + nucleobase formation + nucleobase synthesis biological_process - GO:0046113 - nucleobase catabolic process + GO:0046112 + nucleobase biosynthetic process - + - The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. + The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. GOC:ai @@ -147023,45 +144994,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. - carboxylic acid breakdown - carboxylic acid catabolism - carboxylic acid degradation - biological_process - GO:0046395 - carboxylic acid catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. - ISBN:0198506732 - - - - @@ -147099,145 +145031,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). - heterocycle breakdown - heterocycle catabolism - heterocycle degradation - biological_process - GO:0046700 - heterocycle catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). - GOC:ai - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - positive regulation of lipid anabolism - positive regulation of lipid biosynthesis - positive regulation of lipid formation - positive regulation of lipid synthesis - positive regulation of lipogenesis - up regulation of lipid biosynthetic process - up-regulation of lipid biosynthetic process - upregulation of lipid biosynthetic process - activation of lipid biosynthetic process - stimulation of lipid biosynthetic process - biological_process - GO:0046889 - positive regulation of lipid biosynthetic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - GOC:ai - - - - - positive regulation of lipogenesis - GOC:sl - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - regulation of lipid anabolism - regulation of lipid biosynthesis - regulation of lipid formation - regulation of lipid synthesis - regulation of lipogenesis - biological_process - GO:0046890 - regulation of lipid biosynthetic process - - - - - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - GOC:ai - - - - - regulation of lipogenesis - GOC:sl - - - - @@ -147428,43 +145221,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The creation of a single organelle from two or more organelles. - biological_process - GO:0048284 - - - organelle fusion - - - - - The creation of a single organelle from two or more organelles. - GOC:jid - - - - @@ -147502,49 +145258,81 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + - + - - + + - + + - + - The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei. + + + + + + + The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. + https://github.com/geneontology/go-ontology/issues/24390 biological_process - nuclear membrane fusion during karyogamy - GO:0048288 - nuclear membrane fusion involved in karyogamy + terminal differentiation + GO:0048468 + + cell development - + - The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei. - GOC:jid + The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. + GOC:go_curators - + - nuclear membrane fusion during karyogamy + terminal differentiation GOC:dph GOC:tb + + + + + Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + https://github.com/geneontology/go-ontology/issues/25943 + Wikipedia:Organogenesis + development of an organ + organogenesis + biological_process + GO:0048513 + animal organ development + + + + + Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + GOC:dph + GOC:jid + + + + @@ -147717,6 +145505,124 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + biological_process + GO:0048580 + regulation of post-embryonic development + + + + + Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + down regulation of post-embryonic development + down-regulation of post-embryonic development + downregulation of post-embryonic development + inhibition of post-embryonic development + biological_process + GO:0048581 + negative regulation of post-embryonic development + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + up regulation of post-embryonic development + up-regulation of post-embryonic development + upregulation of post-embryonic development + activation of post-embryonic development + stimulation of post-embryonic development + biological_process + GO:0048582 + positive regulation of post-embryonic development + + + + + Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. + GOC:jid + + + + @@ -147791,7 +145697,24 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. https://github.com/geneontology/go-ontology/issues/26424 development of an anatomical structure @@ -148090,8 +146013,8 @@ For example, A and B may be gene products and binding of B by A positively regul regulation of metalloenzyme activity biological_process GO:0050790 + - regulation of catalytic activity @@ -148105,6 +146028,41 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + biological_process + GO:0050793 + regulation of developmental process + + + + + Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:go_curators + + + + @@ -148171,134 +146129,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - regulation of lipid breakdown - regulation of lipid catabolism - regulation of lipid degradation - biological_process - GO:0050994 - regulation of lipid catabolic process - - - - - Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - GOC:ai - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - down regulation of lipid catabolic process - down-regulation of lipid catabolic process - downregulation of lipid catabolic process - negative regulation of lipid breakdown - negative regulation of lipid catabolism - negative regulation of lipid degradation - inhibition of lipid catabolic process - biological_process - GO:0050995 - negative regulation of lipid catabolic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - GOC:ai - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - positive regulation of lipid breakdown - positive regulation of lipid catabolism - positive regulation of lipid degradation - up regulation of lipid catabolic process - up-regulation of lipid catabolic process - upregulation of lipid catabolic process - activation of lipid catabolic process - stimulation of lipid catabolic process - biological_process - GO:0050996 - positive regulation of lipid catabolic process - - - - - Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. - GOC:ai - - - - @@ -148532,58 +146362,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - down regulation of lipid biosynthetic process - down-regulation of lipid biosynthetic process - downregulation of lipid biosynthetic process - negative regulation of lipid anabolism - negative regulation of lipid biosynthesis - negative regulation of lipid formation - negative regulation of lipid synthesis - negative regulation of lipogenesis - inhibition of lipid biosynthetic process - biological_process - GO:0051055 - negative regulation of lipid biosynthetic process - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. - GOC:ai - - - - - negative regulation of lipogenesis - GOC:sl - - - - @@ -148658,6 +146436,87 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + down regulation of developmental process + down-regulation of developmental process + downregulation of developmental process + inhibition of developmental process + biological_process + GO:0051093 + negative regulation of developmental process + + + + + Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + up regulation of developmental process + up-regulation of developmental process + upregulation of developmental process + activation of developmental process + stimulation of developmental process + biological_process + GO:0051094 + positive regulation of developmental process + + + + + Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:ai + + + + @@ -149266,6 +147125,124 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. + biological_process + GO:0051239 + regulation of multicellular organismal process + + + + + Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. + GOC:ai + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. + up regulation of multicellular organismal process + up-regulation of multicellular organismal process + upregulation of multicellular organismal process + activation of multicellular organismal process + stimulation of multicellular organismal process + biological_process + GO:0051240 + positive regulation of multicellular organismal process + + + + + Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. + down regulation of multicellular organismal process + down-regulation of multicellular organismal process + downregulation of multicellular organismal process + inhibition of multicellular organismal process + biological_process + GO:0051241 + negative regulation of multicellular organismal process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. + GOC:ai + + + + @@ -149678,8 +147655,8 @@ For example, A and B may be gene products and binding of B by A positively regul transferase regulator biological_process GO:0051338 + - This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity @@ -149723,8 +147700,8 @@ For example, A and B may be gene products and binding of B by A positively regul stimulation of transferase activity biological_process GO:0051347 + - This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity @@ -149767,8 +147744,8 @@ For example, A and B may be gene products and binding of B by A positively regul inhibition of transferase activity biological_process GO:0051348 + - This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity @@ -149937,49 +147914,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole. - GO:0042146 - biological_process - heterotypic vacuole fusion (non-autophagic) - heterotypic vacuole fusion, non-autophagic - GO:0051469 - vesicle fusion with vacuole - - - - - The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole. - GOC:ai - - - - @@ -150125,50 +148059,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. - cytoplasmic vesicle localization - establishment and maintenance of vesicle localization - vesicle localisation - biological_process - GO:0051648 - vesicle localization - - - - - Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. - GOC:ai - - - - - vesicle localisation - GOC:mah - - - - @@ -150243,44 +148133,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - The directed movement of a vesicle to a specific location. - establishment of vesicle localisation - biological_process - GO:0051650 - establishment of vesicle localization - - - - - The directed movement of a vesicle to a specific location. - GOC:ai - - - - - establishment of vesicle localisation - GOC:mah - - - - @@ -150937,8 +148789,8 @@ For example, A and B may be gene products and binding of B by A positively regul + - nucleobase-containing small molecule metabolic process @@ -150986,6 +148838,42 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. + biological_process + GO:0060284 + regulation of cell development + + + + + Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. + GOC:dph + GOC:tb + + + + @@ -151074,45 +148962,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. - dph - 2009-05-18T02:29:43Z - biological_process - GO:0060627 - regulation of vesicle-mediated transport - - - - - Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. - GOC:dph - GOC:tb - - - - @@ -151152,7 +149001,6 @@ For example, A and B may be gene products and binding of B by A positively regul - membrane organization @@ -151177,50 +149025,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The membrane organization process that joins two lipid bilayers to form a single membrane. - jl - 2010-02-08T02:48:06Z - GO:0006944 - GO:0044801 - Wikipedia:Lipid_bilayer_fusion - cellular membrane fusion - biological_process - single-organism membrane fusion - GO:0061025 - - membrane fusion - - - - - The membrane organization process that joins two lipid bilayers to form a single membrane. - GOC:dph - GOC:tb - - - - @@ -151690,7 +149494,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + protein-containing complex assembly @@ -151755,7 +149559,6 @@ For example, A and B may be gene products and binding of B by A positively regul - regulation of molecular function @@ -151878,45 +149681,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis. - exocytic constitutive secretory pathway transport vesicle - exocytotic vesicle - cellular_component - GO:0070382 - exocytic vesicle - - - - - A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis. - GOC:kad - GOC:mah - - - - - exocytotic vesicle - GOC:kad - - - - @@ -152446,7 +150210,6 @@ For example, A and B may be gene products and binding of B by A positively regul - The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. mah 2010-10-04T01:51:47Z @@ -152455,12 +150218,6 @@ For example, A and B may be gene products and binding of B by A positively regul cell periphery - - - - The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - GOC:pdt - @@ -152567,7 +150324,7 @@ For example, A and B may be gene products and binding of B by A positively regul protein localization in membrane biological_process GO:0072657 - + protein localization to membrane @@ -153052,46 +150809,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The joining of two lipid bilayers to form a single organelle membrane. - tb - 2009-12-11T11:44:58Z - biological_process - GO:0090174 - organelle membrane fusion - - - - - The joining of two lipid bilayers to form a single organelle membrane. - GOC:ascb_2009 - GOC:dph - GOC:tb - - - - @@ -153115,6 +150832,7 @@ For example, A and B may be gene products and binding of B by A positively regul Any cellular metabolic process involving nucleic acids. + https://github.com/geneontology/go-ontology/issues/26133 tb 2010-04-07T10:18:47Z biological_process @@ -153400,78 +151118,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole. - pr - 2014-02-28T09:49:31Z - biological_process - GO:0097576 - vacuole fusion - - - - - Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole. - GOC:pr - GOC:vw - Wikipedia:Vacuole - - - - - - - - - - - - - - - - - - - - - Any vesicle that is part of the intracellular region. - pr - 2016-03-29T17:39:45Z - cellular_component - GO:0097708 - intracellular vesicle - - - - - Any vesicle that is part of the intracellular region. - GOC:vesicles - - - - @@ -153725,135 +151371,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis. - biological_process - GO:0098876 - vesicle-mediated transport to the plasma membrane - - - - - The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space. - biological_process - GO:0099500 - vesicle fusion to plasma membrane - - - - - Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space. - GOC:aruk - GOC:bc - ISBN:0071120009 - PMID:18618940 - - - - - - - - - - - - - - - - - - - - - - - - - - A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. - cellular_component - GO:0099503 - - secretory vesicle - - - - - A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. - GOC:dos - - - - @@ -153975,7 +151492,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -153990,7 +151507,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154070,138 +151587,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate, or extent of lipid transporter activity. - kmv - 2018-07-06T18:53:55Z - biological_process - GO:0110112 - - regulation of lipid transporter activity - - - - - Any process that modulates the frequency, rate, or extent of lipid transporter activity. - GOC:BHF - GOC:BHF_miRNA - GOC:rph - PMID:27365390 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that increases the frequency, rate, or extent of lipid transporter activity. - kmv - 2018-07-06T19:14:13Z - biological_process - GO:0110113 - - positive regulation of lipid transporter activity - - - - - Any process that increases the frequency, rate, or extent of lipid transporter activity. - GOC:BHF - GOC:BHF_miRNA - GOC:rph - PMID:27365390 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that decreases the frequency, rate, or extent of lipid transporter activity. - kmv - 2018-07-06T19:21:44Z - biological_process - GO:0110114 - - negative regulation of lipid transporter activity - - - - - Any process that decreases the frequency, rate, or extent of lipid transporter activity. - GOC:BHF - GOC:BHF_miRNA - GOC:rph - PMID:27365390 - - - - + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 @@ -154337,44 +151727,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - The cellular processes that contribute to exocytosis. - pg - 2017-05-15T13:20:45Z - biological_process - GO:0140029 - - exocytic process - - - - - The cellular processes that contribute to exocytosis. - Wikipedia:Exocytosis - - - - @@ -154383,7 +151735,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154392,7 +151744,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154404,7 +151756,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0140096 - catalytic activity, acting on a protein @@ -154425,7 +151776,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154434,7 +151785,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154446,7 +151797,7 @@ For example, A and B may be gene products and binding of B by A positively regul molecular_function GO:0140098 - + catalytic activity, acting on RNA @@ -154480,61 +151831,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Directly binding to a specific protein and delivering it to a specific cellular location. - https://github.com/geneontology/go-ontology/issues/17073 - pg - 2019-04-01T10:41:38Z - Reactome:R-HSA-9662747 - Reactome:R-HSA-9662818 - molecular_function - protein carrier activity - protein transport chaperone - GO:0140318 - Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation. - protein transporter activity - - - - - Directly binding to a specific protein and delivering it to a specific cellular location. - PMID:18706423 - - - - - Reactome:R-HSA-9662747 - iRHOM2 transports ADAM17 from ER to the Golgi-network - - - - - Reactome:R-HSA-9662818 - iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane - - - - @@ -154584,99 +151880,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of a lipid from a cell, into the extracellular region. - pg - 2019-05-22T11:33:07Z - lipid efflux - biological_process - GO:0140353 - lipid export from cell - - - - - The directed movement of a lipid from a cell, into the extracellular region. - GOC:pg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. - pg - 2019-05-22T11:38:15Z - lipid uptake - biological_process - GO:0140354 - lipid import into cell - - - - - The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. - GOC:pg - - - - @@ -154783,7 +151986,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154792,7 +151995,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -154894,6 +152097,7 @@ For example, A and B may be gene products and binding of B by A positively regul + The chemical reactions and pathways resulting in the formation of L-amino acids, the L-enantiomers of amino acids. @@ -154948,6 +152152,8 @@ For example, A and B may be gene products and binding of B by A positively regul + + The chemical reactions and pathways involving any amino acid that is incorporated into protein naturally by ribosomal translation of mRNA, and that has a specific codon for translation from mRNA to protein. https://github.com/geneontology/go-ontology/issues/23268 ew @@ -155657,65 +152863,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. - bf - 2012-09-14T09:05:04Z - organic cyclic compound breakdown - organic cyclic compound catabolism - organic cyclic compound degradation - biological_process - GO:1901361 - organic cyclic compound catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. - GOC:TermGenie - - - - - organic cyclic compound breakdown - GOC:TermGenie - - - - - organic cyclic compound catabolism - GOC:TermGenie - - - - - organic cyclic compound degradation - GOC:TermGenie - - - - @@ -155880,66 +153027,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. - pr - 2012-11-04T15:17:56Z - organonitrogen compound breakdown - organonitrogen compound catabolism - organonitrogen compound degradation - biological_process - GO:1901565 - organonitrogen compound catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. - GOC:TermGenie - GOC:pr - - - - - organonitrogen compound breakdown - GOC:TermGenie - - - - - organonitrogen compound catabolism - GOC:TermGenie - - - - - organonitrogen compound degradation - GOC:TermGenie - - - - @@ -156010,25 +153097,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:36Z @@ -156158,6 +153228,8 @@ For example, A and B may be gene products and binding of B by A positively regul + + @@ -156187,65 +153259,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid. - tb - 2012-11-08T17:39:54Z - alpha-amino acid breakdown - alpha-amino acid catabolism - alpha-amino acid degradation - biological_process - GO:1901606 - alpha-amino acid catabolic process - - - - - The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid. - GOC:TermGenie - - - - - alpha-amino acid breakdown - GOC:TermGenie - - - - - alpha-amino acid catabolism - GOC:TermGenie - - - - - alpha-amino acid degradation - GOC:TermGenie - - - - @@ -156260,7 +153273,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + @@ -156564,179 +153578,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process. - bf - 2013-08-22T14:59:39Z - down regulation of RNA breakdown - down regulation of RNA catabolic process - down regulation of RNA catabolism - down regulation of RNA degradation - down-regulation of RNA breakdown - down-regulation of RNA catabolic process - down-regulation of RNA catabolism - down-regulation of RNA degradation - downregulation of RNA breakdown - downregulation of RNA catabolic process - downregulation of RNA catabolism - downregulation of RNA degradation - negative regulation of RNA breakdown - negative regulation of RNA catabolism - negative regulation of RNA degradation - inhibition of RNA breakdown - inhibition of RNA catabolic process - inhibition of RNA catabolism - inhibition of RNA degradation - biological_process - GO:1902369 - negative regulation of RNA catabolic process - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process. - GOC:TermGenie - GOC:bf - PMID:16640457 - - - - - down regulation of RNA breakdown - GOC:TermGenie - - - - - down regulation of RNA catabolic process - GOC:TermGenie - - - - - down regulation of RNA catabolism - GOC:TermGenie - - - - - down regulation of RNA degradation - GOC:TermGenie - - - - - down-regulation of RNA breakdown - GOC:TermGenie - - - - - down-regulation of RNA catabolic process - GOC:TermGenie - - - - - down-regulation of RNA catabolism - GOC:TermGenie - - - - - down-regulation of RNA degradation - GOC:TermGenie - - - - - downregulation of RNA breakdown - GOC:TermGenie - - - - - downregulation of RNA catabolic process - GOC:TermGenie - - - - - downregulation of RNA catabolism - GOC:TermGenie - - - - - downregulation of RNA degradation - GOC:TermGenie - - - - - negative regulation of RNA breakdown - GOC:TermGenie - - - - - negative regulation of RNA catabolism - GOC:TermGenie - - - - - negative regulation of RNA degradation - GOC:TermGenie - - - - - inhibition of RNA breakdown - GOC:TermGenie - - - - - inhibition of RNA catabolic process - GOC:TermGenie - - - - - inhibition of RNA catabolism - GOC:TermGenie - - - - - inhibition of RNA degradation - GOC:TermGenie - - - - @@ -156883,7 +153724,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -157093,7 +153933,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -158451,48 +155290,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - Any vesicle that is part of the extracellular region. - jl - 2014-10-22T14:26:11Z - cellular_component - microparticle - GO:1903561 - extracellular vesicle - - - - - Any vesicle that is part of the extracellular region. - GOC:TermGenie - GOC:pm - GO_REF:0000064 - PMID:24769233 - - - - - microparticle - GOC:vesicles - - - - @@ -158742,495 +155539,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole. - rl - 2015-06-12T09:10:36Z - biological_process - regulation of vacuolar protein breakdown - regulation of vacuolar protein catabolic process - regulation of vacuolar protein catabolism - regulation of vacuolar protein degradation - GO:1904350 - regulation of protein catabolic process in the vacuole - - - - - Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole. - GOC:BHF - GOC:TermGenie - GOC:rl - GO_REF:0000058 - PMID:25635054 - - - - - regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - regulation of vacuolar protein degradation - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole. - rl - 2015-06-12T09:10:42Z - down regulation of protein catabolic process in the vacuole - down-regulation of protein catabolic process in the vacuole - downregulation of protein catabolic process in the vacuole - inhibition of protein catabolic process in the vacuole - biological_process - down regulation of vacuolar protein breakdown - down regulation of vacuolar protein catabolic process - down regulation of vacuolar protein catabolism - down regulation of vacuolar protein degradation - down-regulation of vacuolar protein breakdown - down-regulation of vacuolar protein catabolic process - down-regulation of vacuolar protein catabolism - down-regulation of vacuolar protein degradation - downregulation of vacuolar protein breakdown - downregulation of vacuolar protein catabolic process - downregulation of vacuolar protein catabolism - downregulation of vacuolar protein degradation - inhibition of vacuolar protein breakdown - inhibition of vacuolar protein catabolic process - inhibition of vacuolar protein catabolism - inhibition of vacuolar protein degradation - negative regulation of vacuolar protein breakdown - negative regulation of vacuolar protein catabolic process - negative regulation of vacuolar protein catabolism - negative regulation of vacuolar protein degradation - GO:1904351 - negative regulation of protein catabolic process in the vacuole - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole. - GOC:BHF - GOC:TermGenie - GOC:rl - GO_REF:0000058 - PMID:25635054 - - - - - down regulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - down-regulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - downregulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - inhibition of protein catabolic process in the vacuole - GOC:TermGenie - - - - - down regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - down regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - down regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - down regulation of vacuolar protein degradation - GOC:TermGenie - - - - - down-regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - down-regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - down-regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - down-regulation of vacuolar protein degradation - GOC:TermGenie - - - - - downregulation of vacuolar protein breakdown - GOC:TermGenie - - - - - downregulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - downregulation of vacuolar protein catabolism - GOC:TermGenie - - - - - downregulation of vacuolar protein degradation - GOC:TermGenie - - - - - inhibition of vacuolar protein breakdown - GOC:TermGenie - - - - - inhibition of vacuolar protein catabolic process - GOC:TermGenie - - - - - inhibition of vacuolar protein catabolism - GOC:TermGenie - - - - - inhibition of vacuolar protein degradation - GOC:TermGenie - - - - - negative regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - negative regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - negative regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - negative regulation of vacuolar protein degradation - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole. - rl - 2015-06-12T09:10:49Z - up regulation of protein catabolic process in the vacuole - up-regulation of protein catabolic process in the vacuole - upregulation of protein catabolic process in the vacuole - activation of protein catabolic process in the vacuole - biological_process - activation of vacuolar protein breakdown - activation of vacuolar protein catabolic process - activation of vacuolar protein catabolism - activation of vacuolar protein degradation - positive regulation of vacuolar protein breakdown - positive regulation of vacuolar protein catabolic process - positive regulation of vacuolar protein catabolism - positive regulation of vacuolar protein degradation - up regulation of vacuolar protein breakdown - up regulation of vacuolar protein catabolic process - up regulation of vacuolar protein catabolism - up regulation of vacuolar protein degradation - up-regulation of vacuolar protein breakdown - up-regulation of vacuolar protein catabolic process - up-regulation of vacuolar protein catabolism - up-regulation of vacuolar protein degradation - upregulation of vacuolar protein breakdown - upregulation of vacuolar protein catabolic process - upregulation of vacuolar protein catabolism - upregulation of vacuolar protein degradation - GO:1904352 - positive regulation of protein catabolic process in the vacuole - - - - - Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole. - GOC:BHF - GOC:TermGenie - GOC:rl - GO_REF:0000058 - PMID:25635054 - - - - - up regulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - up-regulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - upregulation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - activation of protein catabolic process in the vacuole - GOC:TermGenie - - - - - activation of vacuolar protein breakdown - GOC:TermGenie - - - - - activation of vacuolar protein catabolic process - GOC:TermGenie - - - - - activation of vacuolar protein catabolism - GOC:TermGenie - - - - - activation of vacuolar protein degradation - GOC:TermGenie - - - - - positive regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - positive regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - positive regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - positive regulation of vacuolar protein degradation - GOC:TermGenie - - - - - up regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - up regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - up regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - up regulation of vacuolar protein degradation - GOC:TermGenie - - - - - up-regulation of vacuolar protein breakdown - GOC:TermGenie - - - - - up-regulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - up-regulation of vacuolar protein catabolism - GOC:TermGenie - - - - - up-regulation of vacuolar protein degradation - GOC:TermGenie - - - - - upregulation of vacuolar protein breakdown - GOC:TermGenie - - - - - upregulation of vacuolar protein catabolic process - GOC:TermGenie - - - - - upregulation of vacuolar protein catabolism - GOC:TermGenie - - - - - upregulation of vacuolar protein degradation - GOC:TermGenie - - - - @@ -160050,186 +156358,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of membrane invagination. - bf - 2016-04-18T15:43:54Z - biological_process - GO:1905153 - regulation of membrane invagination - - - - - Any process that modulates the frequency, rate or extent of membrane invagination. - GOC:PARL - GOC:TermGenie - GOC:bf - GO_REF:0000058 - PMID:26589353 - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination. - bf - 2016-04-18T15:44:04Z - down regulation of membrane invagination - down-regulation of membrane invagination - downregulation of membrane invagination - inhibition of membrane invagination - biological_process - GO:1905154 - negative regulation of membrane invagination - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination. - GOC:PARL - GOC:TermGenie - GOC:bf - GO_REF:0000058 - PMID:26589353 - - - - - down regulation of membrane invagination - GOC:TermGenie - - - - - down-regulation of membrane invagination - GOC:TermGenie - - - - - downregulation of membrane invagination - GOC:TermGenie - - - - - inhibition of membrane invagination - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of membrane invagination. - bf - 2016-04-18T15:44:12Z - up regulation of membrane invagination - up-regulation of membrane invagination - upregulation of membrane invagination - activation of membrane invagination - biological_process - GO:1905155 - positive regulation of membrane invagination - - - - - Any process that activates or increases the frequency, rate or extent of membrane invagination. - GOC:PARL - GOC:TermGenie - GOC:bf - GO_REF:0000058 - - - - - up regulation of membrane invagination - GOC:TermGenie - - - - - up-regulation of membrane invagination - GOC:TermGenie - - - - - upregulation of membrane invagination - GOC:TermGenie - - - - - activation of membrane invagination - GOC:TermGenie - - - - @@ -160613,258 +156741,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - Any process that modulates the frequency, rate or extent of lipid localization. - rz - 2017-02-21T12:12:22Z - regulation of lipid localisation - biological_process - GO:1905952 - regulation of lipid localization - - - - - Any process that modulates the frequency, rate or extent of lipid localization. - GOC:TermGenie - GO_REF:0000058 - PMID:17564681 - - - - - regulation of lipid localisation - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. - rz - 2017-02-21T12:12:41Z - down regulation of lipid localisation - down regulation of lipid localization - down-regulation of lipid localisation - down-regulation of lipid localization - downregulation of lipid localisation - downregulation of lipid localization - negative regulation of lipid localisation - inhibition of lipid localisation - inhibition of lipid localization - biological_process - GO:1905953 - negative regulation of lipid localization - - - - - Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. - GOC:TermGenie - GO_REF:0000058 - PMID:17564681 - - - - - down regulation of lipid localisation - GOC:TermGenie - - - - - down regulation of lipid localization - GOC:TermGenie - - - - - down-regulation of lipid localisation - GOC:TermGenie - - - - - down-regulation of lipid localization - GOC:TermGenie - - - - - downregulation of lipid localisation - GOC:TermGenie - - - - - downregulation of lipid localization - GOC:TermGenie - - - - - negative regulation of lipid localisation - GOC:TermGenie - - - - - inhibition of lipid localisation - GOC:TermGenie - - - - - inhibition of lipid localization - GOC:TermGenie - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process that activates or increases the frequency, rate or extent of lipid localization. - rz - 2017-02-21T12:12:49Z - positive regulation of lipid localisation - up regulation of lipid localisation - up regulation of lipid localization - up-regulation of lipid localisation - up-regulation of lipid localization - upregulation of lipid localisation - upregulation of lipid localization - activation of lipid localisation - activation of lipid localization - biological_process - GO:1905954 - positive regulation of lipid localization - - - - - Any process that activates or increases the frequency, rate or extent of lipid localization. - GOC:TermGenie - GO_REF:0000058 - PMID:17564681 - - - - - positive regulation of lipid localisation - GOC:TermGenie - - - - - up regulation of lipid localisation - GOC:TermGenie - - - - - up regulation of lipid localization - GOC:TermGenie - - - - - up-regulation of lipid localisation - GOC:TermGenie - - - - - up-regulation of lipid localization - GOC:TermGenie - - - - - upregulation of lipid localisation - GOC:TermGenie - - - - - upregulation of lipid localization - GOC:TermGenie - - - - - activation of lipid localisation - GOC:TermGenie - - - - - activation of lipid localization - GOC:TermGenie - - - - @@ -160903,45 +156779,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells. - bhm - 2014-03-26T14:23:27Z - cellular_component - GO:1990351 - An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay). - transporter complex - - - - - A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells. - GOC:bhm - PMID:15449578 - - - - @@ -161056,6 +156893,44 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of multicellular organismal development. + tb + 2010-08-05T11:25:59Z + biological_process + GO:2000026 + regulation of multicellular organismal development + + + + + Any process that modulates the frequency, rate or extent of multicellular organismal development. + GOC:obol + + + + @@ -161183,8 +157058,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + @@ -161257,7 +157133,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + @@ -161331,7 +157208,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + @@ -161405,7 +157283,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -161665,6 +157542,8 @@ For example, A and B may be gene products and binding of B by A positively regul GC_ID:1 + PMID:30365038 + PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -161679,6 +157558,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1206794 + Ecdysozoa + + + + @@ -161698,6 +157590,289 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + true yeasts + ncbi_taxonomy + NCBITaxon:147537 + Saccharomycotina + + + + + true yeasts + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Archiascomycota + NCBITaxon:147554 + Schizosaccharomycetes + + + + + Archiascomycota + + + + + + + + + + + GC_ID:1 + PMID:10874751 + PMID:11557979 + ncbi_taxonomy + NCBITaxon:197562 + Pancrustacea + + + + + + + + + + GC_ID:1 + PMID:11557979 + PMID:9727836 + mandibulates + ncbi_taxonomy + NCBITaxon:197563 + Mandibulata + + + + + mandibulates + + + + + + + + + + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11542017 + PMID:11542087 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:270744 + PMID:32628106 + PMID:36748408 + PMID:7520741 + PMID:8123559 + PMID:8186100 + PMID:8590690 + PMID:9103655 + PMID:9336922 + eubacteria + ncbi_taxonomy + Monera + Procaryotae + Prokaryota + Prokaryotae + bacteria + prokaryote + prokaryotes + NCBITaxon:2 + Bacteria + + + + + eubacteria + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + bacteria + + + + + + prokaryote + + + + + + prokaryotes + + + + + + + + + + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11541975 + PMID:11542064 + PMID:11542149 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:25527841 + PMID:270744 + PMID:32628106 + PMID:36748408 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + ncbi_taxonomy + Archaebacteria + Mendosicutes + Metabacteria + Monera + Procaryotae + Prokaryota + Prokaryotae + archaea + prokaryote + prokaryotes + NCBITaxon:2157 + Archaea + + + + + Archaebacteria + + + + + + Mendosicutes + + + + + + Metabacteria + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + archaea + + + + + + prokaryote + + + + + + prokaryotes + + + + + @@ -161727,7 +157902,7 @@ For example, A and B may be gene products and binding of B by A positively regul eukaryotes - + @@ -161789,6 +157964,117 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + metazoans + multicellular animals + ncbi_taxonomy + Animalia + animals + NCBITaxon:33208 + Metazoa + + + + + metazoans + + + + + + multicellular animals + + + + + + Animalia + + + + + + animals + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33213 + Bilateria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33317 + Protostomia + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:34346 + Schizosaccharomycetales + + + + + + + + + + GC_ID:1 + PMID:15689432 + PMID:16151185 + PMID:17010206 + PMID:17051209 + PMID:17572334 + ncbi_taxonomy + NCBITaxon:451864 + Dikarya + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:451866 + Taphrinomycotina + + + + @@ -161818,6 +158104,417 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + PMID:17572334 + ascomycetes + sac fungi + ncbi_taxonomy + ascomycete fungi + NCBITaxon:4890 + Ascomycota + + + + + ascomycetes + + + + + + sac fungi + + + + + + ascomycete fungi + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Hemiascomycetes + NCBITaxon:4891 + Saccharomycetes + + + + + Hemiascomycetes + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Endomycetales + budding yeasts + NCBITaxon:4892 + Saccharomycetales + + + + + Endomycetales + + + + + + budding yeasts + + + + + + + + + + + NCBITaxon:221665 + NCBITaxon:44280 + GC_ID:1 + ncbi_taxonomy + NCBITaxon:4893 + Saccharomycetaceae + + + + + + + + + + GC_ID:1 + fission yeasts + ncbi_taxonomy + Schizosaccharomycetoideae + NCBITaxon:4894 + Schizosaccharomycetaceae + + + + + fission yeasts + + + + + + Schizosaccharomycetoideae + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:4895 + Schizosaccharomyces + + + + + + + + + + NCBITaxon:45042 + GC_ID:1 + fission yeast + ncbi_taxonomy + Schizosaccharomyces malidevorans + NCBITaxon:4896 + Schizosaccharomyces pombe + + + + + fission yeast + + + + + + Schizosaccharomyces malidevorans + + + + + + + + + + + NCBITaxon:36915 + GC_ID:1 + ncbi_taxonomy + Pachytichospora + NCBITaxon:4930 + Saccharomyces + + + + + Pachytichospora + + + + + + + + + + + NCBITaxon:41870 + GC_ID:1 + Saccharomyces cerevisiae 'var. diastaticus' + baker's yeast + brewer's yeast + ncbi_taxonomy + Candida robusta + Mycoderma cerevisiae + Saccharomyces capensis + Saccharomyces diastaticus + Saccharomyces italicus + Saccharomyces oviformis + Saccharomyces uvarum var. melibiosus + NCBITaxon:4932 + Saccharomyces cerevisiae + + + + + Saccharomyces cerevisiae 'var. diastaticus' + + + + + + baker's yeast + + + + + + brewer's yeast + + + + + + Candida robusta + + + + + + Mycoderma cerevisiae + + + + + + Saccharomyces capensis + + + + + + Saccharomyces diastaticus + + + + + + Saccharomyces italicus + + + + + + Saccharomyces oviformis + + + + + + Saccharomyces uvarum var. melibiosus + + + + + + + + + + + GC_ID:1 + true insects + ncbi_taxonomy + insects + NCBITaxon:50557 + Insecta + + + + + true insects + + + + + + insects + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:6072 + Eumetazoa + + + + + + + + + + GC_ID:1 + arthropods + ncbi_taxonomy + arthropods + NCBITaxon:6656 + Arthropoda + + + + + arthropods + + + + + + arthropods + + + + + + + + + + + GC_ID:1 + insects + ncbi_taxonomy + Atelocerata + Tracheata + Uniramia + hexapods + NCBITaxon:6960 + Hexapoda + + + + + insects + + + + + + Atelocerata + + + + + + Tracheata + + + + + + Uniramia + + + + + + hexapods + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:716545 + saccharomyceta + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:88770 + Panarthropoda + + + + @@ -163355,6 +160052,45 @@ See https://github.com/pato-ontology/pato/issues/331. + + + + + An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. + quality + PATO:0001992 + + + cellularity + + + + + An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. + PATOC:GVG + + + + + + + + + A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. + quality + PATO:0001993 + + multicellular + + + + + A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. + PATOC:GVG + + + + @@ -203315,7 +200051,7 @@ See https://github.com/pato-ontology/pato/issues/331. - + A single species cell morphology phenotype in which fungal hyphae form an increased number of branches. alaynecuzick 2020-03-04T14:33:49Z @@ -206889,6 +203625,394 @@ occurs to a lesser extent than normal. + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001411 + resistance to dalfopristin + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to dalfopristin. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001412 + sensitive to dalfopristin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to dalfopristin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-05T09:44:00Z + single_species_phenotype + PHIPO:0001413 + normal growth on dalfopristin + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001414 + resistance to thifluzamide + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to thifluzamide. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001415 + sensitive to thifluzamide + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to thifluzamide (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001416 + normal growth on thifluzamide + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to penflufen. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001417 + resistance to penflufen + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to penflufen. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001418 + sensitive to penflufen + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to penflufen (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001419 + normal growth on penflufen + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to flutolanil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001420 + resistance to flutolanil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to flutolanil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001421 + sensitive to flutolanil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to flutolanil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-07T11:32:37Z + single_species_phenotype + PHIPO:0001422 + normal growth on flutolanil + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to imazalil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001423 + resistance to imazalil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to imazalil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001424 + sensitive to imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to imazalil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-12T10:06:39Z + single_species_phenotype + PHIPO:0001425 + normal growth on imazalil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fludioxonil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-02-28T09:44:54Z + single_species_phenotype + normal growth on fludioxonil + + + + + + + + + A single species cell morphology phenotype in which fungal hyphae branching is abnormal. + alaynecuzick + 2024-03-04T15:00:58Z + single_species_phenotype + abnormal hyphal branching + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to brefeldin A (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:12:17Z + single_species_phenotype + normal growth on brefeldin A + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to fluconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-12T15:14:22Z + single_species_phenotype + normal growth on fluconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to ipconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001430 + resistance to ipconazole + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to ipconazole. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001431 + sensitive to ipconazole + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to ipconazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001432 + normal growth on ipconazole + + + + + + + + + A growth phenotype which describes the resistance of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001433 + resistance to cyprodinil + + + + + + + + + A growth phenotype which describes the sensitivity of individuals or populations after exposure to cyprodinil. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow. + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001434 + sensitive to cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to cyprodinil (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-18T13:26:33Z + single_species_phenotype + PHIPO:0001435 + normal growth on cyprodinil + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to caspofungin (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001436 + normal growth on caspofungin + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to terbinafine (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001437 + normal growth on terbinafine + + + + + + + + + A growth phenotype which describes the absence of change of individuals or populations after exposure to bifonazole (i.e. indistinguishable from wild type). + alaynecuzick + 2024-03-27T11:45:23Z + single_species_phenotype + PHIPO:0001438 + normal growth on bifonazole + + + + @@ -207100,6 +204224,7 @@ occurs to a lesser extent than normal. + BFO:0000003 uberon UBERON:0000000 @@ -207163,6 +204288,12 @@ occurs to a lesser extent than normal. Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 + + + + FBbt:00007001 + + @@ -207172,6 +204303,107 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + adult stage + BTO:0001043 + BilaDO:0000004 + EFO:0001272 + FBdv:00005369 + WBls:0000041 + XtroDO:0000084 + fully formed animal stage + juvenile-adult stage + uberon + UBERON:0000066 + + fully formed stage + https://github.com/obophenotype/uberon/issues/566 + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + BilaDO:0000002 + EV:0300001 + FBdv:00005289 + FMA:72652 + HsapDv:0000002 + MmusDv:0000002 + OGES:000000 + OGES:000022 + SCTID:296280003 + WBls:0000003 + WBls:0000092 + WBls:0000102 + XAO:1000012 + embryonic stage + uberon + embryogenesis + UBERON:0000068 + embryo stage + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + http://orcid.org/0000-0002-6601-2165 + + + + @@ -207211,6 +204443,49 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + Stage succeeding embryo, including mature structure. + In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) + BilaDO:0000003 + OGES:000010 + OGES:000014 + OGES:000024 + WBls:0000022 + WBls:0000093 + WBls:0000103 + postembryonic stage + post-hatching stage + uberon + postembryonic + UBERON:0000092 + post-embryonic stage + https://github.com/obophenotype/uberon/issues/344 + + + + + Stage succeeding embryo, including mature structure. + https://orcid.org/0000-0002-6601-2165 + + + + @@ -207306,6 +204581,149 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + BILS:0000106 + BilaDO:0000005 + EFO:0001322 + EHDAA:27 + FBdv:00005288 + IDOMAL:0000302 + NCIT:C12601 + PdumDv:0000100 + VHOG:0000745 + Wikipedia:Zygote + XAO:1000001 + ZFS:0000001 + 1-cell stage + fertilized egg stage + one cell stage + uberon + fertilized egg stage + one-cell stage + zygote + zygotum + UBERON:0000106 + + zygote stage + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + Wikipedia:Zygote + + + + + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + 2012-09-17 + VHOG:0000745 + VHOG + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 + http://bgee.unil.ch/ + + + + + IDOMAL:0000302 + + + https://github.com/biopragmatics/biomappings + + + + + fertilized egg stage + BTO:0000854 + + + + + one-cell stage + VHOG:0000745 + + + + + zygote + VHOG:0000745 + + + + + zygotum + Wikipedia:Zygote + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + BILS:0000111 + BilaDO:0000010 + HsapDv:0000015 + MmusDv:0000018 + OGES:000005 + OGES:000032 + Wikipedia:Organogenesis + uberon + segmentation stage + UBERON:0000111 + organogenesis stage + https://github.com/obophenotype/developmental-stage-ontologies/issues/84 + https://github.com/obophenotype/uberon/issues/533 + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + Wikipedia:Organogenesis + + + + @@ -207338,6 +204756,248 @@ occurs to a lesser extent than normal. Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 + + + + FBbt:00007016 + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + TODO - split body and mc organism? body continues after death stage + + + + organismal + organism + AAO:0010026 + AEO:0000191 + BILA:0000012 + BIRNLEX:18 + BSA:0000038 + BTO:0000042 + CARO:0000012 + EFO:0002906 + EHDAA2:0003103 + EHDAA2:0003191 + EHDAA:1 + EMAPA:25765 + EV:0100016 + FBbt:00000001 + FMA:256135 + HAO:0000012 + NCIT:C13041 + SCTID:243928005 + TADS:0000001 + TAO:0001094 + TGMA:0001832 + VHOG:0000671 + WBbt:0007833 + Wikipedia:Multi-cellular_organism + XAO:0003004 + ZFA:0001094 + galen:Organism + ncithesaurus:Whole_Organism + multi-cellular organism + uberon + Koerper + body + whole body + whole organism + UBERON:0000468 + + + + + + multicellular organism + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + CARO:0000012 + Wikipedia:Multi-cellular_organism + http://orcid.org/0000-0001-9114-8737 + + + + + organism + FBbt:00000001 + VHOG:0000671 + WBbt:0007833 + + + + + FBbt:00000001 + + + + + + multi-cellular organism + CARO:0000012 + + + + + Koerper + BTO:0001489 + + + + + body + AEO:0000103 + BIRNLEX:18 + FMA:256135 + NCIT:C13041 + + + + + whole body + BTO:0001489 + + + + + whole organism + FBbt:00000001 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + embryonic + Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo + AAO:0011035 + AEO:0000169 + BILA:0000056 + BSA:0000039 + BTO:0000379 + CALOHA:TS-0229 + EFO:0001367 + EHDAA2:0000002 + EHDAA2_RETIRED:0003236 + EHDAA:38 + EMAPA:16039 + FBbt:00000052 + FMA:69068 + GAID:963 + IDOMAL:0000646 + MAT:0000226 + MESH:D004622 + MIAA:0000019 + NCIT:C28147 + OGEM:000001 + SCTID:57991002 + UMLS:C0013935 + VHOG:0001766 + Wikipedia:Embryo + XAO:0000113 + ZFA:0000103 + http://neurolex.org/wiki/Category:Embryonic_organism + embryonic organism + uberon + developing organism + developmental tissue + UBERON:0000922 + + + + + embryo + https://github.com/obophenotype/uberon/issues/503 + https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg + + + + + Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + BTO:0000379 + FB:FBrf0039741 + FB:FBrf0041814 + GO:0009790 + Wikipedia:Embryo + + + + + Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo + ZFA + + + + + FBbt:00000052 + + + + + + IDOMAL:0000646 + + + https://github.com/biopragmatics/biomappings + + + + + UMLS:C0013935 + ncithesaurus:Embryo + + + + + embryonic organism + BILA:0000056 + + + + + developing organism + BILA:0000056 + @@ -207351,6 +205011,7 @@ occurs to a lesser extent than normal. AAO:0010841 AEO:0000000 + BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 @@ -207379,6 +205040,12 @@ occurs to a lesser extent than normal. FMA:62955 http://orcid.org/0000-0001-9114-8737 + + + + FBbt:10000000 + + @@ -207388,6 +205055,133 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + + + + + A multicellular organism that existence_starts_with a post-embryonic stage. + MA:0002405 + postnatal organism + TS28 mouse + post-hatching organism + post-natal organism + postnatal mouse + uberon + UBERON:0009953 + post-embryonic organism + https://github.com/obophenotype/uberon/issues/667 + + + + + A multicellular organism that existence_starts_with a post-embryonic stage. + OBOL:automatic + + + + + TS28 mouse + MA:0002405 + + + + + post-hatching organism + https://orcid.org/0000-0002-6601-2165 + + + + + post-natal organism + https://orcid.org/0000-0002-6601-2165 + + + + + postnatal mouse + MA:0002405 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that has more than one cell as a part. + + + + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + + multicellular anatomical structure + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + + + + + FBbt:00100313 + + + + + + multicellular structure + FBbt:00100313 + + + + @@ -207743,6 +205537,36 @@ occurs to a lesser extent than normal. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -207814,6 +205638,16 @@ occurs to a lesser extent than normal. + + + + + + + + + + @@ -207847,10 +205681,10 @@ occurs to a lesser extent than normal. /////////////////////////////////////////////////////////////////////////////////////// --> - + - + @@ -207868,66 +205702,54 @@ occurs to a lesser extent than normal. - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - + - - - - - - - - - @@ -207940,8 +205762,8 @@ occurs to a lesser extent than normal. - - + + @@ -207951,7 +205773,7 @@ occurs to a lesser extent than normal. - + @@ -207961,7 +205783,7 @@ occurs to a lesser extent than normal. - + @@ -207978,8 +205800,8 @@ occurs to a lesser extent than normal. - - + + @@ -208241,7 +206063,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208251,8 +206073,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208262,8 +206084,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208280,8 +206102,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208300,7 +206122,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208310,8 +206132,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208321,8 +206143,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208339,8 +206161,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208356,8 +206178,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208367,7 +206189,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208377,8 +206199,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208388,8 +206210,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208408,8 +206230,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208427,8 +206249,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208438,8 +206260,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208449,8 +206271,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208467,8 +206289,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208485,8 +206307,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208496,8 +206318,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208507,8 +206329,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208525,8 +206347,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208543,8 +206365,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208554,8 +206376,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208565,8 +206387,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208583,8 +206405,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208600,9 +206422,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208611,9 +206433,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208628,8 +206450,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208645,9 +206467,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208656,9 +206478,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208673,8 +206495,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208690,9 +206512,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208701,9 +206523,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208718,8 +206540,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208735,9 +206557,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208746,9 +206568,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208763,8 +206585,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208780,9 +206602,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208791,9 +206613,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208808,8 +206630,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -208825,9 +206647,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208836,9 +206658,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208853,7 +206675,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208863,7 +206685,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208881,9 +206703,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208892,9 +206714,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208909,7 +206731,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208919,7 +206741,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208936,7 +206758,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208947,7 +206769,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -208980,9 +206802,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -208991,9 +206813,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209008,8 +206830,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -209024,9 +206846,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209035,9 +206857,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209051,9 +206873,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209068,7 +206890,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -209079,7 +206901,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -209095,7 +206917,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -209112,9 +206934,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209123,9 +206945,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -209157,8 +206979,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -209168,8 +206990,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl index 199e740..262030f 100644 --- a/src/ontology/imports/chebi_import.owl +++ b/src/ontology/imports/chebi_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-01-31") + +Annotation( ) +Annotation(owl:versionInfo "2024-04-04") Declaration(Class()) Declaration(Class()) @@ -208,6 +208,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3956,6 +3957,7 @@ AnnotationAssertion(rdfs:label "amm SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -7802,6 +7804,23 @@ SubClassOf( ) SubClassOf( ) +# Class: (NMR chemical shift reference compound) + +AnnotationAssertion( "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift reference compounds") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift standards") +AnnotationAssertion(Annotation( "ChEBI") "NMR internal standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR internal standards") +AnnotationAssertion(Annotation( "ChEBI") "NMR reference standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR reference standards") +AnnotationAssertion( "CHEBI:228364") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "NMR chemical shift reference compound") +SubClassOf( ) +SubClassOf( ) + # Class: (biphenyls) AnnotationAssertion( "Benzenoid aromatic compounds containing two phenyl or substituted-phenyl groups which are joined together by a single bond.") @@ -10116,6 +10135,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phosphoric acid") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -17273,8 +17293,15 @@ SubClassOf( (alpha-amino-acid residue) +AnnotationAssertion( "An amino-acid residue derived from an alpha-amino acid.") +AnnotationAssertion( "0") +AnnotationAssertion( "C2H2NOR") +AnnotationAssertion( "56.043") +AnnotationAssertion( "56.01364") +AnnotationAssertion( "*-NC([*])C(-*)=O") AnnotationAssertion( "chebi_ontology") AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid residues") +AnnotationAssertion(Annotation( "UniProt") "an alpha-amino acid residue") AnnotationAssertion( "CHEBI:33710") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alpha-amino-acid residue") diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl index 7855ebb..e8814fa 100644 --- a/src/ontology/imports/cl_import.owl +++ b/src/ontology/imports/cl_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-01-31") + +Annotation( ) +Annotation(owl:versionInfo "2024-04-04") Declaration(Class()) Declaration(Class()) @@ -50,7 +50,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -547,6 +546,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -567,6 +567,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -580,8 +581,8 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -595,7 +596,6 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -640,6 +640,9 @@ Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) ############################ # Annotation Properties ############################ @@ -678,6 +681,10 @@ AnnotationAssertion(rdfs:label "def SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -708,6 +715,10 @@ SubAnnotationPropertyOf( < SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -760,13 +771,13 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: () -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: () -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: () @@ -816,10 +827,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -3077,6 +3084,7 @@ AnnotationAssertion( "VHOG:0001533") AnnotationAssertion( "WBbt:0004017") AnnotationAssertion( "XAO:0003012") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).") AnnotationAssertion(rdfs:label "cell") @@ -3090,6 +3098,7 @@ DisjointClasses( "GOC:tfm") Annotation( "ISBN:0721662544") "A cell that specializes in controlled release of one or more substances.") AnnotationAssertion( "BTO:0003659") AnnotationAssertion( "FMA:86916") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "secretory cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -3144,6 +3153,7 @@ SubClassOf( ObjectSomeValuesFrom( (eukaryotic cell) AnnotationAssertion( "MESH:D005057") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eukaryotic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -3184,6 +3194,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2017-01-30T18:53:32Z"^^xsd:dateTime) AnnotationAssertion( "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "https://github.com/obophenotype/cell-ontology/issues/448") AnnotationAssertion(rdfs:label "abnormal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -3213,22 +3224,13 @@ SubClassOf( (precursor cell) AnnotationAssertion(Annotation( "GOC:dos") "A cell that, by division or terminal differentiation, can give rise to other cell types.") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.") AnnotationAssertion(rdfs:label "precursor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (increased nucleus size) - -AnnotationAssertion(Annotation( "GOC:tfm") "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.") -AnnotationAssertion( ) -AnnotationAssertion( "2009-12-23T10:53:24Z") -AnnotationAssertion(rdfs:label "increased nucleus size") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (reproduction) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.") @@ -3360,8 +3362,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "DNA binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -3387,8 +3389,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "RNA binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -3459,7 +3461,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.") AnnotationAssertion(rdfs:label "transporter activity") SubClassOf( ) @@ -3523,7 +3525,7 @@ SubClassOf( ObjectSomeValuesFrom( (cellular_component) -AnnotationAssertion(Annotation( "GOC:pdt") "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).") +AnnotationAssertion(Annotation( "GOC:pdt") "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17729"^^xsd:anyURI) AnnotationAssertion( "GO:0008372") AnnotationAssertion( "NIF_Subcellular:sao1337158144") @@ -3559,8 +3561,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.") AnnotationAssertion(rdfs:label "extracellular region") SubClassOf( ) @@ -3639,8 +3641,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cytoplasm") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -3693,8 +3695,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "plasma membrane") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -3737,8 +3739,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "carbohydrate metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -3834,8 +3836,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lipid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -3872,7 +3874,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.") AnnotationAssertion(rdfs:label "transport") SubClassOf( ) @@ -3909,7 +3911,7 @@ AnnotationAssertion( "GOC:al") "copper-induced intracellular protein transport") AnnotationAssertion( "GO:0006886") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intracellular protein transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -4288,8 +4290,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lipid binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -4622,7 +4624,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "RNA metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -4699,8 +4701,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "transferase activity") SubClassOf( ) @@ -4737,8 +4739,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hydrolase activity") SubClassOf( ) @@ -4892,7 +4894,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children.") AnnotationAssertion(rdfs:label "protein catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -5229,7 +5231,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein modification process") SubClassOf( ) SubClassOf( ) @@ -5242,7 +5244,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0043062") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "extracellular structure organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -5251,6 +5253,7 @@ SubClassOf( ObjectSomeValuesFrom( (macromolecule metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "GO:0034960") AnnotationAssertion( "GO:0043283") AnnotationAssertion( "GO:0044259") @@ -5260,6 +5263,7 @@ AnnotationAssertion( "multicellular organismal macromolecule metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043170") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macromolecule metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -5276,7 +5280,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle") SubClassOf( ) @@ -5409,9 +5413,11 @@ SubClassOf( (primary metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "http://www.metacyc.org") "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "primary metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044238") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "primary metabolic process") SubClassOf( ) @@ -5550,9 +5556,11 @@ SubClassOf( (anatomical structure development) AnnotationAssertion(Annotation( "GO_REF:0000021") "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "development of an anatomical structure") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048856") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -5849,7 +5857,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "membrane organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -5931,7 +5939,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein-containing complex assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -6016,6 +6024,7 @@ SubClassOf( ObjectSomeValuesFrom( (organic substance metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-08T03:32:18Z") AnnotationAssertion( "organic molecular entity metabolic process") @@ -6023,6 +6032,7 @@ AnnotationAssertion( "organic substance metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071704") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic substance metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -6075,7 +6085,7 @@ SubClassOf( (cell periphery) -AnnotationAssertion(Annotation( "GOC:pdt") "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.") +AnnotationAssertion(Annotation( "GOC:pdt") "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.") AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-04T01:51:47Z") AnnotationAssertion( "cellular_component") @@ -6106,7 +6116,7 @@ AnnotationAssertion(Annotation( "protein localization in membrane") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072657") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein localization to membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -6396,6 +6406,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:kmv") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24200"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "kmv") AnnotationAssertion( "2019-08-12T18:01:37Z") AnnotationAssertion( "cellular_component") @@ -6444,7 +6455,7 @@ AnnotationAssertion( AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140096") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "catalytic activity, acting on a protein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -6459,7 +6470,7 @@ AnnotationAssertion( AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140097") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "catalytic activity, acting on DNA") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -6475,7 +6486,7 @@ AnnotationAssertion( AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140098") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "catalytic activity, acting on RNA") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -7606,7 +7617,7 @@ AnnotationAssertion( "CARO:0000003") AnnotationAssertion( "EHDAA2:0003003") AnnotationAssertion( "EMAPA:0") -AnnotationAssertion( "FBbt:00007001") +AnnotationAssertion(Annotation( ) "FBbt:00007001") AnnotationAssertion( "FMA:305751") AnnotationAssertion( "FMA:67135") AnnotationAssertion( "GAID:781") @@ -7791,7 +7802,7 @@ AnnotationAssertion( "EFO:0001322") AnnotationAssertion( "EHDAA:27") AnnotationAssertion( "FBdv:00005288") -AnnotationAssertion(Annotation( "https://orcid.org/0000-0003-4423-4370") "IDOMAL:0000302") +AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0000302") AnnotationAssertion( "NCIT:C12601") AnnotationAssertion( "PdumDv:0000100") AnnotationAssertion( "VHOG:0000745") @@ -7805,7 +7816,7 @@ AnnotationAssertion( "fertilized egg stage") AnnotationAssertion(Annotation( "VHOG:0000745") "one-cell stage") AnnotationAssertion(Annotation( "VHOG:0000745") "zygote") -AnnotationAssertion(Annotation( "Wikipedia:Zygote") Annotation( ) "zygotum") +AnnotationAssertion(Annotation( "Wikipedia:Zygote") Annotation( ) "zygotum") AnnotationAssertion( "UBERON:0000106") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "zygote stage") @@ -7848,7 +7859,7 @@ AnnotationAssertion( "BILA:0000006") AnnotationAssertion( "CARO:0000006") AnnotationAssertion( "EHDAA2:0003006") -AnnotationAssertion( "FBbt:00007016") +AnnotationAssertion(Annotation( ) "FBbt:00007016") AnnotationAssertion( "FMA:67165") AnnotationAssertion( "HAO:0000006") AnnotationAssertion( "TAO:0001836") @@ -7884,7 +7895,7 @@ AnnotationAssertion( "EHDAA:1") AnnotationAssertion( "EMAPA:25765") AnnotationAssertion( "EV:0100016") -AnnotationAssertion( "FBbt:00000001") +AnnotationAssertion(Annotation( ) "FBbt:00000001") AnnotationAssertion( "FMA:256135") AnnotationAssertion( "HAO:0000012") AnnotationAssertion( "NCIT:C13041") @@ -7930,10 +7941,10 @@ AnnotationAssertion( "EHDAA2_RETIRED:0003236") AnnotationAssertion( "EHDAA:38") AnnotationAssertion( "EMAPA:16039") -AnnotationAssertion( "FBbt:00000052") +AnnotationAssertion(Annotation( ) "FBbt:00000052") AnnotationAssertion( "FMA:69068") AnnotationAssertion( "GAID:963") -AnnotationAssertion(Annotation( "https://orcid.org/0000-0003-4423-4370") "IDOMAL:0000646") +AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0000646") AnnotationAssertion( "MAT:0000226") AnnotationAssertion( "MESH:D004622") AnnotationAssertion( "MIAA:0000019") @@ -7976,7 +7987,7 @@ AnnotationAssertion( "BIRNLEX:6") AnnotationAssertion( "CARO:0000000") AnnotationAssertion( "EHDAA2:0002229") -AnnotationAssertion( "FBbt:10000000") +AnnotationAssertion(Annotation( ) "FBbt:10000000") AnnotationAssertion( "FMA:62955") AnnotationAssertion( "HAO:0000000") AnnotationAssertion( "MA:0000001") @@ -8017,7 +8028,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "CARO:0010000") -AnnotationAssertion( "FBbt:00100313") +AnnotationAssertion(Annotation( ) "FBbt:00100313") AnnotationAssertion(Annotation( "FBbt:00100313") "multicellular structure") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010000") @@ -8160,6 +8171,7 @@ EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(2 ))) EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(1 ))) EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectMinCardinality(2 ))) +EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -8168,6 +8180,7 @@ SubClassOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index 7957f58..1bcffc6 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-01-31") +Annotation(owl:versionInfo "2024-04-04") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index f6d856f..f3f5ef0 100644 --- a/src/ontology/imports/ido_import.owl +++ b/src/ontology/imports/ido_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-01-31") +Annotation(owl:versionInfo "2024-04-04") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index f96094b..5e3654c 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-01-31") + +Annotation( ) +Annotation(owl:versionInfo "2024-04-04") Declaration(Class()) Declaration(Class()) @@ -34,12 +34,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -229,21 +229,28 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -255,7 +262,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -268,7 +274,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -278,12 +283,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -291,38 +291,32 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -334,7 +328,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -342,11 +335,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -356,26 +349,19 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -386,11 +372,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -398,39 +381,22 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -446,30 +412,22 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -480,7 +438,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -494,7 +451,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -507,57 +463,51 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -565,19 +515,18 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -592,6 +541,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -605,13 +557,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -627,10 +576,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -641,7 +589,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -663,38 +610,25 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -705,20 +639,15 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -734,13 +663,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -749,21 +674,15 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -772,10 +691,38 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -834,6 +781,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -880,11 +829,20 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -913,6 +871,8 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -937,10 +897,12 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -983,6 +945,12 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -1019,7 +987,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -1059,6 +1026,8 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -1071,6 +1040,9 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -1086,6 +1058,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -1099,13 +1072,13 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -1121,7 +1094,10 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -1133,12 +1109,15 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -1151,13 +1130,16 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) ############################ # Annotation Properties ############################ @@ -1166,6 +1148,14 @@ Declaration(AnnotationProperty() AnnotationAssertion(rdfs:label "definition") +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -1208,6 +1198,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -1260,30 +1254,30 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) +# Annotation Property: () -# Annotation Property: () +SubAnnotationPropertyOf( ) -SubAnnotationPropertyOf( ) - -# Annotation Property: () +# Annotation Property: () -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: () SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: () -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: () SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -1340,49 +1334,33 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: () -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: () -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) -# Annotation Property: (creator) +# Annotation Property: () -AnnotationAssertion( "http://purl.org/dc/elements/1.1/creator") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-creator") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-creator") -AnnotationAssertion(rdfs:label "creator") +SubAnnotationPropertyOf( ) -# Annotation Property: (description) +# Annotation Property: () -AnnotationAssertion( "http://purl.org/dc/elements/1.1/description") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-description") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-description") -AnnotationAssertion(rdfs:label "description") +SubAnnotationPropertyOf( ) -# Annotation Property: (title) +# Annotation Property: () + +SubAnnotationPropertyOf( ) -AnnotationAssertion( "http://purl.org/dc/elements/1.1/title") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-title") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-title") -AnnotationAssertion(rdfs:label "title") +# Annotation Property: (created by) -# Annotation Property: (license) +AnnotationAssertion(rdfs:label "created by") -AnnotationAssertion( "http://purl.org/dc/terms/license") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dcterms-license") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dcterms-license") -AnnotationAssertion(rdfs:label "license") +# Annotation Property: (creation date) + +AnnotationAssertion(rdfs:label "creation date") # Annotation Property: (has_alternative_id) @@ -1412,6 +1390,10 @@ AnnotationAssertion(rdfs:label "has_related_synonym") +# Annotation Property: (id) + +AnnotationAssertion(rdfs:label "id") + # Annotation Property: (in_subset) AnnotationAssertion(rdfs:label "in_subset") @@ -1445,7 +1427,6 @@ AnnotationAssertion( "BFO:0000050") AnnotationAssertion( "external") AnnotationAssertion( "quality") -AnnotationAssertion( "uberon") AnnotationAssertion( "part_of") AnnotationAssertion( ) AnnotationAssertion( ) @@ -1457,6 +1438,7 @@ AnnotationAssertion(rdfs:label "par AnnotationAssertion(rdfs:label "part_of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -1479,7 +1461,6 @@ AnnotationAssertion( "BFO:0000051") AnnotationAssertion( "external") AnnotationAssertion( "quality") -AnnotationAssertion( "uberon") AnnotationAssertion( "has_part") AnnotationAssertion( ) AnnotationAssertion( ) @@ -1498,10 +1479,9 @@ AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) AnnotationAssertion( "is preceded by"@en) AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") AnnotationAssertion( "BFO:0000062") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "preceded_by") AnnotationAssertion( ) AnnotationAssertion( "preceded_by") @@ -1519,7 +1499,6 @@ AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) AnnotationAssertion( "BFO:0000063") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "precedes") AnnotationAssertion( ) AnnotationAssertion( "precedes") @@ -1548,6 +1527,7 @@ AnnotationAssertion(rdfs:comment "P AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) AnnotationAssertion(rdfs:label "occurs in") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -1556,14 +1536,9 @@ ObjectPropertyRange( "site of"@en) AnnotationAssertion( "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) -AnnotationAssertion( "BFO:0000067") -AnnotationAssertion( "uberon") -AnnotationAssertion( "contains_process") -AnnotationAssertion( "contains_process") AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "contains process"@en) -AnnotationAssertion(rdfs:label "contains process") # Object Property: (results in fission of) @@ -1618,7 +1593,6 @@ AnnotationAssertion( "participates_in"@en) AnnotationAssertion( "RO:0000056") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "participates_in") AnnotationAssertion( "participates_in") AnnotationAssertion(rdfs:label "participates in"@en) @@ -1636,7 +1610,7 @@ AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion( "RO:0000057") AnnotationAssertion( "external") AnnotationAssertion( "has_participant") @@ -1700,12 +1674,7 @@ AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) AnnotationAssertion( "has_quality"@en) -AnnotationAssertion( "RO:0000086") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_quality") -AnnotationAssertion( "has_quality") AnnotationAssertion(rdfs:label "has quality"@en) -AnnotationAssertion(rdfs:label "has quality") SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -1740,7 +1709,7 @@ SubObjectPropertyOf( (has regulatory component activity) AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) AnnotationAssertion( "RO:0002013") AnnotationAssertion( "external") @@ -1753,7 +1722,7 @@ SubObjectPropertyOf( (has negative regulatory component activity) AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) AnnotationAssertion( "RO:0002014") AnnotationAssertion( "external") @@ -1767,7 +1736,7 @@ SubObjectPropertyOf( (has positive regulatory component activity) AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") AnnotationAssertion(rdfs:label "has positive regulatory component activity") @@ -1776,7 +1745,7 @@ SubObjectPropertyOf( (has component activity) -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") AnnotationAssertion(rdfs:label "has component activity") @@ -1785,7 +1754,7 @@ SubObjectPropertyOf( (has component process) AnnotationAssertion( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "has component process") SubObjectPropertyOf( ) @@ -1794,17 +1763,17 @@ ObjectPropertyRange( (directly regulated by) -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( "GOC:dos") rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") AnnotationAssertion(rdfs:label "directly regulated by") SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (directly negatively regulated by) -AnnotationAssertion(Annotation( "GOC:dos") "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") -AnnotationAssertion( "dos") +AnnotationAssertion(Annotation( ) "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "directly negatively regulated by") SubObjectPropertyOf( ) @@ -1812,8 +1781,8 @@ InverseObjectProperties( (directly positively regulated by) -AnnotationAssertion(Annotation( "GOC:dos") "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") -AnnotationAssertion( "dos") +AnnotationAssertion(Annotation( ) "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "directly positively regulated by") SubObjectPropertyOf( ) @@ -1821,14 +1790,35 @@ InverseObjectProperties( (has effector activity) -AnnotationAssertion(Annotation( "GOC:dos") "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") -AnnotationAssertion( "dos") +AnnotationAssertion(Annotation( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") AnnotationAssertion(rdfs:label "has effector activity") SubObjectPropertyOf( ) FunctionalObjectProperty() +# Object Property: (before or simultaneous with) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "<="@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Primitive instance level timing relation between events") +AnnotationAssertion(rdfs:label "before or simultaneous with"@en) +SubObjectPropertyOf( ) + +# Object Property: (simultaneous with) + +AnnotationAssertion( "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time.") +AnnotationAssertion( ) +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en) +AnnotationAssertion(rdfs:label "simultaneous with"@en) +SubObjectPropertyOf( ) +SymmetricObjectProperty() +TransitiveObjectProperty() + # Object Property: (ends after) AnnotationAssertion( "David Osumi-Sutherland") @@ -1844,7 +1834,6 @@ AnnotationAssertion( "starts_at_end_of") AnnotationAssertion( "RO:0002087") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) @@ -1878,7 +1867,6 @@ AnnotationAssertion( ) AnnotationAssertion( "RO:0002131") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "overlaps") AnnotationAssertion( ) AnnotationAssertion( ) @@ -1900,10 +1888,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002160") -AnnotationAssertion( "uberon") -AnnotationAssertion( "only_in_taxon") -AnnotationAssertion( "only_in_taxon") AnnotationAssertion(rdfs:label "only in taxon") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -1916,15 +1900,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002162") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_taxon") AnnotationAssertion( ) -AnnotationAssertion( "in_taxon") AnnotationAssertion(rdfs:comment "Connects a biological entity to its taxon of origin.") AnnotationAssertion(rdfs:label "in taxon") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (has component) @@ -1935,7 +1916,6 @@ AnnotationAssertion( ) AnnotationAssertion( "RO:0002180") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "has_component") AnnotationAssertion( ) AnnotationAssertion( "has_component") @@ -2023,7 +2003,6 @@ AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") AnnotationAssertion( "RO:0002215") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "capable_of") AnnotationAssertion( ) AnnotationAssertion( "capable_of") @@ -2040,7 +2019,6 @@ AnnotationAssertion( "has function in") AnnotationAssertion( "RO:0002216") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion(rdfs:label "capable of part of"@en) @@ -2069,13 +2047,8 @@ AnnotationAssertion( ) AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "Allen") -AnnotationAssertion( "RO:0002223") -AnnotationAssertion( "uberon") -AnnotationAssertion( "starts") AnnotationAssertion( ) -AnnotationAssertion( "starts") AnnotationAssertion(rdfs:label "starts"@en) -AnnotationAssertion(rdfs:label "starts") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -2090,7 +2063,6 @@ AnnotationAssertion( "started by") AnnotationAssertion( "RO:0002224") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "starts_with") AnnotationAssertion( ) AnnotationAssertion( "starts_with") @@ -2106,13 +2078,8 @@ AnnotationAssertion( "inverse of ends with") AnnotationAssertion( ) AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "RO:0002229") -AnnotationAssertion( "uberon") -AnnotationAssertion( "ends") AnnotationAssertion( ) -AnnotationAssertion( "ends") AnnotationAssertion(rdfs:label "ends"@en) -AnnotationAssertion(rdfs:label "ends") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -2126,7 +2093,6 @@ AnnotationAssertion( "finished by") AnnotationAssertion( "RO:0002230") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "ends_with") AnnotationAssertion( ) AnnotationAssertion( "ends_with") @@ -2186,6 +2152,7 @@ AnnotationAssertion( "has_input") AnnotationAssertion(rdfs:label "has input"@en) AnnotationAssertion(rdfs:label "has input") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -2206,6 +2173,7 @@ AnnotationAssertion( "has_output") AnnotationAssertion(rdfs:label "has output"@en) AnnotationAssertion(rdfs:label "has output") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -2225,7 +2193,7 @@ AnnotationAssertion( "affects") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (results in developmental progression of) @@ -2243,8 +2211,28 @@ AnnotationAssertion(rdfs:label "resu AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) - -# Object Property: (results in formation of) +ObjectPropertyRange( ) + +# Object Property: (results in development of) + +AnnotationAssertion( "every flower development (GO:0009908) results in development of some flower (PO:0009046)"@en) +AnnotationAssertion( ) +AnnotationAssertion( "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.") +AnnotationAssertion( ) +AnnotationAssertion( "http://www.geneontology.org/GO.doc.development.shtml"^^xsd:anyURI) +AnnotationAssertion( "RO:0002296") +AnnotationAssertion( "external") +AnnotationAssertion( "results_in_development_of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "results_in_development_of") +AnnotationAssertion(rdfs:label "results in development of"@en) +AnnotationAssertion(rdfs:label "results in development of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (results in formation of anatomical entity) AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") @@ -2258,7 +2246,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_formation_of") -AnnotationAssertion(rdfs:label "results in formation of"@en) +AnnotationAssertion(rdfs:label "results in formation of anatomical entity"@en) AnnotationAssertion(rdfs:label "results in formation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2277,6 +2265,7 @@ AnnotationAssertion( "causally_upstream_of,_positive_effect") AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2292,6 +2281,7 @@ AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of,_negative_effect") AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2307,6 +2297,25 @@ AnnotationAssertion(rdfs:label "char AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) +# Object Property: (results in acquisition of features of) + +AnnotationAssertion( "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.") +AnnotationAssertion( "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity") +AnnotationAssertion( ) +AnnotationAssertion( "GOC:mtg_berkeley_2013") +AnnotationAssertion( "RO:0002315") +AnnotationAssertion( "external") +AnnotationAssertion( "results_in_acquisition_of_features_of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "results_in_acquisition_of_features_of") +AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) +AnnotationAssertion(rdfs:label "results in acquisition of features of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + # Object Property: (evolutionarily related to) AnnotationAssertion( "A relationship that holds via some environmental process") @@ -2342,6 +2351,7 @@ AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enables"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -2350,12 +2360,7 @@ InverseObjectProperties( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") AnnotationAssertion( ) AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") -AnnotationAssertion( "RO:0002328") -AnnotationAssertion( "uberon") -AnnotationAssertion( "functionally_related_to") -AnnotationAssertion( "functionally_related_to") AnnotationAssertion(rdfs:label "functionally related to"@en) -AnnotationAssertion(rdfs:label "functionally related to") # Object Property: (part of structure that is capable of) @@ -2372,7 +2377,7 @@ AnnotationAssertion( "actively involved in") AnnotationAssertion( "enables part of") AnnotationAssertion(rdfs:label "involved in"@en) -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2382,6 +2387,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2483,14 +2489,9 @@ SubObjectPropertyOf( "inverse of has input") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002352") -AnnotationAssertion( "uberon") -AnnotationAssertion( "input_of") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "input_of") AnnotationAssertion(rdfs:label "input of"@en) -AnnotationAssertion(rdfs:label "input of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2500,7 +2501,6 @@ AnnotationAssertion( ) AnnotationAssertion( "RO:0002353") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "output_of") AnnotationAssertion( ) AnnotationAssertion( ) @@ -2552,6 +2552,7 @@ AnnotationAssertion( "indirectly activates") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -2563,6 +2564,7 @@ AnnotationAssertion( "indirectly inhibits") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -2687,12 +2689,13 @@ SubObjectPropertyOf( (is active in) AnnotationAssertion( "A protein that enables activity in a cytosol.") -AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dos") "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") +AnnotationAssertion(Annotation( ) Annotation( ) "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") AnnotationAssertion( ) AnnotationAssertion( "executes activity in") AnnotationAssertion( "enables activity in") AnnotationAssertion(rdfs:comment "") AnnotationAssertion(rdfs:label "is active in") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Is_active_in"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2801,14 +2804,58 @@ AnnotationAssertion(rdfs:label "rela ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (existence starts during) + +AnnotationAssertion( "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "existence starts during") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (existence starts with) + +AnnotationAssertion( "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "existence starts with") +SubObjectPropertyOf( ) + +# Object Property: (existence overlaps) + +AnnotationAssertion( "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") +AnnotationAssertion(rdfs:label "existence overlaps") +SubObjectPropertyOf( ) + +# Object Property: (existence ends during) + +AnnotationAssertion( "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") +AnnotationAssertion(rdfs:label "existence ends during") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (existence ends with) + +AnnotationAssertion( "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") +AnnotationAssertion(rdfs:label "existence ends with") +SubObjectPropertyOf( ) + +# Object Property: (existence starts during or after) + +AnnotationAssertion( "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") +AnnotationAssertion(rdfs:label "existence starts during or after") +SubObjectPropertyOf( ) + # Object Property: (existence ends during or before) AnnotationAssertion( "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002497") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_ends_during_or_before") -AnnotationAssertion( "existence_ends_during_or_before") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence ends during or before") SubObjectPropertyOf( ) @@ -3019,6 +3066,7 @@ AnnotationAssertion( ) AnnotationAssertion( "directly_positively_regulates") AnnotationAssertion(rdfs:label "directly positively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3036,6 +3084,7 @@ AnnotationAssertion( ) AnnotationAssertion( "directly_negatively_regulates") AnnotationAssertion(rdfs:label "directly negatively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3046,7 +3095,6 @@ AnnotationAssertion( ) AnnotationAssertion( "RO:0003000") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "produces") AnnotationAssertion( ) AnnotationAssertion( "produces") @@ -3064,7 +3112,6 @@ AnnotationAssertion( ) AnnotationAssertion( "RO:0003001") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "produced_by") AnnotationAssertion( ) AnnotationAssertion( "produced_by") @@ -3088,7 +3135,7 @@ SubObjectPropertyOf( (has primary output) -AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:kva") Annotation( "GOC:pt") Annotation(rdfs:comment "PMID:27812932") "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.") +AnnotationAssertion(Annotation( ) Annotation( "GOC:dph") Annotation( "GOC:kva") Annotation( "GOC:pt") Annotation(rdfs:comment "PMID:27812932") "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.") AnnotationAssertion( ) AnnotationAssertion( "2018-12-13T11:26:32Z"^^xsd:dateTime) AnnotationAssertion( "RO:0004008") @@ -3102,7 +3149,7 @@ SubObjectPropertyOf( (has primary input) -AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:kva") Annotation( "GOC:pt") Annotation(rdfs:comment "PMID:27812932") "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.") +AnnotationAssertion(Annotation( ) Annotation( "GOC:dph") Annotation( "GOC:kva") Annotation( "GOC:pt") Annotation(rdfs:comment "PMID:27812932") "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.") AnnotationAssertion( ) AnnotationAssertion( "2018-12-13T11:26:56Z"^^xsd:dateTime) AnnotationAssertion( "RO:0004009") @@ -3129,7 +3176,7 @@ AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (acts upstream of or within, negative effect) @@ -3139,6 +3186,7 @@ AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (acts upstream of, positive effect) @@ -3149,7 +3197,7 @@ AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3161,7 +3209,7 @@ AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3171,6 +3219,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (causally upstream of or within, positive effect) @@ -3179,6 +3228,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (regulates activity of) @@ -3190,25 +3240,10 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (results in fusion of) - -AnnotationAssertion( "pg") -AnnotationAssertion( "2021-02-26T07:28:29Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0012008") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_fusion_of") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "results_in_fusion_of") -AnnotationAssertion(rdfs:label "results in fusion of"@en) -AnnotationAssertion(rdfs:label "results in fusion of") -SubObjectPropertyOf( ) - # Object Property: (indirectly causally upstream of) AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion( "pg") +AnnotationAssertion( ) AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) SubObjectPropertyOf( ) @@ -3216,7 +3251,7 @@ SubObjectPropertyOf( (indirectly regulates) AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( "pg") +AnnotationAssertion( ) AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "indirectly regulates"@en) SubObjectPropertyOf( ) @@ -3265,7 +3300,7 @@ AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z") +AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) @@ -3383,7 +3418,8 @@ DisjointClasses( ObjectSomeValuesFro # Class: (independent continuant) -AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion( "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) AnnotationAssertion(rdfs:label "independent continuant"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -3391,7 +3427,8 @@ DisjointClasses( (process) -AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion( "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) @@ -3417,7 +3454,8 @@ SubClassOf( ObjectAllValuesFrom( (specifically dependent continuant) -AnnotationAssertion( "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -3426,8 +3464,7 @@ SubClassOf( ObjectAllValuesFrom( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) AnnotationAssertion(rdfs:label "role"@en) -EquivalentClasses( ) -SubClassOf( ) +SubClassOf( ) # Class: (function) @@ -3662,6 +3699,7 @@ AnnotationAssertion(rdfs:label "amm SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -3752,21 +3790,6 @@ AnnotationAssertion( "donor") SubClassOf( ) -# Class: (lipid) - -AnnotationAssertion( "'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.") -AnnotationAssertion( "CHEBI:14517") -AnnotationAssertion( "CHEBI:25054") -AnnotationAssertion( "CHEBI:6486") -AnnotationAssertion( "KEGG:C01356") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Lipid") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "lipids") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:18059") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "lipid") -SubClassOf( ) - # Class: (nucleobase) AnnotationAssertion( "That part of DNA or RNA that may be involved in pairing.") @@ -3867,6 +3890,23 @@ AnnotationAssertion( "base") SubClassOf( ) +# Class: (NMR chemical shift reference compound) + +AnnotationAssertion( "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift reference compounds") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift standards") +AnnotationAssertion(Annotation( "ChEBI") "NMR internal standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR internal standards") +AnnotationAssertion(Annotation( "ChEBI") "NMR reference standard") +AnnotationAssertion(Annotation( "ChEBI") "NMR reference standards") +AnnotationAssertion( "CHEBI:228364") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "NMR chemical shift reference compound") +SubClassOf( ) +SubClassOf( ) + # Class: (carbamoyl group) AnnotationAssertion( "The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.") @@ -3968,7 +4008,6 @@ AnnotationAssertion(Annotation( "CHEBI:24432") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "biological role") -SubClassOf( ) SubClassOf( ) # Class: (group) @@ -4266,6 +4305,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phosphoric acid") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -4591,7 +4631,6 @@ AnnotationAssertion( "CHEBI:33232") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "application") -SubClassOf( ) SubClassOf( ) # Class: (fundamental particle) @@ -5238,8 +5277,15 @@ SubClassOf( ObjectSomeValuesFrom( (alpha-amino-acid residue) +AnnotationAssertion( "An amino-acid residue derived from an alpha-amino acid.") +AnnotationAssertion( "0") +AnnotationAssertion( "C2H2NOR") +AnnotationAssertion( "56.043") +AnnotationAssertion( "56.01364") +AnnotationAssertion( "*-NC([*])C(-*)=O") AnnotationAssertion( "chebi_ontology") AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid residues") +AnnotationAssertion(Annotation( "UniProt") "an alpha-amino acid residue") AnnotationAssertion( "CHEBI:33710") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alpha-amino-acid residue") @@ -6068,7 +6114,7 @@ AnnotationAssertion( "CHEBI:50906") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "role") -SubClassOf( ) +SubClassOf( ) # Class: (neurotoxin) @@ -6096,7 +6142,6 @@ AnnotationAssertion( "CHEBI:51086") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chemical role") -SubClassOf( ) SubClassOf( ) # Class: (nitrogen molecular entity) @@ -6602,6 +6647,7 @@ AnnotationAssertion( "VHOG:0001533") AnnotationAssertion( "WBbt:0004017") AnnotationAssertion( "XAO:0003012") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).") AnnotationAssertion(rdfs:label "cell") @@ -6610,27 +6656,112 @@ SubClassOf( ObjectSomeValuesFrom( ) DisjointClasses( ) +# Class: (secretory cell) + +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A cell that specializes in controlled release of one or more substances.") +AnnotationAssertion( "BTO:0003659") +AnnotationAssertion( "FMA:86916") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "secretory cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein secreting cell) + +AnnotationAssertion(rdfs:label "protein secreting cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anucleate cell) + +AnnotationAssertion(Annotation( "FB:ma") "A cell that lacks a nucleus.") +AnnotationAssertion( "FMA:68647") +AnnotationAssertion( "non-nucleated cell") +AnnotationAssertion(rdfs:label "anucleate cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (single nucleate cell) + +AnnotationAssertion(Annotation( "FB:ma") Annotation( "GOC:tfm") "A cell with a single nucleus.") +AnnotationAssertion(rdfs:label "single nucleate cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (binucleate cell) + +AnnotationAssertion(rdfs:label "binucleate cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (multinucleate cell) + +AnnotationAssertion(Annotation( "FB:ma") "A cell with more than one nucleus.") +AnnotationAssertion( "AEO:0000203") +AnnotationAssertion( "WBbt:0008074") +AnnotationAssertion( "syncitium") +AnnotationAssertion( "syncytial cell") +AnnotationAssertion( "syncytium") +AnnotationAssertion(rdfs:label "multinucleate cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (eukaryotic cell) + +AnnotationAssertion( "MESH:D005057") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "eukaryotic cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (fungal cell) + +AnnotationAssertion(rdfs:label "fungal cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (abnormal cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:cg") Annotation( "GOC:wdd") "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models.") AnnotationAssertion( ) AnnotationAssertion( "2017-01-30T18:53:32Z"^^xsd:dateTime) AnnotationAssertion( "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "https://github.com/obophenotype/cell-ontology/issues/448") AnnotationAssertion(rdfs:label "abnormal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (increased nucleus size) +# Class: (nucleate cell) -AnnotationAssertion(Annotation( "GOC:tfm") "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.") -AnnotationAssertion( ) -AnnotationAssertion( "2009-12-23T10:53:24Z") -AnnotationAssertion(rdfs:label "increased nucleus size") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(Annotation( "GOC:tfm") "A cell containing at least one nucleus.") +AnnotationAssertion( ) +AnnotationAssertion( "2010-09-07T03:32:33Z") +AnnotationAssertion( "FMA:67513") +AnnotationAssertion(rdfs:label "nucleate cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (precursor cell) + +AnnotationAssertion(Annotation( "GOC:dos") "A cell that, by division or terminal differentiation, can give rise to other cell types.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.") +AnnotationAssertion(rdfs:label "precursor cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (reproduction) @@ -6661,33 +6792,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (nuclear membrane fusion) - -AnnotationAssertion(Annotation( "GOC:elh") "The joining of 2 or more lipid bilayer membranes that surround the nucleus.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0000740") -AnnotationAssertion(rdfs:label "nuclear membrane fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (karyogamy) - -AnnotationAssertion(Annotation( "GOC:elh") "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei.") -AnnotationAssertion( "GO:0007335") -AnnotationAssertion( "Wikipedia:Karyogamy") -AnnotationAssertion( "nuclear fusion") -AnnotationAssertion( "nuclear fusion during karyogamy") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0000741") -AnnotationAssertion(rdfs:label "karyogamy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (formation of translation initiation ternary complex) AnnotationAssertion(Annotation( "GOC:hjd") "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).") @@ -6700,6 +6804,16 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (embryonic development via the syncytial blastoderm) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:mtg_sensu") "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0001700") +AnnotationAssertion(rdfs:label "embryonic development via the syncytial blastoderm") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + # Class: (peptide secretion) AnnotationAssertion(Annotation( "GOC:add") "The controlled release of a peptide from a cell or a tissue.") @@ -6752,6 +6866,18 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (developmental process involved in reproduction) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:isa_complete") "A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring.") +AnnotationAssertion(Annotation( "GOC:dph") "puberty") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "reproductive developmental process") +AnnotationAssertion( "GO:0003006") +AnnotationAssertion(rdfs:label "developmental process involved in reproduction") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (molecular_function) AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") @@ -6765,7 +6891,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") AnnotationAssertion(rdfs:label "molecular_function") SubClassOf( ) DisjointClasses( ) @@ -6788,57 +6914,10 @@ AnnotationAssertion( "catalytic activity") SubClassOf( ) -# Class: (transporter activity) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dgf") "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.") -AnnotationAssertion( "GO:0005478") -AnnotationAssertion(Annotation(rdfs:label "Virion-associated M2 protein mediated ion infusion") "Reactome:R-HSA-168313") -AnnotationAssertion(Annotation(rdfs:label "SMAD7:SMURF1 complex is exported to the cytosol") "Reactome:R-HSA-178215") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "carrier") -AnnotationAssertion( "GO:0005215") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.") -AnnotationAssertion(rdfs:label "transporter activity") -SubClassOf( ) - -# Class: (lipid transporter activity) - -AnnotationAssertion(Annotation( "GOC:ai") "Enables the directed movement of lipids into, out of or within a cell, or between cells.") -AnnotationAssertion(Annotation(rdfs:label "ABCAs mediate lipid efflux") "Reactome:R-HSA-1369028") -AnnotationAssertion(Annotation(rdfs:label "ABCAs mediate lipid influx") "Reactome:R-HSA-1369052") -AnnotationAssertion(Annotation(rdfs:label "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex") "Reactome:R-HSA-174786") -AnnotationAssertion(Annotation(rdfs:label "ABCA12 transports lipids from cytosol to extracellular region") "Reactome:R-HSA-5682285") -AnnotationAssertion(Annotation(rdfs:label "Defective ABCA12 does not transport lipids from cytosol to extracellular region") "Reactome:R-HSA-5682311") -AnnotationAssertion(Annotation(rdfs:label "Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body") "Reactome:R-HSA-5683672") -AnnotationAssertion(Annotation(rdfs:label "ABCA3 transports PC, PG from ER membrane to lamellar body") "Reactome:R-HSA-5683714") -AnnotationAssertion(Annotation(rdfs:label "Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body") "Reactome:R-HSA-5688397") -AnnotationAssertion(Annotation(rdfs:label "TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane") "Reactome:R-HSA-6801250") -AnnotationAssertion(Annotation(rdfs:label "ABCA5 transports CHOL from lysosomal lumen to cytosol") "Reactome:R-HSA-8848053") -AnnotationAssertion(Annotation(rdfs:label "MTTP lipidates APOB-100, forming a pre-VLDL") "Reactome:R-HSA-8866329") -AnnotationAssertion( "lipophorin") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "apolipoprotein") -AnnotationAssertion( "GO:0005319") -AnnotationAssertion(rdfs:label "lipid transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (cellular_component) -AnnotationAssertion(Annotation( "GOC:pdt") Annotation( "NIF_Subcellular:sao1337158144") "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).") +AnnotationAssertion(Annotation( "GOC:pdt") "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17729"^^xsd:anyURI) AnnotationAssertion( "GO:0008372") AnnotationAssertion( "NIF_Subcellular:sao1337158144") AnnotationAssertion( "cell or subcellular entity") @@ -6852,7 +6931,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") AnnotationAssertion(rdfs:label "cellular_component") SubClassOf( ) DisjointClasses( ) @@ -6873,8 +6952,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.") AnnotationAssertion(rdfs:label "extracellular region") SubClassOf( ) @@ -6953,8 +7032,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cytoplasm") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -7007,8 +7086,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "plasma membrane") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -7016,7 +7095,9 @@ SubClassOf( ObjectSomeValuesFrom( (cell cortex) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0815316194") "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26298"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Cell_cortex") +AnnotationAssertion( "ectoplasm") AnnotationAssertion( "cellular_component") AnnotationAssertion( "cell periphery") AnnotationAssertion( "peripheral cytoplasm") @@ -7064,22 +7145,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (RNA catabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.") -AnnotationAssertion( "RNA breakdown") -AnnotationAssertion( "RNA catabolism") -AnnotationAssertion( "RNA degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006401") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "RNA catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (RNA localization) AnnotationAssertion(Annotation( "GOC:ai") "A process in which RNA is transported to, or maintained in, a specific location.") @@ -7112,7 +7177,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "translation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -7182,9 +7247,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of translation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -7249,14 +7312,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cellular amino acid metabolic process) @@ -7271,31 +7333,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (lipid metabolic process) - -AnnotationAssertion(Annotation( "GOC:ma") "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.") -AnnotationAssertion( "Wikipedia:Lipid_metabolism") -AnnotationAssertion( "lipid metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006629") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "lipid metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (cellular aromatic compound metabolic process) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.") @@ -7337,9 +7374,11 @@ SubClassOf( ObjectSomeValuesFrom( (nitrogen compound metabolic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "nitrogen compound metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006807") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nitrogen compound metabolic process") @@ -7365,7 +7404,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.") AnnotationAssertion(rdfs:label "transport") SubClassOf( ) @@ -7415,20 +7454,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (lipid transport) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006869") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "lipid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (intracellular protein transport) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.") @@ -7437,87 +7462,13 @@ AnnotationAssertion( "GOC:al") "copper-induced intracellular protein transport") AnnotationAssertion( "GO:0006886") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intracellular protein transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (exocytosis) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0716731363") Annotation( "PMID:22323285") "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.") -AnnotationAssertion( "GO:0016194") -AnnotationAssertion( "GO:0016195") -AnnotationAssertion( "Wikipedia:Exocytosis") -AnnotationAssertion( "vesicle exocytosis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "nonselective vesicle exocytosis") -AnnotationAssertion( "GO:0006887") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "exocytosis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (endocytosis) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0198506732") Annotation( "ISBN:0716731363") Annotation( "Wikipedia:Endocytosis") "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24907"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25268"^^xsd:anyURI) -AnnotationAssertion( "GO:0016193") -AnnotationAssertion( "GO:0016196") -AnnotationAssertion( "GO:0098701") -AnnotationAssertion( "Wikipedia:Endocytosis") -AnnotationAssertion( "endocytic import into cell") -AnnotationAssertion( "vesicle endocytosis") -AnnotationAssertion( "plasma membrane invagination") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "nonselective vesicle endocytosis") -AnnotationAssertion( "GO:0006897") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "endocytosis") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (vesicle budding from membrane) - -AnnotationAssertion(Annotation( "GOC:jid") Annotation( "GOC:tb") "The evagination of a membrane, resulting in formation of a vesicle.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2013-12-19T15:26:17Z") -AnnotationAssertion( "GO:0006902") -AnnotationAssertion( "GO:1902591") -AnnotationAssertion( "membrane evagination") -AnnotationAssertion( "vesicle biosynthesis") -AnnotationAssertion( "vesicle formation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "nonselective vesicle assembly") -AnnotationAssertion(Annotation( "GOC:TermGenie") "single organism membrane budding") -AnnotationAssertion( "single-organism membrane budding") -AnnotationAssertion( "vesicle budding") -AnnotationAssertion( "GO:0006900") -AnnotationAssertion(rdfs:label "vesicle budding from membrane") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (vesicle fusion) - -AnnotationAssertion(Annotation( "GOC:jid") "Fusion of the membrane of a transport vesicle with its target membrane.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006906") -AnnotationAssertion(rdfs:label "vesicle fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organelle organization) AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") @@ -7627,20 +7578,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (protein catabolic process in the vacuole) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:vw") "The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "vacuolar protein breakdown") -AnnotationAssertion( "vacuolar protein catabolic process") -AnnotationAssertion( "vacuolar protein catabolism") -AnnotationAssertion( "vacuolar protein degradation") -AnnotationAssertion( "GO:0007039") -AnnotationAssertion(rdfs:label "protein catabolic process in the vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (cell cycle) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:mtg_cell_cycle") "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.") @@ -7680,6 +7617,22 @@ SubClassOf( ) SubClassOf( ) +# Class: (multicellular organism development) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:ems") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21234"^^xsd:anyURI) +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0007275") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term was 'developmental process'.") +AnnotationAssertion(rdfs:label "multicellular organism development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (protein localization) AnnotationAssertion(Annotation( "GOC:ai") "Any process in which a protein is transported to, or maintained in, a specific location.") @@ -7726,7 +7679,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") AnnotationAssertion(rdfs:label "biological_process") SubClassOf( ) @@ -7791,6 +7744,8 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) @@ -7809,25 +7764,11 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (lipid biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.") -AnnotationAssertion( "lipid anabolism") -AnnotationAssertion( "lipid biosynthesis") -AnnotationAssertion( "lipid formation") -AnnotationAssertion( "lipid synthesis") -AnnotationAssertion(Annotation( "GOC:sl") "lipogenesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0008610") -AnnotationAssertion(rdfs:label "lipid biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (amino acid biosynthetic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.") @@ -7842,54 +7783,10 @@ AnnotationAssertion( "GO:0008652") AnnotationAssertion(rdfs:label "amino acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (catabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-10-17T15:52:35Z") -AnnotationAssertion( "GO:0044243") -AnnotationAssertion( "GO:0044712") -AnnotationAssertion( "Wikipedia:Catabolism") -AnnotationAssertion( "breakdown") -AnnotationAssertion( "catabolism") -AnnotationAssertion( "degradation") -AnnotationAssertion( "multicellular organismal catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "single-organism catabolic process") -AnnotationAssertion( "GO:0009056") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "catabolic process") -SubClassOf( ) - -# Class: (macromolecule catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") -AnnotationAssertion( "GO:0043285") -AnnotationAssertion( "GO:0044266") -AnnotationAssertion(Annotation( "GOC:mtg_chebi_dec09") "biopolymer catabolic process") -AnnotationAssertion( "macromolecule breakdown") -AnnotationAssertion( "macromolecule catabolism") -AnnotationAssertion( "macromolecule degradation") -AnnotationAssertion( "multicellular organismal macromolecule catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "cellular macromolecule catabolic process") -AnnotationAssertion( "cellular macromolecule catabolism") -AnnotationAssertion( "cellular macromolecule degradation") -AnnotationAssertion( "GO:0009057") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "macromolecule catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (biosynthetic process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.") @@ -7915,7 +7812,8 @@ SubClassOf( (macromolecule biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") -AnnotationAssertion( "http://amigo.geneontology.org/amigo/term/GO:0070589"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15249"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25418"^^xsd:anyURI) AnnotationAssertion( "GO:0043284") AnnotationAssertion(Annotation( "GOC:mtg_chebi_dec09") "biopolymer biosynthetic process") AnnotationAssertion( "macromolecule anabolism") @@ -7928,26 +7826,10 @@ AnnotationAssertion( "macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (amino acid catabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17904"^^xsd:anyURI) -AnnotationAssertion( "amino acid breakdown") -AnnotationAssertion( "amino acid catabolism") -AnnotationAssertion( "amino acid degradation") -AnnotationAssertion( "cellular amino acid catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0009063") -AnnotationAssertion(rdfs:label "amino acid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (nucleobase metabolic process) AnnotationAssertion(Annotation( "GOC:ma") "The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.") @@ -8009,19 +7891,44 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (amine catabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.") -AnnotationAssertion( "amine breakdown") -AnnotationAssertion( "amine catabolism") -AnnotationAssertion( "amine degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0009310") -AnnotationAssertion(rdfs:label "amine catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (embryo development) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") Annotation( "GOC:mtg_sensu") "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.") +AnnotationAssertion( "GO:0009795") +AnnotationAssertion( "embryogenesis and morphogenesis") +AnnotationAssertion( "Wikipedia:Embryogenesis") +AnnotationAssertion( "embryogenesis") +AnnotationAssertion( "embryonal development") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009790") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "embryo development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (post-embryonic development) + +AnnotationAssertion(Annotation( "GOC:go_curators") "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009791") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "post-embryonic development") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (embryo development ending in birth or egg hatching) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") Annotation( "GOC:mtg_sensu") "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.") +AnnotationAssertion( "embryogenesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009792") +AnnotationAssertion(rdfs:label "embryo development ending in birth or egg hatching") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (regulation of biosynthetic process) @@ -8118,56 +8025,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances.") -AnnotationAssertion( "regulation of breakdown") -AnnotationAssertion( "regulation of catabolism") -AnnotationAssertion( "regulation of degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0009894") -AnnotationAssertion(rdfs:label "regulation of catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.") -AnnotationAssertion( "down regulation of catabolic process") -AnnotationAssertion( "down-regulation of catabolic process") -AnnotationAssertion( "downregulation of catabolic process") -AnnotationAssertion( "negative regulation of breakdown") -AnnotationAssertion( "negative regulation of catabolism") -AnnotationAssertion( "negative regulation of degradation") -AnnotationAssertion( "inhibition of catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0009895") -AnnotationAssertion(rdfs:label "negative regulation of catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.") -AnnotationAssertion( "positive regulation of breakdown") -AnnotationAssertion( "positive regulation of catabolism") -AnnotationAssertion( "positive regulation of degradation") -AnnotationAssertion( "up regulation of catabolic process") -AnnotationAssertion( "up-regulation of catabolic process") -AnnotationAssertion( "upregulation of catabolic process") -AnnotationAssertion( "activation of catabolic process") -AnnotationAssertion( "stimulation of catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0009896") -AnnotationAssertion(rdfs:label "positive regulation of catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (cellular process) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.") @@ -8201,29 +8058,17 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (membrane invagination) - -AnnotationAssertion(Annotation( "GOC:tb") "The infolding of a membrane.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2013-12-02T13:58:34Z") -AnnotationAssertion( "GO:1902534") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "single-organism membrane invagination") -AnnotationAssertion( "GO:0010324") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "membrane invagination") -SubClassOf( ) - # Class: (gene expression) -AnnotationAssertion(Annotation( "GOC:txnOH-2018") Annotation( "PMID:25934543") Annotation( "PMID:31580950") "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.") +AnnotationAssertion(Annotation( "GOC:txnOH-2018") Annotation( "PMID:25934543") Annotation( "PMID:31580950") "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22557"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25419"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Gene_expression") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010467") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gene expression") -SubClassOf( ) +SubClassOf( ) # Class: (regulation of gene expression) @@ -8238,7 +8083,7 @@ AnnotationAssertion( "This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.") AnnotationAssertion(rdfs:label "regulation of gene expression") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of membrane disassembly) @@ -8258,7 +8103,7 @@ AnnotationAssertion( "GO:0010556") AnnotationAssertion(rdfs:label "regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -8269,9 +8114,9 @@ AnnotationAssertion( "GO:0010557") AnnotationAssertion(rdfs:label "positive regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of macromolecule biosynthetic process) @@ -8281,9 +8126,9 @@ AnnotationAssertion( "GO:0010558") AnnotationAssertion(rdfs:label "negative regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of phosphorus metabolic process) @@ -8340,17 +8185,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of ketone catabolic process) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010567") -AnnotationAssertion(rdfs:label "regulation of ketone catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (positive regulation of macromolecule metabolic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") @@ -8391,7 +8225,7 @@ AnnotationAssertion( "positive regulation of gene expression") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of gene expression) @@ -8405,7 +8239,7 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "negative regulation of gene expression") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of organelle organization) @@ -8434,16 +8268,27 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (lipid localization) +# Class: (positive regulation of cell development) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0010720") +AnnotationAssertion(rdfs:label "positive regulation of cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process in which a lipid is transported to, or maintained in, a specific location.") -AnnotationAssertion(Annotation( "GOC:mah") "lipid localisation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010876") -AnnotationAssertion(rdfs:label "lipid localization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of cell development) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0010721") +AnnotationAssertion(rdfs:label "negative regulation of cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cell cycle process) @@ -8485,17 +8330,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (vesicle membrane) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:vesicle") "The lipid bilayer surrounding any membrane-bounded vesicle in the cell.") -AnnotationAssertion( "NIF_Subcellular:sao1153182838") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0012506") -AnnotationAssertion(rdfs:label "vesicle membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (protein transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") @@ -8621,26 +8455,6 @@ AnnotationAssertion( "membrane") SubClassOf( ) -# Class: (lipid catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.") -AnnotationAssertion( "GO:0006724") -AnnotationAssertion( "GO:0044240") -AnnotationAssertion( "Wikipedia:Lipid_catabolism") -AnnotationAssertion( "lipid breakdown") -AnnotationAssertion( "lipid catabolism") -AnnotationAssertion( "lipid degradation") -AnnotationAssertion( "lipolysis") -AnnotationAssertion( "multicellular organism lipid catabolic process") -AnnotationAssertion( "multicellular organismal lipid catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0016042") -AnnotationAssertion(rdfs:label "lipid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (cellular component organization) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:jl") Annotation( "GOC:mah") "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.") @@ -8663,20 +8477,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (vesicle organization) - -AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.") -AnnotationAssertion( "vesicle organisation") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:mah") "vesicle organization and biogenesis") -AnnotationAssertion( "GO:0016050") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "vesicle organization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organic acid biosynthetic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage.") @@ -8694,22 +8494,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (organic acid catabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage.") -AnnotationAssertion( "organic acid breakdown") -AnnotationAssertion( "organic acid catabolism") -AnnotationAssertion( "organic acid degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0016054") -AnnotationAssertion(rdfs:label "organic acid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (RNA metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.") @@ -8720,34 +8504,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "RNA metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (vesicle-mediated transport) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:mah") Annotation( "ISBN:08789310662000") "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.") -AnnotationAssertion( "GO:0006899") -AnnotationAssertion( "vesicle transport") -AnnotationAssertion(Annotation( "GOC:mah") "vesicular transport") -AnnotationAssertion( "nonselective vesicle transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "protein sorting along secretory pathway") -AnnotationAssertion( "vesicle trafficking") -AnnotationAssertion( "GO:0016192") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "vesicle-mediated transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (kinase activity) AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") @@ -8795,8 +8557,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "transferase activity") SubClassOf( ) @@ -8831,24 +8593,11 @@ AnnotationAssertion( "negative regulation of translation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of exocytosis) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of exocytosis.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0017157") -AnnotationAssertion(rdfs:label "regulation of exocytosis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (heterocycle biosynthetic process) AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") @@ -8864,17 +8613,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of lipid metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.") -AnnotationAssertion( "regulation of lipid metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0019216") -AnnotationAssertion(rdfs:label "regulation of lipid metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of nucleobase-containing compound metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.") @@ -8932,22 +8670,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (aromatic compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.") -AnnotationAssertion( "aromatic compound breakdown") -AnnotationAssertion( "aromatic compound catabolism") -AnnotationAssertion( "aromatic compound degradation") -AnnotationAssertion( "aromatic hydrocarbon catabolic process") -AnnotationAssertion( "aromatic hydrocarbon catabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0019439") -AnnotationAssertion(rdfs:label "aromatic compound catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (protein metabolic process) AnnotationAssertion(Annotation( "GOC:ma") "The chemical reactions and pathways involving a protein. Includes protein modification.") @@ -9092,63 +8814,23 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of endocytosis) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of endocytosis.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0030100") -AnnotationAssertion(rdfs:label "regulation of endocytosis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (transport vesicle) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:22160157") "Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.") -AnnotationAssertion( "NIF_Subcellular:sao885490876") -AnnotationAssertion( "constitutive secretory pathway transport vesicle") -AnnotationAssertion( "Golgi to vacuole transport vesicle") -AnnotationAssertion( "Golgi-vacuole transport vesicle") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "secretory vesicle") -AnnotationAssertion( "GO:0030133") -AnnotationAssertion(rdfs:comment "Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'.") -AnnotationAssertion(rdfs:label "transport vesicle") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (protein catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "GO:0044254") -AnnotationAssertion( "GO:0044257") -AnnotationAssertion( "Wikipedia:Protein_catabolism") -AnnotationAssertion( "cellular protein breakdown") -AnnotationAssertion( "cellular protein catabolic process") -AnnotationAssertion( "cellular protein catabolism") -AnnotationAssertion( "cellular protein degradation") -AnnotationAssertion( "protein breakdown") -AnnotationAssertion( "protein catabolism") -AnnotationAssertion( "protein degradation") -AnnotationAssertion( "multicellular organismal protein catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "pheromone catabolic process") -AnnotationAssertion( "pheromone catabolism") -AnnotationAssertion( "GO:0030163") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children.") -AnnotationAssertion(rdfs:label "protein catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (cell differentiation) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24390"^^xsd:anyURI) +AnnotationAssertion( "Wikipedia:Cellular_differentiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0030154") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (membrane disassembly) @@ -9164,16 +8846,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (cytoplasmic vesicle membrane) - -AnnotationAssertion(Annotation( "GOC:mah") "The lipid bilayer surrounding a cytoplasmic vesicle.") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0030659") -AnnotationAssertion(rdfs:label "cytoplasmic vesicle membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organelle membrane) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:mah") "A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.") @@ -9292,59 +8964,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "regulation of cellular breakdown") -AnnotationAssertion( "regulation of cellular catabolism") -AnnotationAssertion( "regulation of cellular degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031329") -AnnotationAssertion(rdfs:label "regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "down regulation of cellular catabolic process") -AnnotationAssertion( "down-regulation of cellular catabolic process") -AnnotationAssertion( "downregulation of cellular catabolic process") -AnnotationAssertion( "negative regulation of cellular breakdown") -AnnotationAssertion( "negative regulation of cellular catabolism") -AnnotationAssertion( "negative regulation of cellular degradation") -AnnotationAssertion( "inhibition of cellular catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031330") -AnnotationAssertion(rdfs:label "negative regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "positive regulation of cellular breakdown") -AnnotationAssertion( "positive regulation of cellular catabolism") -AnnotationAssertion( "positive regulation of cellular degradation") -AnnotationAssertion( "up regulation of cellular catabolic process") -AnnotationAssertion( "up-regulation of cellular catabolic process") -AnnotationAssertion( "upregulation of cellular catabolic process") -AnnotationAssertion( "activation of cellular catabolic process") -AnnotationAssertion( "stimulation of cellular catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031331") -AnnotationAssertion(rdfs:label "positive regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (negative regulation of protein-containing complex assembly) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.") @@ -9379,71 +8998,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of vesicle fusion) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of vesicle fusion.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031338") -AnnotationAssertion(rdfs:label "regulation of vesicle fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of vesicle fusion) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion.") -AnnotationAssertion( "down regulation of vesicle fusion") -AnnotationAssertion( "down-regulation of vesicle fusion") -AnnotationAssertion( "downregulation of vesicle fusion") -AnnotationAssertion( "inhibition of vesicle fusion") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031339") -AnnotationAssertion(rdfs:label "negative regulation of vesicle fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of vesicle fusion) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of vesicle fusion.") -AnnotationAssertion( "up regulation of vesicle fusion") -AnnotationAssertion( "up-regulation of vesicle fusion") -AnnotationAssertion( "upregulation of vesicle fusion") -AnnotationAssertion( "activation of vesicle fusion") -AnnotationAssertion( "stimulation of vesicle fusion") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031340") -AnnotationAssertion(rdfs:label "positive regulation of vesicle fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (cytoplasmic vesicle) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:mah") Annotation( "GOC:vesicles") "A vesicle found in the cytoplasm of a cell.") -AnnotationAssertion( "GO:0016023") -AnnotationAssertion( "NIF_Subcellular:sao180601769") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "cytoplasmic membrane bounded vesicle") -AnnotationAssertion( "cytoplasmic membrane-enclosed vesicle") -AnnotationAssertion( "cytoplasmic, membrane-bounded vesicle") -AnnotationAssertion( "GO:0031410") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cytoplasmic vesicle") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (protein-containing complex localization) AnnotationAssertion(Annotation( "GOC:mah") "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.") @@ -9494,20 +9048,6 @@ AnnotationAssertion(rdfs:label "enve SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (vesicle) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:pz") Annotation( "GOC:vesicles") "Any small, fluid-filled, spherical organelle enclosed by membrane.") -AnnotationAssertion( "GO:0031988") -AnnotationAssertion( "NIF_Subcellular:sao221389602") -AnnotationAssertion( "Wikipedia:Vesicle_(biology)") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "membrane-bounded vesicle") -AnnotationAssertion( "membrane-enclosed vesicle") -AnnotationAssertion( "GO:0031982") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "vesicle") -SubClassOf( ) - # Class: (regulation of nucleobase-containing compound transport) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") @@ -9552,104 +9092,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (intracellular lipid transport) - -AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of lipids within cells.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032365") -AnnotationAssertion(rdfs:label "intracellular lipid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - -# Class: (regulation of lipid transport) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032368") -AnnotationAssertion(rdfs:label "regulation of lipid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of lipid transport) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "down regulation of lipid transport") -AnnotationAssertion( "down-regulation of lipid transport") -AnnotationAssertion( "downregulation of lipid transport") -AnnotationAssertion( "inhibition of lipid transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032369") -AnnotationAssertion(rdfs:label "negative regulation of lipid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of lipid transport) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "up regulation of lipid transport") -AnnotationAssertion( "up-regulation of lipid transport") -AnnotationAssertion( "upregulation of lipid transport") -AnnotationAssertion( "activation of lipid transport") -AnnotationAssertion( "stimulation of lipid transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032370") -AnnotationAssertion(rdfs:label "positive regulation of lipid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (regulation of intracellular lipid transport) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032377") -AnnotationAssertion(rdfs:label "regulation of intracellular lipid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of intracellular lipid transport) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells.") -AnnotationAssertion( "down regulation of intracellular lipid transport") -AnnotationAssertion( "down-regulation of intracellular lipid transport") -AnnotationAssertion( "downregulation of intracellular lipid transport") -AnnotationAssertion( "inhibition of intracellular lipid transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032378") -AnnotationAssertion(rdfs:label "negative regulation of intracellular lipid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of intracellular lipid transport) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells.") -AnnotationAssertion( "up regulation of intracellular lipid transport") -AnnotationAssertion( "up-regulation of intracellular lipid transport") -AnnotationAssertion( "upregulation of intracellular lipid transport") -AnnotationAssertion( "activation of intracellular lipid transport") -AnnotationAssertion( "stimulation of intracellular lipid transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032379") -AnnotationAssertion(rdfs:label "positive regulation of intracellular lipid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of intracellular transport) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the directed movement of substances within cells.") @@ -9694,51 +9136,53 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of transporter activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the activity of a transporter.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032409") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of transporter activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops or reduces the activity of a transporter.") -AnnotationAssertion( "down regulation of transporter activity") -AnnotationAssertion( "down-regulation of transporter activity") -AnnotationAssertion( "downregulation of transporter activity") -AnnotationAssertion( "inhibition of transporter activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032410") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of transporter activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the activity of a transporter.") -AnnotationAssertion( "up regulation of transporter activity") -AnnotationAssertion( "up-regulation of transporter activity") -AnnotationAssertion( "upregulation of transporter activity") -AnnotationAssertion( "activation of transporter activity") -AnnotationAssertion( "stimulation of transporter activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032411") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (multicellular organismal process) + +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T16:07:47Z") +AnnotationAssertion( "GO:0044707") +AnnotationAssertion( "GO:0050874") +AnnotationAssertion( "organismal physiological process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single-multicellular organism process") +AnnotationAssertion( "GO:0032501") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "multicellular organismal process") +SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (developmental process) + +AnnotationAssertion(Annotation( "GOC:isa_complete") "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-12-19T12:21:31Z") +AnnotationAssertion( "GO:0044767") +AnnotationAssertion( "development") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single-organism developmental process") +AnnotationAssertion( "GO:0032502") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "developmental process") +SubClassOf( ) # Class: (protein transport within lipid bilayer) @@ -9771,22 +9215,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.") AnnotationAssertion(rdfs:label "RNA biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of karyogamy) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032871") -AnnotationAssertion(rdfs:label "regulation of karyogamy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of localization) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.") @@ -9996,52 +9430,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of amine catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.") -AnnotationAssertion( "regulation of amine breakdown") -AnnotationAssertion( "regulation of amine catabolism") -AnnotationAssertion( "regulation of amine degradation") -AnnotationAssertion( "regulation of cellular amine catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0033241") -AnnotationAssertion(rdfs:label "regulation of amine catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of amine catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.") -AnnotationAssertion( "negative regulation of amine breakdown") -AnnotationAssertion( "negative regulation of amine catabolism") -AnnotationAssertion( "negative regulation of amine degradation") -AnnotationAssertion( "negative regulation of cellular amine catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0033242") -AnnotationAssertion(rdfs:label "negative regulation of amine catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of amine catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.") -AnnotationAssertion( "positive regulation of amine breakdown") -AnnotationAssertion( "positive regulation of amine catabolism") -AnnotationAssertion( "positive regulation of amine degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0033243") -AnnotationAssertion(rdfs:label "positive regulation of amine catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (protein localization to organelle) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a protein is transported to, or maintained in, a location within an organelle.") @@ -10064,7 +9452,7 @@ AnnotationAssertion( "kinase inhibitor") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033673") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10082,7 +9470,7 @@ AnnotationAssertion( "stimulation of kinase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033674") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10128,53 +9516,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of amide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.") -AnnotationAssertion( "regulation of amide breakdown") -AnnotationAssertion( "regulation of amide catabolism") -AnnotationAssertion( "regulation of amide degradation") -AnnotationAssertion( "regulation of cellular amide catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0034251") -AnnotationAssertion(rdfs:label "regulation of amide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of amide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.") -AnnotationAssertion( "negative regulation of amide breakdown") -AnnotationAssertion( "negative regulation of amide catabolism") -AnnotationAssertion( "negative regulation of cellular amide catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "negative regulation of amide degradation") -AnnotationAssertion( "GO:0034252") -AnnotationAssertion(rdfs:label "negative regulation of amide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of amide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.") -AnnotationAssertion( "positive regulation of amide breakdown") -AnnotationAssertion( "positive regulation of amide catabolism") -AnnotationAssertion( "positive regulation of cellular amide catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "positive regulation of amide degradation") -AnnotationAssertion( "GO:0034253") -AnnotationAssertion(rdfs:label "positive regulation of amide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (protein localization to nucleus) AnnotationAssertion(Annotation( "GOC:ecd") "A process in which a protein transports or maintains the localization of another protein to the nucleus.") @@ -10194,9 +9535,11 @@ SubClassOf( ObjectSomeValuesFrom( (cellular nitrogen compound metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "cellular nitrogen compound metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0034641") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular nitrogen compound metabolic process") SubClassOf( ) @@ -10220,24 +9563,16 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (nucleobase-containing compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.") -AnnotationAssertion( "nucleobase, nucleoside, nucleotide and nucleic acid breakdown") -AnnotationAssertion( "nucleobase, nucleoside, nucleotide and nucleic acid catabolism") -AnnotationAssertion( "nucleobase, nucleoside, nucleotide and nucleic acid degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process") -AnnotationAssertion( "GO:0034655") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "nucleobase-containing compound catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (syncytial nuclear migration) + +AnnotationAssertion(Annotation( "GOC:bf") Annotation( "ISBN:0879694238") Annotation( "PMID:8314839") "The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0035190") +AnnotationAssertion(rdfs:label "syncytial nuclear migration") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (establishment of protein localization to extracellular region) @@ -10253,6 +9588,23 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (positive regulation of embryonic development) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of embryonic development.") +AnnotationAssertion( "up regulation of embryonic development") +AnnotationAssertion( "up-regulation of embryonic development") +AnnotationAssertion( "upregulation of embryonic development") +AnnotationAssertion( "activation of embryonic development") +AnnotationAssertion( "stimulation of embryonic development") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0040019") +AnnotationAssertion(rdfs:label "positive regulation of embryonic development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of meiotic nuclear division) AnnotationAssertion(Annotation( "GOC:ems") Annotation( "GOC:ma") "Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes.") @@ -10281,76 +9633,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (regulation of protein catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "kmv") -AnnotationAssertion( "2014-08-21T15:05:45Z") -AnnotationAssertion( "GO:1903362") -AnnotationAssertion( "GO:2000598") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cellular protein breakdown") -AnnotationAssertion( "regulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cellular protein degradation") -AnnotationAssertion( "regulation of protein breakdown") -AnnotationAssertion( "regulation of protein catabolism") -AnnotationAssertion( "regulation of protein degradation") -AnnotationAssertion(Annotation( "GOC:obol") "regulation of cyclin breakdown") -AnnotationAssertion( "regulation of cyclin catabolic process") -AnnotationAssertion(Annotation( "GOC:obol") "regulation of cyclin catabolism") -AnnotationAssertion(Annotation( "GOC:obol") "regulation of cyclin degradation") -AnnotationAssertion(Annotation( "GOC:obol") "regulation of degradation of cyclin") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0042176") -AnnotationAssertion(rdfs:label "regulation of protein catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of protein catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GOC:obol") Annotation( "GO_REF:0000058") Annotation( "PMID:24785082") "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "GO:1903363") -AnnotationAssertion( "GO:2000599") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular protein degradation") -AnnotationAssertion( "down regulation of protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cellular protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cellular protein degradation") -AnnotationAssertion( "down-regulation of protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cellular protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cellular protein degradation") -AnnotationAssertion( "downregulation of protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of cellular protein breakdown") -AnnotationAssertion( "negative regulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of cellular protein degradation") -AnnotationAssertion( "negative regulation of protein breakdown") -AnnotationAssertion( "negative regulation of protein catabolism") -AnnotationAssertion( "negative regulation of protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cellular protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cellular protein degradation") -AnnotationAssertion( "inhibition of protein catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0042177") -AnnotationAssertion(rdfs:label "negative regulation of protein catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (cellular ketone metabolic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0787650153") "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.") @@ -10382,22 +9664,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (ketone catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.") -AnnotationAssertion( "ketone breakdown") -AnnotationAssertion( "ketone catabolism") -AnnotationAssertion( "ketone degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0042182") -AnnotationAssertion(rdfs:label "ketone catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of phosphorylation) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.") @@ -10474,7 +9740,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0043062") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "extracellular structure organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10498,8 +9764,8 @@ AnnotationAssertion( "upregulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043085") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10522,7 +9788,7 @@ AnnotationAssertion( "negative regulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043086") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10548,6 +9814,7 @@ SubClassOf( ObjectSomeValuesFrom( (macromolecule metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "GO:0034960") AnnotationAssertion( "GO:0043283") AnnotationAssertion( "GO:0044259") @@ -10557,27 +9824,13 @@ AnnotationAssertion( "multicellular organismal macromolecule metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043170") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macromolecule metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (peptide catabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.") -AnnotationAssertion( "peptide breakdown") -AnnotationAssertion( "peptide catabolism") -AnnotationAssertion( "peptide degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0043171") -AnnotationAssertion(rdfs:label "peptide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.") @@ -10588,7 +9841,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle") SubClassOf( ) @@ -10717,7 +9970,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:bf") "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043549") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10748,18 +10001,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (amide catabolic process) - -AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.") -AnnotationAssertion( "cellular amide catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0043605") -AnnotationAssertion(rdfs:label "amide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (protein-containing complex organization) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.") @@ -10848,9 +10089,9 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0044091") AnnotationAssertion(rdfs:label "membrane biogenesis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of molecular function) @@ -10859,7 +10100,7 @@ AnnotationAssertion( "2009-04-21T04:07:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044092") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10872,7 +10113,7 @@ AnnotationAssertion( "2009-04-21T04:11:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044093") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10907,25 +10148,15 @@ SubClassOf( (primary metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "http://www.metacyc.org") "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "primary metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044238") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "primary metabolic process") SubClassOf( ) -# Class: (cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "cellular breakdown") -AnnotationAssertion( "cellular catabolism") -AnnotationAssertion( "cellular degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044248") -AnnotationAssertion(rdfs:label "cellular catabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (cellular biosynthetic process) AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") @@ -10939,18 +10170,6 @@ AnnotationAssertion(rdfs:label "cell SubClassOf( ) SubClassOf( ) -# Class: (cellular nitrogen compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.") -AnnotationAssertion( "nitrogen compound breakdown") -AnnotationAssertion( "nitrogen compound catabolism") -AnnotationAssertion( "nitrogen compound degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044270") -AnnotationAssertion(rdfs:label "cellular nitrogen compound catabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (cellular nitrogen compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.") @@ -10979,19 +10198,6 @@ AnnotationAssertion(rdfs:comment "Sm AnnotationAssertion(rdfs:label "small molecule metabolic process") SubClassOf( ) -# Class: (small molecule catabolic process) - -AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:vw") "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2010-01-26T12:06:10Z") -AnnotationAssertion( "small molecule catabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044282") -AnnotationAssertion(rdfs:comment "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.") -AnnotationAssertion(rdfs:label "small molecule catabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (small molecule biosynthetic process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pde") Annotation( "GOC:vw") "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.") @@ -11000,26 +10206,12 @@ AnnotationAssertion( AnnotationAssertion( "small molecule biosynthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044283") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.") AnnotationAssertion(rdfs:label "small molecule biosynthetic process") SubClassOf( ) SubClassOf( ) -# Class: (plasma membrane fusion) - -AnnotationAssertion(Annotation( "GOC:elh") Annotation( "GOC:mtg_muscle") "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.") -AnnotationAssertion( "GO:0006947") -AnnotationAssertion( "cell fusion") -AnnotationAssertion( "cell-cell fusion") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045026") -AnnotationAssertion(rdfs:label "plasma membrane fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (establishment of protein localization) AnnotationAssertion(Annotation( "GOC:bf") "The directed movement of a protein to a specific location.") @@ -11033,6 +10225,50 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (regulation of cell differentiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045595") +AnnotationAssertion(rdfs:label "regulation of cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of cell differentiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.") +AnnotationAssertion( "down regulation of cell differentiation") +AnnotationAssertion( "down-regulation of cell differentiation") +AnnotationAssertion( "downregulation of cell differentiation") +AnnotationAssertion( "inhibition of cell differentiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045596") +AnnotationAssertion(rdfs:label "negative regulation of cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of cell differentiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of cell differentiation.") +AnnotationAssertion( "up regulation of cell differentiation") +AnnotationAssertion( "up-regulation of cell differentiation") +AnnotationAssertion( "upregulation of cell differentiation") +AnnotationAssertion( "activation of cell differentiation") +AnnotationAssertion( "stimulation of cell differentiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045597") +AnnotationAssertion(rdfs:label "positive regulation of cell differentiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (positive regulation of translation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:go_curators") Annotation( "GOC:tb") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.") @@ -11052,61 +10288,11 @@ AnnotationAssertion( "positive regulation of translation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (positive regulation of protein catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "GO:1903364") -AnnotationAssertion( "GO:2000600") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cellular protein breakdown") -AnnotationAssertion( "positive regulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cellular protein degradation") -AnnotationAssertion( "positive regulation of protein breakdown") -AnnotationAssertion( "positive regulation of protein catabolism") -AnnotationAssertion( "positive regulation of protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cellular protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cellular protein degradation") -AnnotationAssertion( "up regulation of protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cellular protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cellular protein degradation") -AnnotationAssertion( "up-regulation of protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cellular protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cellular protein degradation") -AnnotationAssertion( "upregulation of protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cellular protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cellular protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cellular protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cellular protein degradation") -AnnotationAssertion( "activation of protein catabolic process") -AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of cyclin breakdown") -AnnotationAssertion( "positive regulation of cyclin catabolic process") -AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of cyclin catabolism") -AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of cyclin degradation") -AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of degradation of cyclin") -AnnotationAssertion( "stimulation of protein catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045732") -AnnotationAssertion(rdfs:label "positive regulation of protein catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (negative regulation of cellular amino acid metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid.") @@ -11120,9 +10306,7 @@ AnnotationAssertion( "negative regulation of cellular amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of amino acid metabolic process) @@ -11140,9 +10324,7 @@ AnnotationAssertion( "positive regulation of amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cell cycle) @@ -11180,72 +10362,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of endocytosis) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis.") -AnnotationAssertion( "down regulation of endocytosis") -AnnotationAssertion( "down-regulation of endocytosis") -AnnotationAssertion( "downregulation of endocytosis") -AnnotationAssertion( "inhibition of endocytosis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045806") -AnnotationAssertion(rdfs:label "negative regulation of endocytosis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of endocytosis) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of endocytosis.") -AnnotationAssertion( "up regulation of endocytosis") -AnnotationAssertion( "up-regulation of endocytosis") -AnnotationAssertion( "upregulation of endocytosis") -AnnotationAssertion( "activation of endocytosis") -AnnotationAssertion( "stimulation of endocytosis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045807") -AnnotationAssertion(rdfs:label "positive regulation of endocytosis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of lipid metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids.") -AnnotationAssertion( "down regulation of lipid metabolic process") -AnnotationAssertion( "down-regulation of lipid metabolic process") -AnnotationAssertion( "downregulation of lipid metabolic process") -AnnotationAssertion( "negative regulation of lipid metabolism") -AnnotationAssertion( "inhibition of lipid metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045833") -AnnotationAssertion(rdfs:label "negative regulation of lipid metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of lipid metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids.") -AnnotationAssertion( "positive regulation of lipid metabolism") -AnnotationAssertion( "up regulation of lipid metabolic process") -AnnotationAssertion( "up-regulation of lipid metabolic process") -AnnotationAssertion( "upregulation of lipid metabolic process") -AnnotationAssertion( "activation of lipid metabolic process") -AnnotationAssertion( "stimulation of lipid metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045834") -AnnotationAssertion(rdfs:label "positive regulation of lipid metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (negative regulation of meiotic nuclear division) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis.") @@ -11347,37 +10463,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of exocytosis) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis.") -AnnotationAssertion( "down regulation of exocytosis") -AnnotationAssertion( "down-regulation of exocytosis") -AnnotationAssertion( "downregulation of exocytosis") -AnnotationAssertion( "inhibition of exocytosis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045920") -AnnotationAssertion(rdfs:label "negative regulation of exocytosis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of exocytosis) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of exocytosis.") -AnnotationAssertion( "up regulation of exocytosis") -AnnotationAssertion( "up-regulation of exocytosis") -AnnotationAssertion( "upregulation of exocytosis") -AnnotationAssertion( "activation of exocytosis") -AnnotationAssertion( "stimulation of exocytosis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045921") -AnnotationAssertion(rdfs:label "positive regulation of exocytosis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (negative regulation of nucleobase-containing compound metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.") @@ -11479,6 +10564,32 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of embryonic development) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development.") +AnnotationAssertion( "down regulation of embryonic development") +AnnotationAssertion( "down-regulation of embryonic development") +AnnotationAssertion( "downregulation of embryonic development") +AnnotationAssertion( "inhibition of embryonic development") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045992") +AnnotationAssertion(rdfs:label "negative regulation of embryonic development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of embryonic development) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of embryonic development.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045995") +AnnotationAssertion(rdfs:label "regulation of embryonic development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (nucleobase biosynthetic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.") @@ -11496,22 +10607,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (nucleobase catabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.") -AnnotationAssertion( "nucleobase breakdown") -AnnotationAssertion( "nucleobase catabolism") -AnnotationAssertion( "nucleobase degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0046113") -AnnotationAssertion(rdfs:label "nucleobase catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (carboxylic acid biosynthetic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.") @@ -11527,20 +10622,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (carboxylic acid catabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.") -AnnotationAssertion( "carboxylic acid breakdown") -AnnotationAssertion( "carboxylic acid catabolism") -AnnotationAssertion( "carboxylic acid degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0046395") -AnnotationAssertion(rdfs:label "carboxylic acid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (heterocycle metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") @@ -11553,58 +10634,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (heterocycle catabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") -AnnotationAssertion( "heterocycle breakdown") -AnnotationAssertion( "heterocycle catabolism") -AnnotationAssertion( "heterocycle degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0046700") -AnnotationAssertion(rdfs:label "heterocycle catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of lipid biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.") -AnnotationAssertion( "positive regulation of lipid anabolism") -AnnotationAssertion( "positive regulation of lipid biosynthesis") -AnnotationAssertion( "positive regulation of lipid formation") -AnnotationAssertion( "positive regulation of lipid synthesis") -AnnotationAssertion(Annotation( "GOC:sl") "positive regulation of lipogenesis") -AnnotationAssertion( "up regulation of lipid biosynthetic process") -AnnotationAssertion( "up-regulation of lipid biosynthetic process") -AnnotationAssertion( "upregulation of lipid biosynthetic process") -AnnotationAssertion( "activation of lipid biosynthetic process") -AnnotationAssertion( "stimulation of lipid biosynthetic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0046889") -AnnotationAssertion(rdfs:label "positive regulation of lipid biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (regulation of lipid biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.") -AnnotationAssertion( "regulation of lipid anabolism") -AnnotationAssertion( "regulation of lipid biosynthesis") -AnnotationAssertion( "regulation of lipid formation") -AnnotationAssertion( "regulation of lipid synthesis") -AnnotationAssertion(Annotation( "GOC:sl") "regulation of lipogenesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0046890") -AnnotationAssertion(rdfs:label "regulation of lipid biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (secretion) AnnotationAssertion(Annotation( "GOC:ai") "The controlled release of a substance by a cell or a tissue.") @@ -11641,18 +10670,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (organelle fusion) - -AnnotationAssertion(Annotation( "GOC:jid") "The creation of a single organelle from two or more organelles.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0048284") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organelle fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organelle fission) AnnotationAssertion(Annotation( "GOC:jid") "The creation of two or more organelles by division of one organelle.") @@ -11665,16 +10682,32 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (nuclear membrane fusion involved in karyogamy) - -AnnotationAssertion(Annotation( "GOC:jid") "The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei.") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "nuclear membrane fusion during karyogamy") -AnnotationAssertion( "GO:0048288") -AnnotationAssertion(rdfs:label "nuclear membrane fusion involved in karyogamy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (cell development) + +AnnotationAssertion(Annotation( "GOC:go_curators") "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24390"^^xsd:anyURI) +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "terminal differentiation") +AnnotationAssertion( "GO:0048468") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (animal organ development) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25943"^^xsd:anyURI) +AnnotationAssertion( "Wikipedia:Organogenesis") +AnnotationAssertion( "development of an organ") +AnnotationAssertion( "organogenesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0048513") +AnnotationAssertion(rdfs:label "animal organ development") +SubClassOf( ) # Class: (positive regulation of biological process) @@ -11748,6 +10781,74 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of post-embryonic development) + +AnnotationAssertion(Annotation( "GOC:jid") "Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0048580") +AnnotationAssertion(rdfs:label "regulation of post-embryonic development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of post-embryonic development) + +AnnotationAssertion(Annotation( "GOC:jid") "Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.") +AnnotationAssertion( "down regulation of post-embryonic development") +AnnotationAssertion( "down-regulation of post-embryonic development") +AnnotationAssertion( "downregulation of post-embryonic development") +AnnotationAssertion( "inhibition of post-embryonic development") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0048581") +AnnotationAssertion(rdfs:label "negative regulation of post-embryonic development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of post-embryonic development) + +AnnotationAssertion(Annotation( "GOC:jid") "Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.") +AnnotationAssertion( "up regulation of post-embryonic development") +AnnotationAssertion( "up-regulation of post-embryonic development") +AnnotationAssertion( "upregulation of post-embryonic development") +AnnotationAssertion( "activation of post-embryonic development") +AnnotationAssertion( "stimulation of post-embryonic development") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0048582") +AnnotationAssertion(rdfs:label "positive regulation of post-embryonic development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anatomical structure development) + +AnnotationAssertion(Annotation( "GO_REF:0000021") "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) +AnnotationAssertion( "development of an anatomical structure") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0048856") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anatomical structure development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular developmental process) + +AnnotationAssertion(Annotation( "GOC:isa_complete") "A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0048869") +AnnotationAssertion(rdfs:label "cellular developmental process") +SubClassOf( ) +SubClassOf( ) + # Class: (nucleic acid transport) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "ISBN:0198506732") "The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") @@ -11836,13 +10937,23 @@ AnnotationAssertion( "regulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050790") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of developmental process) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0050793") +AnnotationAssertion(rdfs:label "regulation of developmental process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of cellular process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.") @@ -11856,59 +10967,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of lipid catabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids.") -AnnotationAssertion( "regulation of lipid breakdown") -AnnotationAssertion( "regulation of lipid catabolism") -AnnotationAssertion( "regulation of lipid degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0050994") -AnnotationAssertion(rdfs:label "regulation of lipid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of lipid catabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.") -AnnotationAssertion( "down regulation of lipid catabolic process") -AnnotationAssertion( "down-regulation of lipid catabolic process") -AnnotationAssertion( "downregulation of lipid catabolic process") -AnnotationAssertion( "negative regulation of lipid breakdown") -AnnotationAssertion( "negative regulation of lipid catabolism") -AnnotationAssertion( "negative regulation of lipid degradation") -AnnotationAssertion( "inhibition of lipid catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0050995") -AnnotationAssertion(rdfs:label "negative regulation of lipid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of lipid catabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.") -AnnotationAssertion( "positive regulation of lipid breakdown") -AnnotationAssertion( "positive regulation of lipid catabolism") -AnnotationAssertion( "positive regulation of lipid degradation") -AnnotationAssertion( "up regulation of lipid catabolic process") -AnnotationAssertion( "up-regulation of lipid catabolic process") -AnnotationAssertion( "upregulation of lipid catabolic process") -AnnotationAssertion( "activation of lipid catabolic process") -AnnotationAssertion( "stimulation of lipid catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0050996") -AnnotationAssertion(rdfs:label "positive regulation of lipid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of secretion) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.") @@ -11992,27 +11050,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of lipid biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.") -AnnotationAssertion( "down regulation of lipid biosynthetic process") -AnnotationAssertion( "down-regulation of lipid biosynthetic process") -AnnotationAssertion( "downregulation of lipid biosynthetic process") -AnnotationAssertion( "negative regulation of lipid anabolism") -AnnotationAssertion( "negative regulation of lipid biosynthesis") -AnnotationAssertion( "negative regulation of lipid formation") -AnnotationAssertion( "negative regulation of lipid synthesis") -AnnotationAssertion(Annotation( "GOC:sl") "negative regulation of lipogenesis") -AnnotationAssertion( "inhibition of lipid biosynthetic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051055") -AnnotationAssertion(rdfs:label "negative regulation of lipid biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (meiotic nuclear membrane disassembly) AnnotationAssertion(Annotation( "GOC:bf") "The cell cycle process in which the controlled breakdown of the nuclear membranes during meiotic cell division occurs.") @@ -12042,6 +11079,37 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of developmental process) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).") +AnnotationAssertion( "down regulation of developmental process") +AnnotationAssertion( "down-regulation of developmental process") +AnnotationAssertion( "downregulation of developmental process") +AnnotationAssertion( "inhibition of developmental process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051093") +AnnotationAssertion(rdfs:label "negative regulation of developmental process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of developmental process) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).") +AnnotationAssertion( "up regulation of developmental process") +AnnotationAssertion( "up-regulation of developmental process") +AnnotationAssertion( "upregulation of developmental process") +AnnotationAssertion( "activation of developmental process") +AnnotationAssertion( "stimulation of developmental process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051094") +AnnotationAssertion(rdfs:label "positive regulation of developmental process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of cellular component organization) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.") @@ -12229,9 +11297,11 @@ SubClassOf( ObjectSomeValuesFrom( (establishment of localization) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dos") "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24200"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:mah") "establishment of localisation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051234") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -12251,6 +11321,47 @@ AnnotationAssertion(rdfs:label "esta SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of multicellular organismal process) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051239") +AnnotationAssertion(rdfs:label "regulation of multicellular organismal process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of multicellular organismal process) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.") +AnnotationAssertion( "up regulation of multicellular organismal process") +AnnotationAssertion( "up-regulation of multicellular organismal process") +AnnotationAssertion( "upregulation of multicellular organismal process") +AnnotationAssertion( "activation of multicellular organismal process") +AnnotationAssertion( "stimulation of multicellular organismal process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051240") +AnnotationAssertion(rdfs:label "positive regulation of multicellular organismal process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of multicellular organismal process) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.") +AnnotationAssertion( "down regulation of multicellular organismal process") +AnnotationAssertion( "down-regulation of multicellular organismal process") +AnnotationAssertion( "downregulation of multicellular organismal process") +AnnotationAssertion( "inhibition of multicellular organismal process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051241") +AnnotationAssertion(rdfs:label "negative regulation of multicellular organismal process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of protein metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.") @@ -12394,8 +11505,8 @@ AnnotationAssertion(Annotation( "transferase regulator") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051338") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -12413,8 +11524,8 @@ AnnotationAssertion( "stimulation of transferase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051347") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "positive regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -12432,8 +11543,8 @@ AnnotationAssertion( "inhibition of transferase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051348") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "negative regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -12495,20 +11606,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (vesicle fusion with vacuole) - -AnnotationAssertion(Annotation( "GOC:ai") "The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole.") -AnnotationAssertion( "GO:0042146") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "heterotypic vacuole fusion (non-autophagic)") -AnnotationAssertion( "heterotypic vacuole fusion, non-autophagic") -AnnotationAssertion( "GO:0051469") -AnnotationAssertion(rdfs:label "vesicle fusion with vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organelle localization) AnnotationAssertion(Annotation( "GOC:ai") "Any process in which an organelle is transported to, and/or maintained in, a specific location.") @@ -12559,19 +11656,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (vesicle localization) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location.") -AnnotationAssertion( "cytoplasmic vesicle localization") -AnnotationAssertion( "establishment and maintenance of vesicle localization") -AnnotationAssertion(Annotation( "GOC:mah") "vesicle localisation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051648") -AnnotationAssertion(rdfs:label "vesicle localization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (establishment of localization in cell) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dos") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.") @@ -12590,18 +11674,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) -# Class: (establishment of vesicle localization) - -AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of a vesicle to a specific location.") -AnnotationAssertion(Annotation( "GOC:mah") "establishment of vesicle localisation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051650") -AnnotationAssertion(rdfs:label "establishment of vesicle localization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # Class: (establishment of organelle localization) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of an organelle to a specific location.") @@ -12812,8 +11884,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleobase-containing small molecule metabolic process") SubClassOf( ) SubClassOf( ) @@ -12828,6 +11900,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of cell development) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0060284") +AnnotationAssertion(rdfs:label "regulation of cell development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of cellular localization) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell.") @@ -12840,19 +11922,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of vesicle-mediated transport) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2009-05-18T02:29:43Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0060627") -AnnotationAssertion(rdfs:label "regulation of vesicle-mediated transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (membrane organization) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.") @@ -12872,30 +11941,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "membrane organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (membrane fusion) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The membrane organization process that joins two lipid bilayers to form a single membrane.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2010-02-08T02:48:06Z") -AnnotationAssertion( "GO:0006944") -AnnotationAssertion( "GO:0044801") -AnnotationAssertion( "Wikipedia:Lipid_bilayer_fusion") -AnnotationAssertion( "cellular membrane fusion") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "single-organism membrane fusion") -AnnotationAssertion( "GO:0061025") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "membrane fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (transferase complex, transferring phosphorus-containing groups) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "GOC:dph") "A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") @@ -12984,7 +12035,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein-containing complex assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -13011,7 +12062,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -13039,18 +12089,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (exocytic vesicle) - -AnnotationAssertion(Annotation( "GOC:kad") Annotation( "GOC:mah") "A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.") -AnnotationAssertion( "exocytic constitutive secretory pathway transport vesicle") -AnnotationAssertion(Annotation( "GOC:kad") "exocytotic vesicle") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0070382") -AnnotationAssertion(rdfs:label "exocytic vesicle") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (cellular macromolecule localization) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.") @@ -13106,6 +12144,7 @@ SubClassOf( ObjectSomeValuesFrom( (organic substance metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-08T03:32:18Z") AnnotationAssertion( "organic molecular entity metabolic process") @@ -13113,6 +12152,7 @@ AnnotationAssertion( "organic substance metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071704") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic substance metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -13194,7 +12234,7 @@ SubClassOf( (cell periphery) -AnnotationAssertion(Annotation( "GOC:pdt") "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.") +AnnotationAssertion(Annotation( "GOC:pdt") "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.") AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-04T01:51:47Z") AnnotationAssertion( "cellular_component") @@ -13225,7 +12265,7 @@ AnnotationAssertion(Annotation( "protein localization in membrane") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072657") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein localization to membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -13343,22 +12383,10 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (organelle membrane fusion) - -AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The joining of two lipid bilayers to form a single organelle membrane.") -AnnotationAssertion( "tb") -AnnotationAssertion( "2009-12-11T11:44:58Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0090174") -AnnotationAssertion(rdfs:label "organelle membrane fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (nucleic acid metabolic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any cellular metabolic process involving nucleic acids.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26133"^^xsd:anyURI) AnnotationAssertion( "tb") AnnotationAssertion( "2010-04-07T10:18:47Z") AnnotationAssertion( "biological_process") @@ -13437,31 +12465,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (vacuole fusion) - -AnnotationAssertion(Annotation( "GOC:pr") Annotation( "GOC:vw") Annotation( "Wikipedia:Vacuole") "Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2014-02-28T09:49:31Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0097576") -AnnotationAssertion(rdfs:label "vacuole fusion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (intracellular vesicle) - -AnnotationAssertion(Annotation( "GOC:vesicles") "Any vesicle that is part of the intracellular region.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2016-03-29T17:39:45Z") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0097708") -AnnotationAssertion(rdfs:label "intracellular vesicle") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (plasma membrane region) AnnotationAssertion(Annotation( "GOC:dos") "A membrane that is a (regional) part of the plasma membrane.") @@ -13511,40 +12514,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (vesicle-mediated transport to the plasma membrane) - -AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0098876") -AnnotationAssertion(rdfs:label "vesicle-mediated transport to the plasma membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (vesicle fusion to plasma membrane) - -AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "ISBN:0071120009") Annotation( "PMID:18618940") "Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0099500") -AnnotationAssertion(rdfs:label "vesicle fusion to plasma membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (secretory vesicle) - -AnnotationAssertion(Annotation( "GOC:dos") "A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0099503") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "secretory vesicle") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (cytoplasmic region) AnnotationAssertion(Annotation( "GOC:dos") "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.") @@ -13585,65 +12554,25 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0101025") AnnotationAssertion(rdfs:label "nuclear membrane biogenesis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (regulation of lipid transporter activity) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27365390") "Any process that modulates the frequency, rate, or extent of lipid transporter activity.") -AnnotationAssertion( "kmv") -AnnotationAssertion( "2018-07-06T18:53:55Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0110112") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of lipid transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of lipid transporter activity) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27365390") "Any process that increases the frequency, rate, or extent of lipid transporter activity.") -AnnotationAssertion( "kmv") -AnnotationAssertion( "2018-07-06T19:14:13Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0110113") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of lipid transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of lipid transporter activity) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27365390") "Any process that decreases the frequency, rate, or extent of lipid transporter activity.") -AnnotationAssertion( "kmv") -AnnotationAssertion( "2018-07-06T19:21:44Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0110114") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of lipid transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cellular anatomical entity) AnnotationAssertion(Annotation( "GOC:kmv") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24200"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "kmv") AnnotationAssertion( "2019-08-12T18:01:37Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0110165") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular anatomical entity") SubClassOf( ) +SubClassOf( ) # Class: (meiotic nuclear division) @@ -13660,19 +12589,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (exocytic process) - -AnnotationAssertion(Annotation( "Wikipedia:Exocytosis") "The cellular processes that contribute to exocytosis.") -AnnotationAssertion( "pg") -AnnotationAssertion( "2017-05-15T13:20:45Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0140029") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "exocytic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (catalytic activity, acting on a protein) AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify a protein.") @@ -13682,11 +12598,11 @@ AnnotationAssertion( AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140096") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "catalytic activity, acting on a protein") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (catalytic activity, acting on RNA) @@ -13698,29 +12614,11 @@ AnnotationAssertion( AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140098") AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "catalytic activity, acting on RNA") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (protein transporter activity) - -AnnotationAssertion(Annotation( "PMID:18706423") "Directly binding to a specific protein and delivering it to a specific cellular location.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17073"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2019-04-01T10:41:38Z") -AnnotationAssertion(Annotation(rdfs:label "iRHOM2 transports ADAM17 from ER to the Golgi-network") "Reactome:R-HSA-9662747") -AnnotationAssertion(Annotation(rdfs:label "iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane") "Reactome:R-HSA-9662818") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "protein carrier activity") -AnnotationAssertion( "protein transport chaperone") -AnnotationAssertion( "GO:0140318") -AnnotationAssertion(rdfs:comment "Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation.") -AnnotationAssertion(rdfs:label "protein transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (export from cell) @@ -13737,33 +12635,6 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (lipid export from cell) - -AnnotationAssertion(Annotation( "GOC:pg") "The directed movement of a lipid from a cell, into the extracellular region.") -AnnotationAssertion( "pg") -AnnotationAssertion( "2019-05-22T11:33:07Z") -AnnotationAssertion( "lipid efflux") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0140353") -AnnotationAssertion(rdfs:label "lipid export from cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - -# Class: (lipid import into cell) - -AnnotationAssertion(Annotation( "GOC:pg") "The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.") -AnnotationAssertion( "pg") -AnnotationAssertion( "2019-05-22T11:38:15Z") -AnnotationAssertion( "lipid uptake") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0140354") -AnnotationAssertion(rdfs:label "lipid import into cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (nuclear protein-containing complex) AnnotationAssertion(Annotation( "GOC:pg") "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus.") @@ -13800,9 +12671,9 @@ AnnotationAssertion( AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140640") AnnotationAssertion(rdfs:label "catalytic activity, acting on a nucleic acid") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of protein localization to nucleus) @@ -13954,22 +12825,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (organic cyclic compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2012-09-14T09:05:04Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic cyclic compound breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic cyclic compound catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic cyclic compound degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901361") -AnnotationAssertion(rdfs:label "organic cyclic compound catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organic cyclic compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the formation of organic cyclic compound.") @@ -13990,33 +12845,19 @@ SubClassOf( ObjectSomeValuesFrom( (organonitrogen compound metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways involving organonitrogen compound.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-04T15:17:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901564") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (organonitrogen compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2012-11-04T15:17:56Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901565") -AnnotationAssertion(rdfs:label "organonitrogen compound catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organonitrogen compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the formation of organonitrogen compound.") @@ -14034,26 +12875,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (organic substance catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2012-11-05T11:04:36Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity breakdown") -AnnotationAssertion( "organic molecular entity catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity degradation") -AnnotationAssertion( "organic substance breakdown") -AnnotationAssertion( "organic substance catabolism") -AnnotationAssertion( "organic substance degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901575") -AnnotationAssertion(rdfs:label "organic substance catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organic substance biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.") @@ -14089,22 +12910,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (alpha-amino acid catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid.") -AnnotationAssertion( "tb") -AnnotationAssertion( "2012-11-08T17:39:54Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "alpha-amino acid breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "alpha-amino acid catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "alpha-amino acid degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901606") -AnnotationAssertion(rdfs:label "alpha-amino acid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (alpha-amino acid biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the formation of an alpha-amino acid.") @@ -14118,7 +12923,7 @@ AnnotationAssertion( "GO:1901607") AnnotationAssertion(rdfs:label "alpha-amino acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -14170,38 +12975,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of RNA catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "PMID:16640457") "Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2013-08-22T14:59:39Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of RNA breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of RNA catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of RNA catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of RNA degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of RNA breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of RNA catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of RNA catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of RNA degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of RNA breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of RNA catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of RNA degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of RNA breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of RNA catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of RNA catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of RNA degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1902369") -AnnotationAssertion(rdfs:label "negative regulation of RNA catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (catalytic complex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "PMID:8077207") "A protein complex which is capable of catalytic activity.") @@ -14251,7 +13024,6 @@ AnnotationAssertion( "negative regulation of RNA biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -14290,7 +13062,6 @@ AnnotationAssertion( "positive regulation of RNA biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -14554,19 +13325,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (extracellular vesicle) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pm") Annotation( "GO_REF:0000064") Annotation( "PMID:24769233") "Any vesicle that is part of the extracellular region.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2014-10-22T14:26:11Z") -AnnotationAssertion( "cellular_component") -AnnotationAssertion(Annotation( "GOC:vesicles") "microparticle") -AnnotationAssertion( "GO:1903561") -AnnotationAssertion(rdfs:label "extracellular vesicle") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (regulation of plasma membrane organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24514900") "Any process that modulates the frequency, rate or extent of plasma membrane organization.") @@ -14627,96 +13385,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of protein catabolic process in the vacuole) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:25635054") "Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole.") -AnnotationAssertion( "rl") -AnnotationAssertion( "2015-06-12T09:10:36Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vacuolar protein degradation") -AnnotationAssertion( "GO:1904350") -AnnotationAssertion(rdfs:label "regulation of protein catabolic process in the vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of protein catabolic process in the vacuole) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:25635054") "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole.") -AnnotationAssertion( "rl") -AnnotationAssertion( "2015-06-12T09:10:42Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein catabolic process in the vacuole") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of protein catabolic process in the vacuole") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of protein catabolic process in the vacuole") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of protein catabolic process in the vacuole") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vacuolar protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of vacuolar protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of vacuolar protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of vacuolar protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of vacuolar protein degradation") -AnnotationAssertion( "GO:1904351") -AnnotationAssertion(rdfs:label "negative regulation of protein catabolic process in the vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of protein catabolic process in the vacuole) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:25635054") "Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole.") -AnnotationAssertion( "rl") -AnnotationAssertion( "2015-06-12T09:10:49Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of protein catabolic process in the vacuole") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of protein catabolic process in the vacuole") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of protein catabolic process in the vacuole") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of protein catabolic process in the vacuole") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of vacuolar protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of vacuolar protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of vacuolar protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of vacuolar protein degradation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of vacuolar protein breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of vacuolar protein catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of vacuolar protein catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of vacuolar protein degradation") -AnnotationAssertion( "GO:1904352") -AnnotationAssertion(rdfs:label "positive regulation of protein catabolic process in the vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of protein localization to cell periphery) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18216290") "Any process that modulates the frequency, rate or extent of protein localization to cell periphery.") @@ -14887,52 +13555,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of membrane invagination) - -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:26589353") "Any process that modulates the frequency, rate or extent of membrane invagination.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2016-04-18T15:43:54Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905153") -AnnotationAssertion(rdfs:label "regulation of membrane invagination") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of membrane invagination) - -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:26589353") "Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2016-04-18T15:44:04Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of membrane invagination") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of membrane invagination") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of membrane invagination") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of membrane invagination") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905154") -AnnotationAssertion(rdfs:label "negative regulation of membrane invagination") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of membrane invagination) - -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of membrane invagination.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2016-04-18T15:44:12Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of membrane invagination") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of membrane invagination") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of membrane invagination") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of membrane invagination") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905155") -AnnotationAssertion(rdfs:label "positive regulation of membrane invagination") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of protein localization to membrane) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:26911690") "Any process that modulates the frequency, rate or extent of protein localization to membrane.") @@ -15015,63 +13637,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of lipid localization) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17564681") "Any process that modulates the frequency, rate or extent of lipid localization.") -AnnotationAssertion( "rz") -AnnotationAssertion( "2017-02-21T12:12:22Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of lipid localisation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905952") -AnnotationAssertion(rdfs:label "regulation of lipid localization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of lipid localization) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17564681") "Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization.") -AnnotationAssertion( "rz") -AnnotationAssertion( "2017-02-21T12:12:41Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lipid localization") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lipid localization") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of lipid localization") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of lipid localization") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905953") -AnnotationAssertion(rdfs:label "negative regulation of lipid localization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of lipid localization) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17564681") "Any process that activates or increases the frequency, rate or extent of lipid localization.") -AnnotationAssertion( "rz") -AnnotationAssertion( "2017-02-21T12:12:49Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lipid localization") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of lipid localization") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of lipid localization") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of lipid localisation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of lipid localization") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905954") -AnnotationAssertion(rdfs:label "positive regulation of lipid localization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (transferase complex) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:16540464") "A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).") @@ -15084,19 +13649,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (transporter complex) - -AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:15449578") "A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2014-03-26T14:23:27Z") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:1990351") -AnnotationAssertion(rdfs:comment "An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay).") -AnnotationAssertion(rdfs:label "transporter complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (protein localization to cell periphery) AnnotationAssertion(Annotation( "PMID:18216290") "A process in which a protein is transported to, or maintained in, the cell periphery.") @@ -15145,6 +13697,19 @@ AnnotationAssertion(rdfs:label "ribo SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of multicellular organismal development) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of multicellular organismal development.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2010-08-05T11:25:59Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2000026") +AnnotationAssertion(rdfs:label "regulation of multicellular organismal development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of reproductive process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of reproductive process.") @@ -15197,8 +13762,9 @@ AnnotationAssertion( "GO:2000282") AnnotationAssertion(rdfs:label "regulation of cellular amino acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of amino acid biosynthetic process) @@ -15216,7 +13782,8 @@ AnnotationAssertion( "negative regulation of amino acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15235,7 +13802,8 @@ AnnotationAssertion( "positive regulation of amino acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15253,19 +13821,29 @@ AnnotationAssertion( "regulation of RNA biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (root) AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:30365038") +AnnotationAssertion( "PMID:32761142") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "all") AnnotationAssertion( "NCBITaxon:1") AnnotationAssertion(rdfs:label "root") SubClassOf( ) +# Class: (Ecdysozoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:1206794") +AnnotationAssertion(rdfs:label "Ecdysozoa") +SubClassOf( ) + # Class: (cellular organisms) AnnotationAssertion( "GC_ID:1") @@ -15275,6 +13853,139 @@ AnnotationAssertion( "cellular organisms") SubClassOf( ) +# Class: (Saccharomycotina) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "true yeasts") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:147537") +AnnotationAssertion(rdfs:label "Saccharomycotina") +SubClassOf( ) + +# Class: (Schizosaccharomycetes) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Archiascomycota") +AnnotationAssertion( "NCBITaxon:147554") +AnnotationAssertion(rdfs:label "Schizosaccharomycetes") +SubClassOf( ) + +# Class: (Pancrustacea) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:10874751") +AnnotationAssertion( "PMID:11557979") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:197562") +AnnotationAssertion(rdfs:label "Pancrustacea") +SubClassOf( ) + +# Class: (Mandibulata) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:11557979") +AnnotationAssertion( "PMID:9727836") +AnnotationAssertion(Annotation( ) "mandibulates") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:197563") +AnnotationAssertion(rdfs:label "Mandibulata") +SubClassOf( ) + +# Class: (Bacteria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:11") +AnnotationAssertion( "PMID:10425795") +AnnotationAssertion( "PMID:10425796") +AnnotationAssertion( "PMID:10425797") +AnnotationAssertion( "PMID:10490293") +AnnotationAssertion( "PMID:10843050") +AnnotationAssertion( "PMID:10939651") +AnnotationAssertion( "PMID:10939673") +AnnotationAssertion( "PMID:10939677") +AnnotationAssertion( "PMID:11211268") +AnnotationAssertion( "PMID:11321083") +AnnotationAssertion( "PMID:11321113") +AnnotationAssertion( "PMID:11411719") +AnnotationAssertion( "PMID:11540071") +AnnotationAssertion( "PMID:11542017") +AnnotationAssertion( "PMID:11542087") +AnnotationAssertion( "PMID:11760965") +AnnotationAssertion( "PMID:12054223") +AnnotationAssertion( "PMID:2112744") +AnnotationAssertion( "PMID:270744") +AnnotationAssertion( "PMID:32628106") +AnnotationAssertion( "PMID:36748408") +AnnotationAssertion( "PMID:7520741") +AnnotationAssertion( "PMID:8123559") +AnnotationAssertion( "PMID:8186100") +AnnotationAssertion( "PMID:8590690") +AnnotationAssertion( "PMID:9103655") +AnnotationAssertion( "PMID:9336922") +AnnotationAssertion(Annotation( ) "eubacteria") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Monera") +AnnotationAssertion(Annotation( ) "Procaryotae") +AnnotationAssertion(Annotation( ) "Prokaryota") +AnnotationAssertion(Annotation( ) "Prokaryotae") +AnnotationAssertion(Annotation( ) "bacteria") +AnnotationAssertion(Annotation( ) "prokaryote") +AnnotationAssertion(Annotation( ) "prokaryotes") +AnnotationAssertion( "NCBITaxon:2") +AnnotationAssertion(rdfs:label "Bacteria") +SubClassOf( ) + +# Class: (Archaea) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:11") +AnnotationAssertion( "PMID:10425795") +AnnotationAssertion( "PMID:10425796") +AnnotationAssertion( "PMID:10425797") +AnnotationAssertion( "PMID:10490293") +AnnotationAssertion( "PMID:10843050") +AnnotationAssertion( "PMID:10939651") +AnnotationAssertion( "PMID:10939673") +AnnotationAssertion( "PMID:10939677") +AnnotationAssertion( "PMID:11211268") +AnnotationAssertion( "PMID:11321083") +AnnotationAssertion( "PMID:11321113") +AnnotationAssertion( "PMID:11411719") +AnnotationAssertion( "PMID:11540071") +AnnotationAssertion( "PMID:11541975") +AnnotationAssertion( "PMID:11542064") +AnnotationAssertion( "PMID:11542149") +AnnotationAssertion( "PMID:11760965") +AnnotationAssertion( "PMID:12054223") +AnnotationAssertion( "PMID:2112744") +AnnotationAssertion( "PMID:25527841") +AnnotationAssertion( "PMID:270744") +AnnotationAssertion( "PMID:32628106") +AnnotationAssertion( "PMID:36748408") +AnnotationAssertion( "PMID:8123559") +AnnotationAssertion( "PMID:8590690") +AnnotationAssertion( "PMID:9103655") +AnnotationAssertion( "PMID:9336922") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Archaebacteria") +AnnotationAssertion(Annotation( ) "Mendosicutes") +AnnotationAssertion(Annotation( ) "Metabacteria") +AnnotationAssertion(Annotation( ) "Monera") +AnnotationAssertion(Annotation( ) "Procaryotae") +AnnotationAssertion(Annotation( ) "Prokaryota") +AnnotationAssertion(Annotation( ) "Prokaryotae") +AnnotationAssertion(Annotation( ) "archaea") +AnnotationAssertion(Annotation( ) "prokaryote") +AnnotationAssertion(Annotation( ) "prokaryotes") +AnnotationAssertion( "NCBITaxon:2157") +AnnotationAssertion(rdfs:label "Archaea") +SubClassOf( ) + # Class: (Eukaryota) AnnotationAssertion( ) @@ -15282,7 +13993,7 @@ AnnotationAssertion( "PMID:23020233") AnnotationAssertion( "PMID:30257078") AnnotationAssertion(Annotation( ) "eucaryotes") -AnnotationAssertion(Annotation( ) "eukaryotes") +AnnotationAssertion(Annotation( ) "eukaryotes") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Eucarya") AnnotationAssertion(Annotation( ) "Eucaryotae") @@ -15304,6 +14015,69 @@ AnnotationAssertion( "Opisthokonta") SubClassOf( ) +# Class: (Metazoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "metazoans") +AnnotationAssertion(Annotation( ) "multicellular animals") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Animalia") +AnnotationAssertion(Annotation( ) "animals") +AnnotationAssertion( "NCBITaxon:33208") +AnnotationAssertion(rdfs:label "Metazoa") +SubClassOf( ) + +# Class: (Bilateria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:33213") +AnnotationAssertion(rdfs:label "Bilateria") +SubClassOf( ) + +# Class: (Protostomia) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:33317") +AnnotationAssertion(rdfs:label "Protostomia") +SubClassOf( ) + +# Class: (Schizosaccharomycetales) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:34346") +AnnotationAssertion(rdfs:label "Schizosaccharomycetales") +SubClassOf( ) + +# Class: (Dikarya) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:15689432") +AnnotationAssertion( "PMID:16151185") +AnnotationAssertion( "PMID:17010206") +AnnotationAssertion( "PMID:17051209") +AnnotationAssertion( "PMID:17572334") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:451864") +AnnotationAssertion(rdfs:label "Dikarya") +SubClassOf( ) + +# Class: (Taphrinomycotina) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:451866") +AnnotationAssertion(rdfs:label "Taphrinomycotina") +SubClassOf( ) + # Class: (Fungi) AnnotationAssertion( ) @@ -15317,6 +14091,177 @@ AnnotationAssertion( "Fungi") SubClassOf( ) +# Class: (Ascomycota) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:17572334") +AnnotationAssertion(Annotation( ) "ascomycetes") +AnnotationAssertion(Annotation( ) "sac fungi") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "ascomycete fungi") +AnnotationAssertion( "NCBITaxon:4890") +AnnotationAssertion(rdfs:label "Ascomycota") +SubClassOf( ) + +# Class: (Saccharomycetes) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Hemiascomycetes") +AnnotationAssertion( "NCBITaxon:4891") +AnnotationAssertion(rdfs:label "Saccharomycetes") +SubClassOf( ) + +# Class: (Saccharomycetales) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Endomycetales") +AnnotationAssertion(Annotation( ) "budding yeasts") +AnnotationAssertion( "NCBITaxon:4892") +AnnotationAssertion(rdfs:label "Saccharomycetales") +SubClassOf( ) + +# Class: (Saccharomycetaceae) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:221665") +AnnotationAssertion( "NCBITaxon:44280") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:4893") +AnnotationAssertion(rdfs:label "Saccharomycetaceae") +SubClassOf( ) + +# Class: (Schizosaccharomycetaceae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "fission yeasts") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Schizosaccharomycetoideae") +AnnotationAssertion( "NCBITaxon:4894") +AnnotationAssertion(rdfs:label "Schizosaccharomycetaceae") +SubClassOf( ) + +# Class: (Schizosaccharomyces) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:4895") +AnnotationAssertion(rdfs:label "Schizosaccharomyces") +SubClassOf( ) + +# Class: (Schizosaccharomyces pombe) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:45042") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "fission yeast") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Schizosaccharomyces malidevorans") +AnnotationAssertion( "NCBITaxon:4896") +AnnotationAssertion(rdfs:label "Schizosaccharomyces pombe") +SubClassOf( ) + +# Class: (Saccharomyces) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:36915") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Pachytichospora") +AnnotationAssertion( "NCBITaxon:4930") +AnnotationAssertion(rdfs:label "Saccharomyces") +SubClassOf( ) + +# Class: (Saccharomyces cerevisiae) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:41870") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Saccharomyces cerevisiae 'var. diastaticus'") +AnnotationAssertion(Annotation( ) "baker's yeast") +AnnotationAssertion(Annotation( ) "brewer's yeast") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Candida robusta") +AnnotationAssertion(Annotation( ) "Mycoderma cerevisiae") +AnnotationAssertion(Annotation( ) "Saccharomyces capensis") +AnnotationAssertion(Annotation( ) "Saccharomyces diastaticus") +AnnotationAssertion(Annotation( ) "Saccharomyces italicus") +AnnotationAssertion(Annotation( ) "Saccharomyces oviformis") +AnnotationAssertion(Annotation( ) "Saccharomyces uvarum var. melibiosus") +AnnotationAssertion( "NCBITaxon:4932") +AnnotationAssertion(rdfs:label "Saccharomyces cerevisiae") +SubClassOf( ) + +# Class: (Insecta) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "true insects") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "insects") +AnnotationAssertion( "NCBITaxon:50557") +AnnotationAssertion(rdfs:label "Insecta") +SubClassOf( ) + +# Class: (Eumetazoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6072") +AnnotationAssertion(rdfs:label "Eumetazoa") +SubClassOf( ) + +# Class: (Arthropoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "arthropods") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "arthropods") +AnnotationAssertion( "NCBITaxon:6656") +AnnotationAssertion(rdfs:label "Arthropoda") +SubClassOf( ) + +# Class: (Hexapoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "insects") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Atelocerata") +AnnotationAssertion(Annotation( ) "Tracheata") +AnnotationAssertion(Annotation( ) "Uniramia") +AnnotationAssertion(Annotation( ) "hexapods") +AnnotationAssertion( "NCBITaxon:6960") +AnnotationAssertion(rdfs:label "Hexapoda") +SubClassOf( ) + +# Class: (saccharomyceta) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:716545") +AnnotationAssertion(rdfs:label "saccharomyceta") +SubClassOf( ) + +# Class: (Panarthropoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:88770") +AnnotationAssertion(rdfs:label "Panarthropoda") +SubClassOf( ) + # Class: (quality) AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") @@ -16073,6 +15018,25 @@ AnnotationAssertion( "multinucleate") SubClassOf( ) +# Class: (cellularity) + +AnnotationAssertion(Annotation( "PATOC:GVG") "An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0001992") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cellularity") +SubClassOf( ) + +# Class: (multicellular) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0001993") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "multicellular") +SubClassOf( ) + # Class: (organismal quality) AnnotationAssertion(Annotation( "PATOC:CJM") "A quality that inheres in an entire organism or part of an organism.") @@ -16631,6 +15595,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( "BFO:0000003") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000000") AnnotationAssertion( ) @@ -16650,7 +15615,7 @@ AnnotationAssertion( "CARO:0000003") AnnotationAssertion( "EHDAA2:0003003") AnnotationAssertion( "EMAPA:0") -AnnotationAssertion( "FBbt:00007001") +AnnotationAssertion(Annotation( ) "FBbt:00007001") AnnotationAssertion( "FMA:305751") AnnotationAssertion( "FMA:67135") AnnotationAssertion( "GAID:781") @@ -16674,6 +15639,57 @@ AnnotationAssertion(rdfs:label " SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (fully formed stage) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.") +AnnotationAssertion( "adult stage") +AnnotationAssertion( "BTO:0001043") +AnnotationAssertion( "BilaDO:0000004") +AnnotationAssertion( "EFO:0001272") +AnnotationAssertion( "FBdv:00005369") +AnnotationAssertion( "WBls:0000041") +AnnotationAssertion( "XtroDO:0000084") +AnnotationAssertion( "fully formed animal stage") +AnnotationAssertion( "juvenile-adult stage") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0000066") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "fully formed stage") +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/566"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (embryo stage) + +AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A life cycle stage that starts with fertilization and ends with the fully formed embryo.") +AnnotationAssertion( "BilaDO:0000002") +AnnotationAssertion( "EV:0300001") +AnnotationAssertion( "FBdv:00005289") +AnnotationAssertion( "FMA:72652") +AnnotationAssertion( "HsapDv:0000002") +AnnotationAssertion( "MmusDv:0000002") +AnnotationAssertion( "OGES:000000") +AnnotationAssertion( "OGES:000022") +AnnotationAssertion( "SCTID:296280003") +AnnotationAssertion( "WBls:0000003") +AnnotationAssertion( "WBls:0000092") +AnnotationAssertion( "WBls:0000102") +AnnotationAssertion( "XAO:1000012") +AnnotationAssertion( "embryonic stage") +AnnotationAssertion( "uberon") +AnnotationAssertion( "embryogenesis") +AnnotationAssertion( "UBERON:0000068") +AnnotationAssertion(rdfs:label "embryo stage") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + # Class: (death stage) AnnotationAssertion(Annotation( "XAO:0000437") "End of the life of an organism.") @@ -16692,6 +15708,29 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (post-embryonic stage) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Stage succeeding embryo, including mature structure.") +AnnotationAssertion( "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)") +AnnotationAssertion( "BilaDO:0000003") +AnnotationAssertion( "OGES:000010") +AnnotationAssertion( "OGES:000014") +AnnotationAssertion( "OGES:000024") +AnnotationAssertion( "WBls:0000022") +AnnotationAssertion( "WBls:0000093") +AnnotationAssertion( "WBls:0000103") +AnnotationAssertion( "postembryonic stage") +AnnotationAssertion( "post-hatching stage") +AnnotationAssertion( "uberon") +AnnotationAssertion( "postembryonic") +AnnotationAssertion( "UBERON:0000092") +AnnotationAssertion(rdfs:label "post-embryonic stage") +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/344"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (life cycle) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.") @@ -16752,6 +15791,61 @@ AnnotationAssertion(rdfs:label " SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (zygote stage) + +AnnotationAssertion(Annotation( "Wikipedia:Zygote") "A stage at which the organism is a single cell produced by means of sexual reproduction.") +AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000745") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107") Annotation( "http://bgee.unil.ch/") "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]") +AnnotationAssertion( "BILS:0000106") +AnnotationAssertion( "BilaDO:0000005") +AnnotationAssertion( "EFO:0001322") +AnnotationAssertion( "EHDAA:27") +AnnotationAssertion( "FBdv:00005288") +AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0000302") +AnnotationAssertion( "NCIT:C12601") +AnnotationAssertion( "PdumDv:0000100") +AnnotationAssertion( "VHOG:0000745") +AnnotationAssertion( "Wikipedia:Zygote") +AnnotationAssertion( "XAO:1000001") +AnnotationAssertion( "ZFS:0000001") +AnnotationAssertion( "1-cell stage") +AnnotationAssertion(Annotation( "BTO:0000854") "fertilized egg stage") +AnnotationAssertion( "one cell stage") +AnnotationAssertion( "uberon") +AnnotationAssertion( "fertilized egg stage") +AnnotationAssertion(Annotation( "VHOG:0000745") "one-cell stage") +AnnotationAssertion(Annotation( "VHOG:0000745") "zygote") +AnnotationAssertion(Annotation( "Wikipedia:Zygote") Annotation( ) "zygotum") +AnnotationAssertion( "UBERON:0000106") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "zygote stage") +AnnotationAssertion(rdfs:seeAlso ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organogenesis stage) + +AnnotationAssertion(Annotation( "Wikipedia:Organogenesis") "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.") +AnnotationAssertion( "BILS:0000111") +AnnotationAssertion( "BilaDO:0000010") +AnnotationAssertion( "HsapDv:0000015") +AnnotationAssertion( "MmusDv:0000018") +AnnotationAssertion( "OGES:000005") +AnnotationAssertion( "OGES:000032") +AnnotationAssertion( "Wikipedia:Organogenesis") +AnnotationAssertion( "uberon") +AnnotationAssertion( "segmentation stage") +AnnotationAssertion( "UBERON:0000111") +AnnotationAssertion(rdfs:label "organogenesis stage") +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84"^^xsd:anyURI) +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/533"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (material anatomical entity) AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Anatomical entity that has mass.") @@ -16763,7 +15857,7 @@ AnnotationAssertion( "BILA:0000006") AnnotationAssertion( "CARO:0000006") AnnotationAssertion( "EHDAA2:0003006") -AnnotationAssertion( "FBbt:00007016") +AnnotationAssertion(Annotation( ) "FBbt:00007016") AnnotationAssertion( "FMA:67165") AnnotationAssertion( "HAO:0000006") AnnotationAssertion( "TAO:0001836") @@ -16777,6 +15871,107 @@ AnnotationAssertion(rdfs:label " SubClassOf( ) SubClassOf( ) +# Class: (multicellular organism) + +AnnotationAssertion(Annotation( "CARO:0000012") Annotation( "Wikipedia:Multi-cellular_organism") Annotation( "http://orcid.org/0000-0001-9114-8737") "Anatomical structure that is an individual member of a species and consists of more than one cell.") +AnnotationAssertion( "TODO - split body and mc organism? body continues after death stage") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "organismal") +AnnotationAssertion(Annotation( "FBbt:00000001") Annotation( "VHOG:0000671") Annotation( "WBbt:0007833") "organism") +AnnotationAssertion( "AAO:0010026") +AnnotationAssertion( "AEO:0000191") +AnnotationAssertion( "BILA:0000012") +AnnotationAssertion( "BIRNLEX:18") +AnnotationAssertion( "BSA:0000038") +AnnotationAssertion( "BTO:0000042") +AnnotationAssertion( "CARO:0000012") +AnnotationAssertion( "EFO:0002906") +AnnotationAssertion( "EHDAA2:0003103") +AnnotationAssertion( "EHDAA2:0003191") +AnnotationAssertion( "EHDAA:1") +AnnotationAssertion( "EMAPA:25765") +AnnotationAssertion( "EV:0100016") +AnnotationAssertion(Annotation( ) "FBbt:00000001") +AnnotationAssertion( "FMA:256135") +AnnotationAssertion( "HAO:0000012") +AnnotationAssertion( "NCIT:C13041") +AnnotationAssertion( "SCTID:243928005") +AnnotationAssertion( "TADS:0000001") +AnnotationAssertion( "TAO:0001094") +AnnotationAssertion( "TGMA:0001832") +AnnotationAssertion( "VHOG:0000671") +AnnotationAssertion( "WBbt:0007833") +AnnotationAssertion( "Wikipedia:Multi-cellular_organism") +AnnotationAssertion( "XAO:0003004") +AnnotationAssertion( "ZFA:0001094") +AnnotationAssertion( "galen:Organism") +AnnotationAssertion( "ncithesaurus:Whole_Organism") +AnnotationAssertion(Annotation( "CARO:0000012") "multi-cellular organism") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "BTO:0001489") "Koerper") +AnnotationAssertion(Annotation( "AEO:0000103") Annotation( "BIRNLEX:18") Annotation( "FMA:256135") Annotation( "NCIT:C13041") "body") +AnnotationAssertion(Annotation( "BTO:0001489") "whole body") +AnnotationAssertion(Annotation( "FBbt:00000001") "whole organism") +AnnotationAssertion( "UBERON:0000468") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "multicellular organism") +SubClassOf( ) + +# Class: (embryo) + +AnnotationAssertion(Annotation( "BTO:0000379") Annotation( "FB:FBrf0039741") Annotation( "FB:FBrf0041814") Annotation( "GO:0009790") Annotation( "Wikipedia:Embryo") "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.") +AnnotationAssertion( "embryonic") +AnnotationAssertion(Annotation( "ZFA") "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo") +AnnotationAssertion( "AAO:0011035") +AnnotationAssertion( "AEO:0000169") +AnnotationAssertion( "BILA:0000056") +AnnotationAssertion( "BSA:0000039") +AnnotationAssertion( "BTO:0000379") +AnnotationAssertion( "CALOHA:TS-0229") +AnnotationAssertion( "EFO:0001367") +AnnotationAssertion( "EHDAA2:0000002") +AnnotationAssertion( "EHDAA2_RETIRED:0003236") +AnnotationAssertion( "EHDAA:38") +AnnotationAssertion( "EMAPA:16039") +AnnotationAssertion(Annotation( ) "FBbt:00000052") +AnnotationAssertion( "FMA:69068") +AnnotationAssertion( "GAID:963") +AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0000646") +AnnotationAssertion( "MAT:0000226") +AnnotationAssertion( "MESH:D004622") +AnnotationAssertion( "MIAA:0000019") +AnnotationAssertion( "NCIT:C28147") +AnnotationAssertion( "OGEM:000001") +AnnotationAssertion( "SCTID:57991002") +AnnotationAssertion(Annotation( "ncithesaurus:Embryo") "UMLS:C0013935") +AnnotationAssertion( "VHOG:0001766") +AnnotationAssertion( "Wikipedia:Embryo") +AnnotationAssertion( "XAO:0000113") +AnnotationAssertion( "ZFA:0000103") +AnnotationAssertion( "http://neurolex.org/wiki/Category:Embryonic_organism") +AnnotationAssertion(Annotation( "BILA:0000056") "embryonic organism") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "BILA:0000056") "developing organism") +AnnotationAssertion( "developmental tissue") +AnnotationAssertion( "UBERON:0000922") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "embryo") +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/503"^^xsd:anyURI) +AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg"^^xsd:anyURI) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (anatomical entity) AnnotationAssertion(Annotation( "FMA:62955") Annotation( "http://orcid.org/0000-0001-9114-8737") "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.") @@ -16785,11 +15980,12 @@ AnnotationAssertion( ) AnnotationAssertion( "AAO:0010841") AnnotationAssertion( "AEO:0000000") +AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "BILA:0000000") AnnotationAssertion( "BIRNLEX:6") AnnotationAssertion( "CARO:0000000") AnnotationAssertion( "EHDAA2:0002229") -AnnotationAssertion( "FBbt:10000000") +AnnotationAssertion(Annotation( ) "FBbt:10000000") AnnotationAssertion( "FMA:62955") AnnotationAssertion( "HAO:0000000") AnnotationAssertion( "MA:0000001") @@ -16806,6 +16002,42 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anatomical entity") +# Class: (post-embryonic organism) + +AnnotationAssertion(Annotation( "OBOL:automatic") "A multicellular organism that existence_starts_with a post-embryonic stage.") +AnnotationAssertion( "MA:0002405") +AnnotationAssertion( "postnatal organism") +AnnotationAssertion(Annotation( "MA:0002405") "TS28 mouse") +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "post-hatching organism") +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "post-natal organism") +AnnotationAssertion(Annotation( "MA:0002405") "postnatal mouse") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0009953") +AnnotationAssertion(rdfs:label "post-embryonic organism") +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/667"^^xsd:anyURI) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (multicellular anatomical structure) + +AnnotationAssertion(Annotation( "CARO:0010000") "An anatomical structure that has more than one cell as a part.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "CARO:0010000") +AnnotationAssertion(Annotation( ) "FBbt:00100313") +AnnotationAssertion(Annotation( "FBbt:00100313") "multicellular structure") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0010000") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "multicellular anatomical structure") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + EquivalentClasses(ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(2 ))) @@ -16813,16 +16045,20 @@ EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectMinCardinality(2 ))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) @@ -16833,7 +16069,6 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -16885,40 +16120,44 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 09c61ab..94b9c7d 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-01-31") + +Annotation( ) +Annotation(owl:versionInfo "2024-04-04") Declaration(Class()) Declaration(Class()) @@ -358,6 +358,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) @@ -384,6 +385,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -427,9 +429,11 @@ AnnotationAssertion( "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) +AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -465,6 +469,8 @@ AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has characteristic"@en) +AnnotationAssertion(rdfs:label "has characteristic") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -492,7 +498,9 @@ AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (function of) @@ -940,6 +948,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:label "enabled by") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1584,6 +1593,7 @@ AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) # Class: (disposition) @@ -1594,6 +1604,7 @@ DisjointClasses( (realizable entity) AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(rdfs:label "realizable"@en) AnnotationAssertion(rdfs:label "realizable entity"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -1605,13 +1616,17 @@ AnnotationAssertion(rdfs:label "qua SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) -# Class: (specifically dependent continuant) +# Class: (characteristic) AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(rdfs:label "characteristic"@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/OBOFoundry/COB/issues/65") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (role) @@ -1633,6 +1648,7 @@ SubClassOf( (cell) AnnotationAssertion(Annotation( "CARO:mah") "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") +AnnotationAssertion( "A material entity that has a plasma membrane and results from cellular division.") AnnotationAssertion( "CALOHA:TS-2035") AnnotationAssertion( "FBbt:00007002") AnnotationAssertion( "FMA:68646") @@ -1642,7 +1658,10 @@ AnnotationAssertion( "VHOG:0001533") AnnotationAssertion( "WBbt:0004017") AnnotationAssertion( "XAO:0003012") +AnnotationAssertion(rdfs:comment "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.") AnnotationAssertion(rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).") +AnnotationAssertion(rdfs:comment "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.") +AnnotationAssertion(rdfs:label "cell"@en) AnnotationAssertion(rdfs:label "cell") SubClassOf( ) @@ -1652,7 +1671,11 @@ AnnotationAssertion(Annotation( "molecular function") AnnotationAssertion( "GO:0003674") AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:comment "This is the same as GO molecular function") +AnnotationAssertion(rdfs:label "gene product or complex activity"@en) AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) +DisjointClasses( ) # Class: (nucleus) @@ -1662,11 +1685,14 @@ AnnotationAssertion( "cell nucleus") AnnotationAssertion(Annotation( "GOC:al") Annotation( "GOC:mah") Annotation( "GOC:vw") Annotation( "PMID:15030757") "horsetail nucleus") AnnotationAssertion( "GO:0005634") +AnnotationAssertion(rdfs:label "cell nucleus"@en) AnnotationAssertion(rdfs:label "nucleus") +SubClassOf( ) # Class: (biological_process) AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.") AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:05:24Z") AnnotationAssertion( "Wikipedia:Biological_process") @@ -1675,8 +1701,12 @@ AnnotationAssertion( "single organism process") AnnotationAssertion( "single-organism process") AnnotationAssertion( "GO:0008150") +AnnotationAssertion(rdfs:comment "A biological process is an evolved process") AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:label "biological process"@en) AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (kinase activity) @@ -1720,7 +1750,6 @@ AnnotationAssertion( "CARO:0000003") AnnotationAssertion( "EHDAA2:0003003") AnnotationAssertion( "EMAPA:0") -AnnotationAssertion( "FBbt:00007001") AnnotationAssertion( "FMA:305751") AnnotationAssertion( "FMA:67135") AnnotationAssertion( "GAID:781") @@ -1752,7 +1781,6 @@ AnnotationAssertion( "BILA:0000006") AnnotationAssertion( "CARO:0000006") AnnotationAssertion( "EHDAA2:0003006") -AnnotationAssertion( "FBbt:00007016") AnnotationAssertion( "FMA:67165") AnnotationAssertion( "HAO:0000006") AnnotationAssertion( "TAO:0001836") @@ -1772,11 +1800,11 @@ AnnotationAssertion( ) AnnotationAssertion( "AAO:0010841") AnnotationAssertion( "AEO:0000000") +AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "BILA:0000000") AnnotationAssertion( "BIRNLEX:6") AnnotationAssertion( "CARO:0000000") AnnotationAssertion( "EHDAA2:0002229") -AnnotationAssertion( "FBbt:10000000") AnnotationAssertion( "FMA:62955") AnnotationAssertion( "HAO:0000000") AnnotationAssertion( "MA:0000001") @@ -1919,30 +1947,30 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/so_import.owl b/src/ontology/imports/so_import.owl index 8914c15..8be1696 100644 --- a/src/ontology/imports/so_import.owl +++ b/src/ontology/imports/so_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-01-31") +Annotation(owl:versionInfo "2024-04-04") Declaration(ObjectProperty()) Declaration(AnnotationProperty()) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index beb2447..67a0a07 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-01-31") + +Annotation(owl:versionInfo "2024-04-04") Declaration(Class()) Declaration(Class())