From d81617dac9fe8490a8fe31f974ffe99ab70e0a90 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Wed, 16 Nov 2022 22:21:50 +0200 Subject: [PATCH] Update rlease --- bspo-base.json | 231 +++++++++++-- bspo-base.obo | 58 +++- bspo-base.owl | 155 +++++++-- bspo-full.json | 484 ++++++++++++++++++++++++---- bspo-full.obo | 143 ++++++-- bspo-full.owl | 394 +++++++++++++++++++--- bspo.json | 484 ++++++++++++++++++++++++---- bspo.obo | 143 ++++++-- bspo.owl | 394 +++++++++++++++++++--- src/ontology/imports/omo_import.owl | 4 +- src/ontology/imports/ro_import.owl | 233 +++++++++++-- 11 files changed, 2353 insertions(+), 370 deletions(-) diff --git a/bspo-base.json b/bspo-base.json index 74e2e12..7e3b26f 100644 --- a/bspo-base.json +++ b/bspo-base.json @@ -141,6 +141,11 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/BSPO_0020001" }, + { + "obj": "http://purl.obolibrary.org/obo/BFO_0000050", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/BSPO_0030006" + }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000051", "pred": "inverseOf", @@ -1576,6 +1581,11 @@ "pred": "inverseOf", "sub": "http://purl.obolibrary.org/obo/BSPO_0000114" }, + { + "obj": "http://purl.obolibrary.org/obo/BSPO_0000123", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/BSPO_0030004" + }, { "obj": "http://purl.obolibrary.org/obo/BSPO_0000124", "pred": "subPropertyOf", @@ -1596,6 +1606,11 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/BSPO_0000121" }, + { + "obj": "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/BSPO_0030005" + }, { "obj": "http://purl.obolibrary.org/obo/BSPO_0000129", "pred": "http://purl.obolibrary.org/obo/RO_0002131", @@ -1796,6 +1811,16 @@ "pred": "inverseOf", "sub": "http://purl.obolibrary.org/obo/BSPO_0015016" }, + { + "obj": "http://purl.obolibrary.org/obo/BSPO_0015101", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/BSPO_0030003" + }, + { + "obj": "http://purl.obolibrary.org/obo/BSPO_0030006", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/BSPO_0030007" + }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000000", "pred": "http://purl.obolibrary.org/obo/BSPO_0015006", @@ -2698,11 +2723,11 @@ "restrictions": [ { "fillerId": "http://purl.obolibrary.org/obo/BSPO_0000013", - "propertyId": "http://purl.obolibrary.org/obo/bspo#parallel_to" + "propertyId": "http://purl.obolibrary.org/obo/BSPO_0001102" }, { "fillerId": "http://purl.obolibrary.org/obo/BSPO_0000016", - "propertyId": "http://purl.obolibrary.org/obo/bspo#parallel_to" + "propertyId": "http://purl.obolibrary.org/obo/BSPO_0001102" }, { "fillerId": "http://purl.obolibrary.org/obo/BSPO_0000017", @@ -2963,10 +2988,10 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-10-07" + "val": "2022-11-16" } ], - "version": "http://purl.obolibrary.org/obo/bspo/releases/2022-10-07/bspo-base.json" + "version": "http://purl.obolibrary.org/obo/bspo/releases/2022-11-16/bspo-base.json" }, "nodes": [ { @@ -7684,6 +7709,25 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/BSPO_0001102", + "lbl": "parallel to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "spatial" + } + ], + "definition": { + "val": "x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.", + "xrefs": [ + "BSPO:curators" + ] + } + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/BSPO_0001106", "lbl": "proximalmost part of", @@ -8518,6 +8562,166 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/BSPO_0030003", + "lbl": "dorsalmost part of", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0003-2699-3066" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "spatial" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "dorsalmost_part_of" + } + ], + "definition": { + "val": "x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y", + "xrefs": [ + "https://orcid.org/0000-0003-2699-3066" + ] + }, + "xrefs": [ + { + "val": "BSPO:0030003" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/BSPO_0030004", + "lbl": "anteriormost part of", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0003-2699-3066" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "spatial" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "anteriormost_part_of" + } + ], + "definition": { + "val": "x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y", + "xrefs": [ + "https://orcid.org/0000-0003-2699-3066" + ] + }, + "xrefs": [ + { + "val": "BSPO:0030004" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/BSPO_0030005", + "lbl": "lateralmost part of", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0003-2699-3066" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "spatial" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "lateralmost_part_of" + } + ], + "definition": { + "val": "x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y", + "xrefs": [ + "https://orcid.org/0000-0003-2699-3066" + ] + }, + "xrefs": [ + { + "val": "BSPO:0030005" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/BSPO_0030006", + "lbl": "in medial side of", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0003-2699-3066" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "spatial" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "in_medial_side_of" + } + ], + "definition": { + "val": "X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion.", + "xrefs": [ + "https://orcid.org/0000-0003-2699-3066" + ] + }, + "xrefs": [ + { + "val": "BSPO:0030006" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/BSPO_0030007", + "lbl": "medialmost part of", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0003-2699-3066" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "spatial" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "medialmost_part_of" + } + ], + "definition": { + "val": "x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y", + "xrefs": [ + "https://orcid.org/0000-0003-2699-3066" + ] + }, + "xrefs": [ + { + "val": "BSPO:0030007" + } + ] + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/BSPO_1000000", "lbl": "preaxial to", @@ -8743,25 +8947,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/bspo#parallel_to", - "lbl": "parallel to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "spatial" - } - ], - "definition": { - "val": "x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.", - "xrefs": [ - "BSPO:curators" - ] - } - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/bspo#vertebrate", "lbl": "synonym typically used in the context of vertebrate anatomy", diff --git a/bspo-base.obo b/bspo-base.obo index 3306275..8e2b098 100644 --- a/bspo-base.obo +++ b/bspo-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: bspo/releases/2022-10-07/bspo-base.owl +data-version: bspo/releases/2022-11-16/bspo-base.owl synonymtypedef: human "synonym typically used in the context of human anatomy" NARROW synonymtypedef: vertebrate "synonym typically used in the context of vertebrate anatomy" NARROW default-namespace: spatial @@ -11,7 +11,7 @@ property_value: http://purl.org/dc/elements/1.1/title "Biological Spatial Ontolo 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/ property_value: IAO:0000700 CARO:0000000 -property_value: owl:versionInfo "2022-10-07" xsd:string +property_value: owl:versionInfo "2022-11-16" xsd:string [Term] id: BSPO:0000000 @@ -1263,9 +1263,9 @@ synonym: "median plane" EXACT [] synonym: "sagittal section" EXACT [] xref: FMA:11361 intersection_of: BSPO:0000400 ! anatomical plane +intersection_of: BSPO:0001102 BSPO:0000013 ! parallel to anterior-posterior axis +intersection_of: BSPO:0001102 BSPO:0000016 ! parallel to dorsal-ventral axis intersection_of: orthogonal_to BSPO:0000017 ! left-right axis -intersection_of: parallel_to BSPO:0000013 ! anterior-posterior axis -intersection_of: parallel_to BSPO:0000016 ! dorsal-ventral axis [Term] id: BSPO:0000671 @@ -1517,6 +1517,11 @@ is_transitive: true created_by: Jennifer Girón creation_date: 2021-04-21T01:01:01Z +[Typedef] +id: BSPO:0001102 +name: parallel to +def: "x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross." [BSPO:curators] + [Typedef] id: BSPO:0020001 name: in central side of @@ -1558,6 +1563,14 @@ property_value: seeAlso FBql:00005863 is_transitive: true inverse_of: posterior_to ! posterior to +[Typedef] +id: anteriormost_part_of +name: anteriormost part of +def: "x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y" [https://orcid.org/0000-0003-2699-3066] +xref: BSPO:0030004 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 +is_a: in_anterior_side_of ! in anterior side of + [Typedef] id: approximately_perpendicular_to name: approximately perpendicular to @@ -1610,6 +1623,14 @@ property_value: seeAlso FBql:00005865 is_transitive: true inverse_of: ventral_to ! ventral to +[Typedef] +id: dorsalmost_part_of +name: dorsalmost part of +def: "x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y" [https://orcid.org/0000-0003-2699-3066] +xref: BSPO:0030003 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 +is_a: in_dorsal_side_of ! in dorsal side of + [Typedef] id: finishes_axis name: finishes axis @@ -1780,6 +1801,14 @@ property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-pai is_a: in_lateral_side_of ! in lateral side of disjoint_from: in_right_side_of ! in right side of +[Typedef] +id: in_medial_side_of +name: in medial side of +def: "X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion." [https://orcid.org/0000-0003-2699-3066] +xref: BSPO:0030006 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 +is_a: part_of ! part of + [Typedef] id: in_posterior_side_of name: in posterior side of @@ -1832,6 +1861,14 @@ property_value: seeAlso FBql:00005850 is_symmetric: true disjoint_from: contralateral_to ! contralateral to +[Typedef] +id: lateralmost_part_of +name: lateralmost part of +def: "x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y" [https://orcid.org/0000-0003-2699-3066] +xref: BSPO:0030005 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 +is_a: in_lateral_side_of ! in lateral side of + [Typedef] id: left_of name: left of @@ -1840,6 +1877,14 @@ xref: BSPO:0000110 is_transitive: true inverse_of: right_of ! right of +[Typedef] +id: medialmost_part_of +name: medialmost part of +def: "x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y" [https://orcid.org/0000-0003-2699-3066] +xref: BSPO:0030007 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 +is_a: in_medial_side_of ! in medial side of + [Typedef] id: obsolete_surrounded_by name: obsolete surrounded_by @@ -1884,11 +1929,6 @@ def: "x overlaps y iff they have some part in common." [BSPO:cjm] comment: "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] xref: RO:0002131 -[Typedef] -id: parallel_to -name: parallel to -def: "x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross." [BSPO:curators] - [Typedef] id: part_of name: part of diff --git a/bspo-base.owl b/bspo-base.owl index d042e53..9c9332a 100644 --- a/bspo-base.owl +++ b/bspo-base.owl @@ -14,7 +14,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Biological Spatial Ontology @@ -23,7 +23,7 @@ * BSPO:$sequence(7,0,999999999)$ spatial based on FBql - 2022-10-07 + 2022-11-16 @@ -877,6 +877,23 @@ + + + + x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. + spatial + parallel_to + parallel to + + + + + x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. + BSPO:curators + + + + @@ -1448,6 +1465,111 @@ + + + + + x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y + + BSPO:0030003 + spatial + dorsalmost_part_of + dorsalmost_part_of + dorsalmost part of + + + + + x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y + + BSPO:0030004 + spatial + anteriormost_part_of + anteriormost_part_of + anteriormost part of + + + + + x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y + + BSPO:0030005 + spatial + lateralmost_part_of + lateralmost_part_of + lateralmost part of + + + + + x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion. + + BSPO:0030006 + spatial + in_medial_side_of + in_medial_side_of + in medial side of + + + + + X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion. + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y + + BSPO:0030007 + spatial + medialmost_part_of + medialmost_part_of + medialmost part of + + + + + x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + @@ -1510,23 +1632,6 @@ - - - - x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. - spatial - parallel_to - parallel to - - - - - x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. - BSPO:curators - - - - + + + + + @@ -1249,6 +1255,23 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. + spatial + parallel_to + parallel to + + + + + x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. + BSPO:curators + + + + @@ -1820,6 +1843,111 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y + + BSPO:0030003 + spatial + dorsalmost_part_of + dorsalmost_part_of + dorsalmost part of + + + + + x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y + + BSPO:0030004 + spatial + anteriormost_part_of + anteriormost_part_of + anteriormost part of + + + + + x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y + + BSPO:0030005 + spatial + lateralmost_part_of + lateralmost_part_of + lateralmost part of + + + + + x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion. + + BSPO:0030006 + spatial + in_medial_side_of + in_medial_side_of + in medial side of + + + + + X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion. + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y + + BSPO:0030007 + spatial + medialmost_part_of + medialmost_part_of + medialmost part of + + + + + x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + @@ -2333,9 +2461,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -2358,7 +2484,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -2382,7 +2508,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2553,6 +2679,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -2568,9 +2695,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. cjm - holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect @@ -2635,6 +2764,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -2801,18 +2931,75 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -2825,6 +3012,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -2834,8 +3027,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -2849,8 +3041,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -2864,7 +3055,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -3116,7 +3307,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -3216,7 +3407,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) 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. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -3324,7 +3515,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) 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 P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -3341,7 +3532,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) 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 P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -3481,6 +3672,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + @@ -3552,23 +3768,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. - spatial - parallel_to - parallel to - - - - - x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. - BSPO:curators - - - - + + + + + @@ -1249,6 +1255,23 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. + spatial + parallel_to + parallel to + + + + + x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. + BSPO:curators + + + + @@ -1820,6 +1843,111 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y + + BSPO:0030003 + spatial + dorsalmost_part_of + dorsalmost_part_of + dorsalmost part of + + + + + x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y + + BSPO:0030004 + spatial + anteriormost_part_of + anteriormost_part_of + anteriormost part of + + + + + x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y + + BSPO:0030005 + spatial + lateralmost_part_of + lateralmost_part_of + lateralmost part of + + + + + x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion. + + BSPO:0030006 + spatial + in_medial_side_of + in_medial_side_of + in medial side of + + + + + X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion. + https://orcid.org/0000-0003-2699-3066 + + + + + + + + + x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y + + BSPO:0030007 + spatial + medialmost_part_of + medialmost_part_of + medialmost part of + + + + + x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y + https://orcid.org/0000-0003-2699-3066 + + + + @@ -2333,9 +2461,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -2358,7 +2484,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -2382,7 +2508,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -2553,6 +2679,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -2568,9 +2695,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. cjm - holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect @@ -2635,6 +2764,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -2801,18 +2931,75 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -2825,6 +3012,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -2834,8 +3027,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -2849,8 +3041,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -2864,7 +3055,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -3116,7 +3307,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -3216,7 +3407,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) 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. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -3324,7 +3515,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) 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 P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -3341,7 +3532,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) 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 P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -3481,6 +3672,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + @@ -3552,23 +3768,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. - spatial - parallel_to - parallel to - - - - - x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. - BSPO:curators - - - - + + + + + @@ -966,9 +972,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -991,7 +995,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1015,7 +1019,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -1180,6 +1184,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -1195,9 +1200,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. cjm - holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect @@ -1262,6 +1269,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -1428,18 +1436,75 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -1452,6 +1517,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -1461,8 +1532,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -1476,8 +1546,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -1491,7 +1560,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -1743,7 +1812,7 @@ For example, A and B may be gene products and binding of B by A positively regul - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -1843,7 +1912,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly regulates process(P2) 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. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -1951,7 +2020,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly postively regulates process(P2) 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 P1 directly positively regulates P2. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -1968,7 +2037,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Process(P1) directly negatively regulates process(P2) 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 P1 directly negatively regulates P2. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -2108,6 +2177,31 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + 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 + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + @@ -2607,6 +2701,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -2616,6 +2716,9 @@ For example, A and B may be gene products and binding of B by A positively regul + + + @@ -3613,6 +3716,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -3789,6 +3936,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +