Merge pull request #46 from mcwdsi/fix-pato-import

fixes #44 by making PATO import a separate ODK (filter) import. Makin…
mcwdsi · Dec 24, 2024 · 555cc58 · 555cc58
2 parents 7f0f99e + a9a2b86
commit 555cc58
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diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -29,5 +29,5 @@ jobs:
       - name: Run ontology QC checks
         env:
           DEFAULT_BRANCH: main
-        run: echo "DRON in its current form is too big for GitHub Actions"
+        run: echo "DrOn in its current form is too big for GitHub Actions."
 
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -27,6 +27,7 @@ These are the current imports in DRON
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
 | chebi | http://purl.obolibrary.org/obo/chebi.owl | slme |
 | pr | http://purl.obolibrary.org/obo/pr.owl | slme |
+| pato | http://purl.obolibrary.org/obo/pato.owl | filter |
 
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -16,7 +16,7 @@
 # 3. [Update repo to latest ODK](update_repo)
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                082560e7167e4c838bb11575d493a5b738d1886fb5b1721258c2e706584f371f
+CONFIG_HASH=                19da4684159be042a50f7d4b9fa0ec9d7698d4c5d70529e63b99f62140d7e4a1
 
 
 # ----------------------------------------
@@ -165,7 +165,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro apollo_sv go iao obi uo ogms bfo omo chebi pr
+IMPORTS =  ro apollo_sv go iao obi uo ogms bfo omo chebi pr pato
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -425,6 +425,16 @@ $(IMPORTDIR)/pr_import.owl: $(MIRRORDIR)/pr.owl $(IMPORTDIR)/pr_terms_combined.t
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
+## Module for ontology: pato
+
+$(IMPORTDIR)/pato_import.owl: $(MIRRORDIR)/pato.owl $(IMPORTDIR)/pato_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
+    extract -T $(IMPORTDIR)/pato_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
+    remove --base-iri http://purl.obolibrary.org/obo/PATO_ --axioms external --preserve-structure false --trim false \
+		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115  -T $(IMPORTDIR)/pato_terms_combined.txt --select complement \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
+		$(ANNOTATE_CONVERT_FILE); fi
+
 
 .PHONY: refresh-imports
 refresh-imports:
@@ -589,6 +599,14 @@ mirror-pr:
 endif
 
 
+## ONTOLOGY: pato
+.PHONY: mirror-pato
+.PRECIOUS: $(MIRRORDIR)/pato.owl
+mirror-pato: | $(TMPDIR)
+	curl -L $(OBOBASE)/pato.owl --create-dirs -o $(TMPDIR)/pato-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/pato-download.owl -o $(TMPDIR)/$@.owl
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -14,7 +14,7 @@
   <uri name="http://purl.obolibrary.org/obo/dron/imports/ogms_import.owl" uri="imports/ogms_import.owl"/>
   <uri name="http://purl.obolibrary.org/obo/dron/imports/iao_import.owl" uri="imports/iao_import.owl"/>
   <uri name="http://purl.obolibrary.org/obo/dron/imports/uo_import.owl" uri="imports/uo_import.owl"/>
-
+  <uri name="http://purl.obolibrary.org/obo/dron/imports/pato_import.owl" uri="imports/pato_import.owl"/>  
 <!--  <uri name="http://purl.obolibrary.org/obo/dron/dron-chebi.owl" uri="components/dron-chebi.owl"/>-->
 
   <!--  <uri name="http://purl.obolibrary.org/obo/dron/dron-hand.owl" uri="components/dron-hand.owl"/>-->

diff --git a/src/ontology/dron-edit.owl b/src/ontology/dron-edit.owl
@@ -20,6 +20,7 @@ Import(<http://purl.obolibrary.org/obo/dron/imports/iao_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/obi_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/ogms_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/omo_import.owl>)
+Import(<http://purl.obolibrary.org/obo/dron/imports/pato_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/pr_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/ro_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/uo_import.owl>)
@@ -342,23 +343,23 @@ Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#sho
 
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> "has_alternative_id")
 
-# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (has cross-reference)
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (database_cross_reference)
 
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "database_cross_reference")
 
-# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> (has exact synonym)
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> (has_exact_synonym)
 
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> "has_exact_synonym")
 
-# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> (has narrow synonym)
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> (has_narrow_synonym)
 
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> "has_narrow_synonym")
 
 # Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> (has_obo_namespace)
 
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> "has_obo_namespace")
 
-# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> (has related synonym)
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> (has_related_synonym)
 
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> "has_related_synonym")
 
@@ -454,7 +455,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_135198> ObjectSomeValuesFrom(<h
 
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_135556> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/DRON_00000072>))
 
-# Class: <http://purl.obolibrary.org/obo/CHEBI_135621> (metaclazepam)
+# Class: <http://purl.obolibrary.org/obo/CHEBI_135621> (Metaclazepam hydrochloride)
 
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_135621> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/DRON_00000072>))
 
@@ -2061,6 +2062,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0005488> <http://purl.obolibrary.org/obo/go#goslim_pir>)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0005488> <http://purl.obolibrary.org/obo/go#goslim_plant>)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0005488> <http://purl.obolibrary.org/obo/go#gosubset_prok>)
+SubClassOf(<http://purl.obolibrary.org/obo/GO_0005488> <http://purl.obolibrary.org/obo/GO_0008150>)
 
 # Class: <http://purl.obolibrary.org/obo/GO_0005515> (protein binding)
 
@@ -2106,6 +2108,11 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.ob
 # Class: <http://purl.obolibrary.org/obo/IAO_0000009> (datum label)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/IAO_0000009> <http://purl.obolibrary.org/obo/IAO_0000122>)
+SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000009> <http://purl.obolibrary.org/obo/IAO_0000030>)
+
+# Class: <http://purl.obolibrary.org/obo/IAO_0000030> (information content entity)
+
+SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000030> <http://purl.obolibrary.org/obo/BFO_0000031>)
 
 # Class: <http://purl.obolibrary.org/obo/OBI_0000011> (planned process)
 
@@ -2127,11 +2134,16 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.ob
 
 SubClassOf(<http://purl.obolibrary.org/obo/OGMS_0000090> <http://purl.obolibrary.org/obo/OBI_0000011>)
 
-# Class: <http://purl.obolibrary.org/obo/PATO_0000125> (<http://purl.obolibrary.org/obo/PATO_0000125>)
+# Class: <http://purl.obolibrary.org/obo/PATO_0000125> (mass)
 
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0000125> <http://purl.obolibrary.org/obo/pato#attribute_slim>)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0000125> <http://purl.obolibrary.org/obo/pato#relational_slim>)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0000125> <http://purl.obolibrary.org/obo/pato#scalar_slim>)
+SubClassOf(<http://purl.obolibrary.org/obo/PATO_0000125> <http://purl.obolibrary.org/obo/PATO_0000001>)
+
+# Class: <http://purl.obolibrary.org/obo/UO_0000000> (unit)
+
+SubClassOf(<http://purl.obolibrary.org/obo/UO_0000000> <http://purl.obolibrary.org/obo/IAO_0000030>)
 
 
 ############################

diff --git a/src/ontology/dron-odk.yaml b/src/ontology/dron-odk.yaml
@@ -49,6 +49,10 @@ import_group:
       module_type: slme
       is_large: TRUE
       use_gzipped: TRUE
+    - id: pato
+      module_type: filter
+      base_iris:
+        - http://purl.obolibrary.org/obo/PATO_
 components:
   products:
     - filename: dron-ingredient.owl

diff --git a/src/ontology/imports/apollo_sv_import.owl b/src/ontology/imports/apollo_sv_import.owl
@@ -7,10 +7,10 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/dron/imports/apollo_sv_import.owl>
-<http://purl.obolibrary.org/obo/dron/releases/2024-12-20/imports/apollo_sv_import.owl>
+<http://purl.obolibrary.org/obo/dron/releases/2024-12-22/imports/apollo_sv_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/apollo_sv/releases/2024-08-15/apollo_sv.owl>)
-Annotation(rdfs:comment "This version of DrOn is current through RxNorm version 20AA_241202F")
-Annotation(owl:versionInfo "2024-12-20")
+Annotation(rdfs:comment "This version of DrOn is current through RxNorm version ")
+Annotation(owl:versionInfo "2024-12-22")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/APOLLO_SV_00000145>))
 Declaration(Class(<http://purl.obolibrary.org/obo/APOLLO_SV_00000335>))

diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl
@@ -7,10 +7,10 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/dron/imports/bfo_import.owl>
-<http://purl.obolibrary.org/obo/dron/releases/2024-12-20/imports/bfo_import.owl>
+<http://purl.obolibrary.org/obo/dron/releases/2024-12-22/imports/bfo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl>)
-Annotation(rdfs:comment "This version of DrOn is current through RxNorm version 20AA_241202F")
-Annotation(owl:versionInfo "2024-12-20")
+Annotation(rdfs:comment "This version of DrOn is current through RxNorm version ")
+Annotation(owl:versionInfo "2024-12-22")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))

diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl
@@ -7,10 +7,10 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/dron/imports/go_import.owl>
-<http://purl.obolibrary.org/obo/dron/releases/2024-12-20/imports/go_import.owl>
+<http://purl.obolibrary.org/obo/dron/releases/2024-12-22/imports/go_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/go/releases/2024-11-03/go.owl>)
-Annotation(rdfs:comment "This version of DrOn is current through RxNorm version 20AA_241202F")
-Annotation(owl:versionInfo "2024-12-20")
+Annotation(rdfs:comment "This version of DrOn is current through RxNorm version ")
+Annotation(owl:versionInfo "2024-12-22")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0003008>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005488>))

diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl
@@ -7,10 +7,10 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/dron/imports/iao_import.owl>
-<http://purl.obolibrary.org/obo/dron/releases/2024-12-20/imports/iao_import.owl>
+<http://purl.obolibrary.org/obo/dron/releases/2024-12-22/imports/iao_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl>)
-Annotation(rdfs:comment "This version of DrOn is current through RxNorm version 20AA_241202F")
-Annotation(owl:versionInfo "2024-12-20")
+Annotation(rdfs:comment "This version of DrOn is current through RxNorm version ")
+Annotation(owl:versionInfo "2024-12-22")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000003>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000009>))

diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl
@@ -7,10 +7,10 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/dron/imports/obi_import.owl>
-<http://purl.obolibrary.org/obo/dron/releases/2024-12-20/imports/obi_import.owl>
+<http://purl.obolibrary.org/obo/dron/releases/2024-12-22/imports/obi_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/obi/2024-12-05/obi.owl>)
-Annotation(rdfs:comment "This version of DrOn is current through RxNorm version 20AA_241202F")
-Annotation(owl:versionInfo "2024-12-20")
+Annotation(rdfs:comment "This version of DrOn is current through RxNorm version ")
+Annotation(owl:versionInfo "2024-12-22")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))

diff --git a/src/ontology/imports/ogms_import.owl b/src/ontology/imports/ogms_import.owl
@@ -7,10 +7,10 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/dron/imports/ogms_import.owl>
-<http://purl.obolibrary.org/obo/dron/releases/2024-12-20/imports/ogms_import.owl>
+<http://purl.obolibrary.org/obo/dron/releases/2024-12-22/imports/ogms_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl>)
-Annotation(rdfs:comment "This version of DrOn is current through RxNorm version 20AA_241202F")
-Annotation(owl:versionInfo "2024-12-20")
+Annotation(rdfs:comment "This version of DrOn is current through RxNorm version ")
+Annotation(owl:versionInfo "2024-12-22")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000090>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))

diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl
@@ -7,10 +7,10 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/dron/imports/omo_import.owl>
-<http://purl.obolibrary.org/obo/dron/releases/2024-12-20/imports/omo_import.owl>
+<http://purl.obolibrary.org/obo/dron/releases/2024-12-22/imports/omo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/omo/releases/2024-11-13/omo.owl>)
-Annotation(rdfs:comment "This version of DrOn is current through RxNorm version 20AA_241202F")
-Annotation(owl:versionInfo "2024-12-20")
+Annotation(rdfs:comment "This version of DrOn is current through RxNorm version ")
+Annotation(owl:versionInfo "2024-12-22")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000027>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000030>))