Fix OMIM part of, refresh exclusions

monarch-initiative · Oct 8, 2022 · 2e0a4bc · 2e0a4bc
1 parent a0b46a4
commit 2e0a4bc
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Showing 28 changed files with 804,085 additions and 358,293 deletions.
diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl
@@ -12,9 +12,9 @@
      xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo-ingest/imports/omo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo-ingest/releases/2022-09-20/imports/omo_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo-ingest/releases/2022-10-07/imports/omo_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/omo/releases/2022-04-27/omo.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-20</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-07</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
@@ -17,9 +17,9 @@
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo-ingest/imports/ro_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo-ingest/releases/2022-09-20/imports/ro_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo-ingest/releases/2022-10-07/imports/ro_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2022-09-07/ro.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-20</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-07</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/src/ontology/mondo-ingest.Makefile b/src/ontology/mondo-ingest.Makefile
@@ -57,6 +57,7 @@ $(COMPONENTSDIR)/ordo.owl: $(TMPDIR)/ordo_relevant_signature.txt config/properti
 		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
 		rename --mappings config/property-map-2.sssom.tsv --allow-missing-entities true \
 		query \
+			--update ../sparql/fix_partof.ru \
 			--update ../sparql/fix_deprecated.ru \
 			--update ../sparql/fix_complex_reification.ru \
 			--update ../sparql/fix_xref_prefixes.ru \
@@ -218,6 +219,9 @@ exclusions-%:
 	$(MAKE) $(REPORTDIR)/$*_exclusion_reasons.ttl
 	$(MAKE) $(REPORTDIR)/$*_excluded_terms_in_mondo_xrefs.tsv
 
+exclusions-all:
+	$(MAKE) $(foreach n,$(ALL_COMPONENT_IDS), exclusions-$(n))
+
 # Exclusions: running for all ontologies
 $(REPORTDIR)/excluded_terms.txt $(REPORTDIR)/exclusion_reasons.robot.template.tsv: $(foreach n,$(ALL_COMPONENT_IDS), $(REPORTDIR)/$(n)_term_exclusions.txt)
 	cat $(REPORTDIR)/*_term_exclusions.txt > $(REPORTDIR)/excluded_terms.txt; \
@@ -296,7 +300,6 @@ tmp/mondo.sssom.ttl: tmp/mondo.sssom.tsv
 # Merge Mondo, precise mappings and mondo-ingest into one coherent whole for the purpose of querying.
 
 tmp/merged.owl: tmp/mondo.owl tmp/mondo-ingest.owl tmp/mondo.sssom.ttl
-	$(ROBOT) merge -i tmp/mondo.owl -i tmp/mondo-ingest.owl -i tmp/mondo.sssom.ttl -o $@
 	$(ROBOT) merge -i tmp/mondo.owl -i tmp/mondo-ingest.owl -i tmp/mondo.sssom.ttl  --add-prefixes config/context.json -o $@
 
 $(REPORTDIR)/mondo_ordo_unsupported_subclass.tsv: ../sparql/mondo-ordo-unsupported-subclass.sparql