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Release 2022 03 31 (easier review) #2376

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Apr 6, 2022
Merged

Release 2022 03 31 (easier review) #2376

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424ec38
Updates to release
matentzn Apr 1, 2022
f6d89d0
Merge branch 'master' into release-2022-03-31
matentzn Apr 1, 2022
7247bbb
Update uberon.Makefile
matentzn Apr 1, 2022
96c3bc9
Update uberon-edit.obo
matentzn Apr 5, 2022
b3a7604
Merge branch 'master' into release-2022-03-31
matentzn Apr 5, 2022
53b0e79
uberon.obo changes
matentzn Apr 5, 2022
dc5c6d2
Revert "Update uberon-edit.obo"
matentzn Apr 5, 2022
2a9b515
Merging in develops from chain is component
matentzn Apr 5, 2022
847b150
Merge branch 'release-2022-03-31' of https://github.com/obophenotype/…
matentzn Apr 5, 2022
7163b00
Update uberon.Makefile
matentzn Apr 5, 2022
404422a
uberon.obo changes 2
matentzn Apr 5, 2022
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4 changes: 2 additions & 2 deletions docs/odk-workflows/RepositoryFileStructure.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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 |
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1,057 changes: 878 additions & 179 deletions imports/cl_import.owl
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13 changes: 3 additions & 10 deletions src/ontology/Makefile
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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13 changes: 13 additions & 0 deletions src/ontology/components/develops-from-chains.owl
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@@ -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>)

)
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