Merge pull request #2376 from obophenotype/release-2022-03-31

Release 2022 03 31 (easier review)
obophenotype · Apr 6, 2022 · cac2b9b · cac2b9b
2 parents a425013 + 404422a
commit cac2b9b
Show file tree

Hide file tree

Showing 8 changed files with 2,238 additions and 1,298 deletions.
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -25,11 +25,11 @@ These are the current imports in UBERON
 | chebi | http://purl.obolibrary.org/obo/chebi.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.owl | None |
 | bfo | http://purl.obolibrary.org/obo/bfo.owl | None |
-| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon.owl | None |
+| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
 | nbo | http://purl.obolibrary.org/obo/nbo.owl | None |
 | ceph | http://purl.obolibrary.org/obo/ceph.owl | None |
 | cteno | http://purl.obolibrary.org/obo/cteno.owl | None |
-| ehdaa2 | http://purl.obolibrary.org/obo/ehdaa2.owl | None |
+| ehdaa2 | https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo | None |
 | emapa | http://purl.obolibrary.org/obo/emapa.owl | None |
 | fbbt | http://purl.obolibrary.org/obo/fbbt.owl | None |
 | fbdv | http://purl.obolibrary.org/obo/fbdv.owl | None |

diff --git a/imports/cl_import.owl b/imports/cl_import.owl
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -280,13 +280,6 @@ $(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_c
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
 		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
-## Module for ontology: ncbitaxon
-
-$(IMPORTDIR)/ncbitaxon_import.owl: $(MIRRORDIR)/ncbitaxon.owl $(IMPORTDIR)/ncbitaxon_terms_combined.txt
-	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/ncbitaxon_terms_combined.txt --force true --individuals include --method BOT \
-		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
-
 .PHONY: refresh-imports
 refresh-imports:
 	make IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B
@@ -374,7 +367,7 @@ mirror-ro: | $(TMPDIR)
 .PHONY: mirror-bspo
 .PRECIOUS: $(MIRRORDIR)/bspo.owl
 mirror-bspo: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/bspo.owl --create-dirs -o $(MIRRORDIR)/bspo.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/bspo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/bspo/bspo-base.owl --create-dirs -o $(MIRRORDIR)/bspo.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/bspo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: chebi
@@ -402,7 +395,7 @@ mirror-bfo: | $(TMPDIR)
 .PHONY: mirror-ncbitaxon
 .PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl
 mirror-ncbitaxon: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(URIBASE)/ncbitaxon.owl.gz --create-dirs -o $(MIRRORDIR)/ncbitaxon.owl.gz --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/ncbitaxon.owl.gz -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: nbo
@@ -430,7 +423,7 @@ mirror-cteno: | $(TMPDIR)
 .PHONY: mirror-ehdaa2
 .PRECIOUS: $(MIRRORDIR)/ehdaa2.owl
 mirror-ehdaa2: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ehdaa2.owl --create-dirs -o $(MIRRORDIR)/ehdaa2.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/ehdaa2.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: emapa

diff --git a/src/ontology/components/develops-from-chains.owl b/src/ontology/components/develops-from-chains.owl
@@ -0,0 +1,13 @@
+Prefix(:=<http://purl.obolibrary.org/obo/uberon/core.owl#>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl>
+
+SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/RO_0002202>) <http://purl.obolibrary.org/obo/RO_0002202>)
+
+)