Merge pull request #316 from mcwdsi/issue-308

updated IAO import to filter module with make_base: true. Then repare…

Author: hoganwr

docs/odk-workflows/RepositoryFileStructure.md

@@ -28,7 +28,7 @@ These are the current imports in OMRSE
 | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | filter |
 | oostt | http://purl.obolibrary.org/obo/oostt.owl | filter |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
-| iao | http://purl.obolibrary.org/obo/iao.owl | mirror |
+| iao | http://purl.obolibrary.org/obo/iao.owl | filter |
 | d-acts | http://purl.obolibrary.org/obo/iao/d-acts.owl | filter |
 | geo | http://purl.obolibrary.org/obo/geo.owl | filter |
 | mf | http://purl.obolibrary.org/obo/mf.owl | filter |

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=                8f3e3334536fd37070740c6e9f4eba111d6ee240094a95f1b91e2b3c52b552e6
+CONFIG_HASH=                027a2056f9a26e4b98ccf68e5955782f997ec0ed3eb75d0555f7b991cf3c861f
 
 
 # ----------------------------------------
@@ -618,12 +618,22 @@ $(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl | all_robot_plugins
 		 repair --merge-axiom-annotations true \
 		 $(ANNOTATE_CONVERT_FILE)
 
-## Module for ontology: iao (mirror)
-$(IMPORTDIR)/iao_import.owl: $(MIRRORDIR)/iao.owl | all_robot_plugins
+## Module for ontology: iao (filter)
+$(IMPORTDIR)/iao_import.owl: $(MIRRORDIR)/iao.owl $(IMPORTDIR)/iao_terms.txt $(IMPORTSEED) | all_robot_plugins
 	$(ROBOT) annotate --input $< --remove-annotations \
+		 odk:normalize --add-source true \
+		 extract --term-file $(IMPORTDIR)/iao_terms.txt $(T_IMPORTSEED) \
+		         --copy-ontology-annotations true --force true --method BOT \
+		 remove --axioms external --preserve-structure false --trim false \
+		        --base-iri http://purl.obolibrary.org/obo/IAO_ \
+		 remove $(foreach p, $(ANNOTATION_PROPERTIES), --term $(p)) \
+		        --term rdfs:label \
+		        --term IAO:0000115 \
+		        --term OMO:0002000 \
+		        --term-file $(IMPORTDIR)/iao_terms.txt $(T_IMPORTSEED) \
+		        --select complement \
 		 odk:normalize --base-iri http://purl.obolibrary.org/obo \
 		               --subset-decls true --synonym-decls true \
-		               --add-source true \
 		 repair --merge-axiom-annotations true \
 		 $(ANNOTATE_CONVERT_FILE)
 
@@ -874,7 +884,7 @@ mirror-omo: | $(TMPDIR)
 .PRECIOUS: $(MIRRORDIR)/iao.owl
 mirror-iao: | $(TMPDIR)
 	curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \
-	$(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/$@.owl
+	$(ROBOT) remove -i $(TMPDIR)/iao-download.owl --base-iri http://purl.obolibrary.org/obo/IAO_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: d-acts

src/ontology/catalog-v001.xml

@@ -18,7 +18,7 @@
     <uri name="http://purl.obolibrary.org/obo/omrse/imports/geo_import.owl" uri="imports/geo_import.owl" />
     <uri name="http://purl.obolibrary.org/obo/omrse/imports/mf_import.owl" uri="imports/mf_import.owl" />
     <uri name="http://purl.obolibrary.org/obo/omrse/imports/occo_import.owl" uri="imports/occo_import.owl" />
-    <uri name="http://purl.obolibrary.org/obo/omrse/language-individuals.owl" uri="components/language/language-individuals.owl" />
+    <uri name="http://purl.obolibrary.org/obo/omrse/components/language/language-individuals.owl" uri="components/language/language-individuals.owl" />
   </group>
   <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/omrse/releases/2025-01-18/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl" />
   <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/omrse/releases/2023-09-08/imports/mf_import.owl" uri="imports/mf_import.owl" />
@@ -46,4 +46,4 @@
     <uri name="http://purl.obolibrary.org/obo/omrse/components/import_terms.owl" uri="components/import_terms.owl" />
     <uri name="http://purl.obolibrary.org/obo/omrse/language-individuals/" uri="components/language/language-individuals.owl" />
   </group>
-</catalog>
+</catalog>

src/ontology/components/language/language-individuals.owl

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
-<rdf:RDF xmlns="http://purl.obolibrary.org/obo/omrse/language-individuals.owl/"
-     xml:base="http://purl.obolibrary.org/obo/omrse/language-individuals.owl/"
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/omrse/components/language/language-individuals.owl/"
+     xml:base="http://purl.obolibrary.org/obo/omrse/components/language/language-individuals.owl/"
      xmlns:dc="http://purl.org/dc/elements/1.1/"
      xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
@@ -12,8 +12,8 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
-     xmlns:language-individuals="http://purl.obolibrary.org/obo/omrse/language-individuals/">
-    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/omrse/language-individuals.owl">
+     xmlns:language-individuals="http://purl.obolibrary.org/obo/omrse/components/language/language-individuals/">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/omrse/components/language/language-individuals.owl">
         <dc:creator xml:lang="en">Mathias Brochhausen</dc:creator>
         <dc:creator xml:lang="en">Matthew Diller</dc:creator>
         <dc:creator xml:lang="en">S. Clint Dowland</dc:creator>

src/ontology/imports/apollo_sv_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/omrse/imports/apollo_sv_import.owl>
-<http://purl.obolibrary.org/obo/omrse/releases/2026-01-06/imports/apollo_sv_import.owl>
+<http://purl.obolibrary.org/obo/omrse/releases/2026-02-04/imports/apollo_sv_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv.owl>)
-Annotation(owl:versionInfo "2026-01-06")
+Annotation(owl:versionInfo "2026-02-04")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/APOLLO_SV_00000032>))
 Declaration(Class(<http://purl.obolibrary.org/obo/APOLLO_SV_00000480>))

src/ontology/imports/bfo_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/omrse/imports/bfo_import.owl>
-<http://purl.obolibrary.org/obo/omrse/releases/2026-01-06/imports/bfo_import.owl>
+<http://purl.obolibrary.org/obo/omrse/releases/2026-02-04/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(owl:versionInfo "2026-01-06")
+Annotation(owl:versionInfo "2026-02-04")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))

src/ontology/imports/d-acts_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/omrse/imports/d-acts_import.owl>
-<http://purl.obolibrary.org/obo/omrse/releases/2026-01-06/imports/d-acts_import.owl>
+<http://purl.obolibrary.org/obo/omrse/releases/2026-02-04/imports/d-acts_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/iao/d-acts/release/2025-08-27/d-acts.owl>)
-Annotation(owl:versionInfo "2026-01-06")
+Annotation(owl:versionInfo "2026-02-04")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000023>))

src/ontology/imports/geo_import.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/omrse/imports/geo_import.owl>
-<http://purl.obolibrary.org/obo/omrse/releases/2026-01-06/imports/geo_import.owl>
-Annotation(owl:versionInfo "2026-01-06")
+<http://purl.obolibrary.org/obo/omrse/releases/2026-02-04/imports/geo_import.owl>
+Annotation(owl:versionInfo "2026-02-04")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/GEO_000000400>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))

src/ontology/imports/go_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/omrse/imports/go_import.owl>
-<http://purl.obolibrary.org/obo/omrse/releases/2026-01-06/imports/go_import.owl>
-Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/go/releases/2025-10-10/go.owl>)
-Annotation(owl:versionInfo "2026-01-06")
+<http://purl.obolibrary.org/obo/omrse/releases/2026-02-04/imports/go_import.owl>
+Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/go/releases/2026-01-23/go.owl>)
+Annotation(owl:versionInfo "2026-02-04")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0007610>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0008150>))
@@ -18,6 +18,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000233>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
 Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>))
 
 
 ############################
@@ -31,6 +32,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <ht
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0007610> "behavioral response to stimulus")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0007610> "behaviour")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0007610> "behavioural response to stimulus")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/GO_0007610> "single-organism behavior")
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0007610> "1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.
 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0007610> "behavior")
@@ -43,6 +45,8 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000233> <http://purl.ob
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/GO_0008150> "Wikipedia:Biological_process")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0008150> "biological process")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/GO_0008150> "physiological process")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/GO_0008150> "single organism process")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/GO_0008150> "single-organism process")
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0008150> "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 <http://purl.obolibrary.org/obo/GO_0008150> "biological_process")