From d524527eafa2050a4c86f080890a1329d929b608 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Sat, 18 Nov 2023 19:24:56 +0000 Subject: [PATCH 1/2] Update the SSSOM plugin. Update to the latest version of the SSSOM plugin. This fixes a bug with the mapping cardinality filter that caused a large part of the CL-ZFA mappings to be ignored. We also use the new features of that version to ensure that the generated mapping sets have a license and an ID. --- src/ontology/uberon.Makefile | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index a9f7f6de1f..3a435269c1 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -119,7 +119,7 @@ export ROBOT_PLUGINS_DIRECTORY # Make sure the SSSOM plugin for ROBOT is available. $(TMPDIR)/plugins/sssom.jar: mkdir -p $(TMPDIR)/plugins - curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.6.0/sssom-robot-plugin-0.6.0.jar + curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.6.1/sssom-robot-plugin-0.6.1.jar # ---------------------------------------- @@ -1251,6 +1251,7 @@ mappings/cl-mappings.sssom.tsv: $(SRC) $(MIRRORDIR)/cl.owl $(TMPDIR)/plugins/sss $(ROBOT) merge -i $(SRC) -i $(MIRRORDIR)/cl.owl --collapse-import-closure false \ remove --base-iri http://purl.obolibrary.org/obo/CL_ --axioms external \ sssom:xref-extract --mapping-file $@ -v --drop-duplicates \ + --set-id "$(ONTBASE)/mappings/cl-mappings.sssom.tsv" \ --prefix 'KUPO: http://purl.obolibrary.org/obo/KUPO_' \ --prefix 'SCTID: http://purl.obolibrary.org/obo/SCTID_' \ > $(REPORTDIR)/cl-xrefs-extraction.txt @@ -1260,6 +1261,7 @@ mappings/cl-mappings.sssom.tsv: $(SRC) $(MIRRORDIR)/cl.owl $(TMPDIR)/plugins/sss mappings/zfa-mappings.sssom.tsv: $(MIRRORDIR)/zfa.owl $(TMPDIR)/plugins/sssom.jar $(ROBOT) sssom:xref-extract -i $(MIRRORDIR)/zfa.owl --mapping-file $@ \ -v --drop-duplicates \ + --set-id "$(ONTBASE)/mappings/zfa-mappings.sssom.tsv" \ > $(REPORTDIR)/zfa-xrefs-extraction.txt endif @@ -1306,10 +1308,10 @@ $(TMPDIR)/bridges: $(SRC) $(TMPDIR)/uberon-mappings.sssom.tsv $(EXTERNAL_SSSOM_S $(CUSTOM_BRIDGES) $(MAKE) $(MIRRORDIR)/cl.owl MIR=true IMP=true $(ROBOT) merge -i $(SRC) -i $(MIRRORDIR)/cl.owl \ - sssom:sssom-inject --sssom $(TMPDIR)/uberon-mappings.sssom.tsv \ - $(foreach set, $(EXTERNAL_SSSOM_SETS), --sssom $(set)) \ - --ruleset $(TMPDIR)/bridges.rules \ - --dispatch-table $(BRIDGEDIR)/bridges.dispatch && \ + sssom:inject --sssom $(TMPDIR)/uberon-mappings.sssom.tsv \ + $(foreach set, $(EXTERNAL_SSSOM_SETS), --sssom $(set)) \ + --ruleset $(TMPDIR)/bridges.rules \ + --dispatch-table $(BRIDGEDIR)/bridges.dispatch && \ touch $@ # The above step creates RDF/XML bridges, turn them to OBO. @@ -1383,12 +1385,12 @@ $(COMPONENTSDIR)/hra_depiction_3d_images.owl: $(TMPDIR)/hra_depiction_3d_images. # component ensures those mappings are visible to Uberon editors and # users. $(COMPONENTSDIR)/mappings.owl: $(SRC) $(EXTERNAL_SSSOM_SETS) $(TMPDIR)/plugins/sssom.jar - $(ROBOT) sssom:sssom-inject -i $< \ - $(foreach set, $(EXTERNAL_SSSOM_SETS), --sssom $(set)) \ - --invert --only-subject-in UBERON \ - --check-subject --drop-duplicate-objects \ - --hasdbxref --no-merge --bridge-file $@ \ - --bridge-iri http://purl.obolibrary.org/obo/uberon/components/mappings.owl + $(ROBOT) sssom:inject -i $< \ + $(foreach set, $(EXTERNAL_SSSOM_SETS), --sssom $(set)) \ + --invert --only-subject-in UBERON \ + --check-subject --drop-duplicate-objects \ + --hasdbxref --no-merge --bridge-file $@ \ + --bridge-iri http://purl.obolibrary.org/obo/uberon/components/mappings.owl # ---------------------------------------- From 7049a1eea4b433d32f968141ae31632b59f920c0 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Sat, 18 Nov 2023 19:31:54 +0000 Subject: [PATCH 2/2] Commit the re-generated bridges. --- src/ontology/bridge/cl-bridge-to-zfa.owl | 9745 ++++++++++++++++- src/ontology/bridge/uberon-bridge-to-caro.owl | 422 +- src/ontology/bridge/uberon-bridge-to-zfa.owl | 27 +- src/ontology/mappings/cl-mappings.sssom.tsv | 2 + src/ontology/mappings/zfa-mappings.sssom.tsv | 2 + 5 files changed, 9911 insertions(+), 287 deletions(-) diff --git a/src/ontology/bridge/cl-bridge-to-zfa.owl b/src/ontology/bridge/cl-bridge-to-zfa.owl index a8fe60f691..f955ab194d 100644 --- a/src/ontology/bridge/cl-bridge-to-zfa.owl +++ b/src/ontology/bridge/cl-bridge-to-zfa.owl @@ -9,7 +9,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/"> - + Melissa Haendel Veri Van Slyke Yvonne Bradford @@ -89,6 +89,24 @@ + + + + + + + + + + + + + + + + + + @@ -107,349 +125,9575 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + 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(zebrafish) - + - + - + @@ -571,18 +9815,18 @@ - visceromotor neuron (zebrafish) + precursor B cell (zebrafish) - + - + - + @@ -590,18 +9834,18 @@ - somatomotor neuron (zebrafish) + transitional stage B cell (zebrafish) - + - + - + @@ -609,18 +9853,18 @@ - pancreatic acinar cell (zebrafish) + immature natural killer cell (zebrafish) - + - + - + @@ -628,18 +9872,18 @@ - pancreatic centro-acinar cell (zebrafish) + mature natural killer cell (zebrafish) - + - + - + @@ -647,18 +9891,18 @@ - pancreatic PP cell (zebrafish) + pro-NK cell (zebrafish) - + - + - + @@ -666,18 +9910,18 @@ - pancreatic D cell (zebrafish) + pro-B cell (zebrafish) - + - + - + @@ -685,18 +9929,18 @@ - notochordal sheath cell (zebrafish) + pro-T cell (zebrafish) - + - + - + @@ -704,18 +9948,18 @@ - structural cell (zebrafish) + thromboblast (zebrafish) - + - + - + @@ -723,18 +9967,18 @@ - spermatid (zebrafish) + neutrophil progenitor cell (zebrafish) - + - + - + @@ -742,18 +9986,18 @@ - embryonic blood vessel endothelial progenitor cell (zebrafish) + myeloblast (zebrafish) - + - + - + @@ -761,18 +10005,18 @@ - enteric neuron (zebrafish) + hematopoietic multipotent progenitor cell (zebrafish) - + - + - + @@ -780,18 +10024,18 @@ - parasympathetic neuron (zebrafish) + lymphoid lineage restricted progenitor cell (zebrafish) - + - + - + @@ -799,18 +10043,18 @@ - sympathetic neuron (zebrafish) + myeloid lineage restricted progenitor cell (zebrafish) - + - + - + @@ -818,18 +10062,18 @@ - hypocretin-secreting neuron (zebrafish) + mononuclear cell (zebrafish) - + - + - + @@ -837,18 +10081,18 @@ - striated muscle cell (zebrafish) + ciliated olfactory receptor neuron (zebrafish) - + - + - + @@ -856,18 +10100,18 @@ - hematopoietic cell (zebrafish) + microvillous olfactory receptor neuron (zebrafish) - + - + - + @@ -875,18 +10119,18 @@ - noradrenergic neuron (zebrafish) + crypt olfactory receptor neuron (zebrafish) - + - + - + @@ -894,18 +10138,18 @@ - oogonial cell (zebrafish) + serotonergic neuron (zebrafish) - + - + - + @@ -913,18 +10157,18 @@ - mural cell (zebrafish) + neuromast mantle cell (zebrafish) - + - + - + @@ -932,18 +10176,18 @@ - germ line stem cell (zebrafish) + neuromast supporting cell (zebrafish) - + - + - + @@ -951,18 +10195,18 @@ - stem cell (zebrafish) + olfactory epithelial supporting cell (zebrafish) - + - + - + @@ -970,18 +10214,18 @@ - premigratory neural crest cell (zebrafish) + interneuromast cell (zebrafish) - + - + - + @@ -989,18 +10233,18 @@ - migratory neural crest cell (zebrafish) + sensory hair cell (zebrafish) - + - + - + @@ -1008,18 +10252,18 @@ - embryonic cell (metazoa) (zebrafish) + neuromast hair cell (zebrafish) - + - + - + @@ -1027,18 +10271,18 @@ - migratory cranial neural crest cell (zebrafish) + slow muscle myoblast (zebrafish) - + - + - + @@ -1046,18 +10290,18 @@ - migratory trunk neural crest cell (zebrafish) + fast muscle myoblast (zebrafish) - + - + - + @@ -1065,18 +10309,18 @@ - stem cell of epidermis (zebrafish) + stretch receptor cell (zebrafish) - + - + - + @@ -1084,7 +10328,7 @@ - Rohon-Beard neuron (zebrafish) + stratified keratinized epithelial stem cell (zebrafish) @@ -1222,25 +10466,6 @@ - - - - - - - - - - - - - - - neurecto-epithelial cell (zebrafish) - - - - diff --git a/src/ontology/bridge/uberon-bridge-to-caro.owl b/src/ontology/bridge/uberon-bridge-to-caro.owl index 73009bee45..ef954fca05 100644 --- a/src/ontology/bridge/uberon-bridge-to-caro.owl +++ b/src/ontology/bridge/uberon-bridge-to-caro.owl @@ -8,7 +8,7 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - + @@ -50,6 +50,33 @@ + + + + + anatomical structure (CARO) + + + + + + + + + organism substance (CARO) + + + + + + + + + anatomical space (CARO) + + + + @@ -68,6 +95,15 @@ + + + + + anatomical line (CARO) + + + + @@ -77,6 +113,78 @@ + + + + + non-material anatomical boundary (CARO) + + + + + + + + + anatomical system (CARO) + + + + + + + + + multicellular organism (CARO) + + + + + + + + + compound organ component (CARO) + + + + + + + + + simple organ (CARO) + + + + + + + + + compound organ (CARO) + + + + + + + + + male organism (CARO) + + + + + + + + + female organism (CARO) + + + + @@ -86,6 +194,42 @@ + + + + + organism subdivision (CARO) + + + + + + + + + acellular anatomical structure (CARO) + + + + + + + + + extraembryonic structure (CARO) + + + + + + + + + tissue (CARO) + + + + @@ -104,6 +248,114 @@ + + + + + anatomical group (CARO) + + + + + + + + + multi-tissue structure (CARO) + + + + + + + + + basal lamina of epithelium (CARO) + + + + + + + + + epithelium (CARO) + + + + + + + + + simple cuboidal epithelium (CARO) + + + + + + + + + simple columnar epithelium (CARO) + + + + + + + + + multilaminar epithelium (CARO) + + + + + + + + + simple squamous epithelium (CARO) + + + + + + + + + atypical epithelium (CARO) + + + + + + + + + cavitated compound organ (CARO) + + + + + + + + + unilaminar epithelium (CARO) + + + + + + + + + solid compound organ (CARO) + + + + @@ -257,12 +509,24 @@ + + + + + + + + + + + + @@ -281,6 +545,18 @@ + + + + + + + + + + + + @@ -293,6 +569,126 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -305,12 +701,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/bridge/uberon-bridge-to-zfa.owl b/src/ontology/bridge/uberon-bridge-to-zfa.owl index 4933c14de4..f0eec6944b 100644 --- a/src/ontology/bridge/uberon-bridge-to-zfa.owl +++ b/src/ontology/bridge/uberon-bridge-to-zfa.owl @@ -9,7 +9,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/"> - + Melissa Haendel Veri Van Slyke Yvonne Bradford @@ -6065,12 +6065,6 @@ - - - - - - @@ -13762,25 +13756,6 @@ - - - - - - - - - - - - - - - yolk (zebrafish) - - - - diff --git a/src/ontology/mappings/cl-mappings.sssom.tsv b/src/ontology/mappings/cl-mappings.sssom.tsv index d93dca9dc4..b3491a2a90 100644 --- a/src/ontology/mappings/cl-mappings.sssom.tsv +++ b/src/ontology/mappings/cl-mappings.sssom.tsv @@ -17,6 +17,8 @@ # WBbt: "http://purl.obolibrary.org/obo/WBbt_" # XAO: "http://purl.obolibrary.org/obo/XAO_" # ZFA: "http://purl.obolibrary.org/obo/ZFA_" +#mapping_set_id: "http://purl.obolibrary.org/obo/uberon/mappings/cl-mappings.sssom.tsv" +#license: "http://creativecommons.org/licenses/by/3.0/" subject_id subject_label predicate_id object_id mapping_justification mapping_cardinality CL:0000000 cell skos:broadMatch VHOG:0001533 semapv:UnspecifiedMatching 1:n CL:0000000 cell skos:exactMatch GO:0005623 semapv:UnspecifiedMatching 1:n diff --git a/src/ontology/mappings/zfa-mappings.sssom.tsv b/src/ontology/mappings/zfa-mappings.sssom.tsv index 62bb303641..6721edffd4 100644 --- a/src/ontology/mappings/zfa-mappings.sssom.tsv +++ b/src/ontology/mappings/zfa-mappings.sssom.tsv @@ -4,6 +4,8 @@ # TAO: "http://purl.obolibrary.org/obo/TAO_" # VSAO: "http://purl.obolibrary.org/obo/VSAO_" # ZFA: "http://purl.obolibrary.org/obo/ZFA_" +#mapping_set_id: "http://purl.obolibrary.org/obo/uberon/mappings/zfa-mappings.sssom.tsv" +#license: "https://creativecommons.org/licenses/by/3.0/" subject_id subject_label predicate_id object_id mapping_justification mapping_cardinality ZFA:0000000 Brachet's cleft semapv:crossSpeciesExactMatch TAO:0000000 semapv:UnspecifiedMatching 1:1 ZFA:0000001 Kupffer's vesicle semapv:crossSpeciesExactMatch TAO:0000001 semapv:UnspecifiedMatching 1:1