Merge pull request #639 from monarch-initiative/update-imports

Add COB, update imports and add constraints on what to pull in, eg BSPO
monarch-initiative · May 6, 2024 · fa6ce0f · fa6ce0f
2 parents 47192e6 + 06e578f
commit fa6ce0f
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diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                9e0aab07905c1d15c732de96a5ca949e9996de50fd7ec4659a0874a075e3bca1
+CONFIG_HASH=                fab3962b1129f1bb5cff3dd83a9e7b702976ffe614b6d7ea307b996f6663b975
 
 
 # ----------------------------------------
@@ -165,7 +165,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  omo go ro so bfo uberon foodon nbo pato hp cl chebi obi ncbitaxon pr
+IMPORTS =  omo cob go ro so bfo uberon foodon nbo pato hp cl chebi obi ncbitaxon pr
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -375,7 +375,7 @@ $(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
 
 $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
-		remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/MPATH_*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>" remove  --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>" remove  --select "<http://birdgenenames.org/cgnc/GeneReport*>" remove  --select "<http://www.ncbi.nlm.nih.gov/gene/*>" remove  --select "<http://purl.obolibrary.org/obo/foodon.owl/FOODON_*>" remove  --select "<http://purl.obolibrary.org/obo/IAO_0000109*>" remove  --select "<http://purl.obolibrary.org/obo/IAO_0000101*>"  \
+		remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/MPATH_*>" remove  --select "<http://purl.obolibrary.org/obo/SEPIO_*>" remove  --select "<http://purl.obolibrary.org/obo/MOD_*>" remove  --select "<http://purl.obolibrary.org/obo/BSPO_*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>" remove  --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>" remove  --select "<http://birdgenenames.org/cgnc/GeneReport*>" remove  --select "<http://www.ncbi.nlm.nih.gov/gene/*>" remove  --select "<http://purl.obolibrary.org/obo/foodon.owl/FOODON_*>" remove  --select "<http://purl.obolibrary.org/obo/IAO_0000109*>" remove  --select "<http://purl.obolibrary.org/obo/IAO_0000101*>"  \
 		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
 		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
@@ -487,6 +487,14 @@ mirror-omo: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl
 
 
+## ONTOLOGY: cob
+.PHONY: mirror-cob
+.PRECIOUS: $(MIRRORDIR)/cob.owl
+mirror-cob: | $(TMPDIR)
+	curl -L $(OBOBASE)/cob.owl --create-dirs -o $(TMPDIR)/cob-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) remove -i $(TMPDIR)/cob-download.owl --base-iri $(OBOBASE)/COB --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
+
+
 ## ONTOLOGY: go
 .PHONY: mirror-go
 .PRECIOUS: $(MIRRORDIR)/go.owl
@@ -806,7 +814,7 @@ ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --tri
 # base: A version of the ontology that does not include any externally imported axioms.
 $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \
-	reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
+	reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms false \
 	relax \
 	reduce -r ELK \
 	remove --base-iri http://purl.obolibrary.org/obo/MAXO_ --axioms external --preserve-structure false --trim false \

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -14,6 +14,7 @@
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/maxo/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/maxo/imports/chebi_import.obo" uri="imports/chebi_import.obo"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/maxo/imports/nbo_import.owl" uri="imports/nbo_import.owl"/>
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/maxo/imports/cob_import.owl" uri="imports/cob_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/maxo/imports/nbo_import.obo" uri="imports/nbo_import.obo"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/maxo/imports/hp_import.owl" uri="imports/hp_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/maxo/imports/hp_import.obo" uri="imports/hp_import.obo"/>

diff --git a/src/ontology/components/maxo-deprecated.owl b/src/ontology/components/maxo-deprecated.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/maxo/components/maxo-deprecated.owl>
-<http://purl.obolibrary.org/obo/maxo/releases/2024-02-05/components/maxo-deprecated.owl>
-Annotation(owl:versionInfo "2024-02-05")
+<http://purl.obolibrary.org/obo/maxo/releases/2024-05-06/components/maxo-deprecated.owl>
+Annotation(owl:versionInfo "2024-05-06")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000008>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000032>))

diff --git a/src/ontology/components/maxo-template.owl b/src/ontology/components/maxo-template.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/maxo/components/maxo-template.owl>
-<http://purl.obolibrary.org/obo/maxo/releases/2024-02-05/components/maxo-template.owl>
-Annotation(owl:versionInfo "2024-02-05")
+<http://purl.obolibrary.org/obo/maxo/releases/2024-05-06/components/maxo-template.owl>
+Annotation(owl:versionInfo "2024-05-06")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000003>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000005>))

diff --git a/src/ontology/components/maxo-xrefs.owl b/src/ontology/components/maxo-xrefs.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/maxo/components/maxo-xrefs.owl>
-<http://purl.obolibrary.org/obo/maxo/releases/2024-02-05/components/maxo-xrefs.owl>
-Annotation(owl:versionInfo "2024-02-05")
+<http://purl.obolibrary.org/obo/maxo/releases/2024-05-06/components/maxo-xrefs.owl>
+Annotation(owl:versionInfo "2024-05-06")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000001>))
 Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))