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Merged
cmungall merged 2 commits into from
Jan 4, 2023
Merged

node identifiers #66

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69841d0
Hacky short term solution for https://github.com/INCATools/ontology-a…
cmungall Jan 4, 2023
25f52d6
regen
cmungall Jan 4, 2023
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8 changes: 4 additions & 4 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,10 @@ selected: $(patsubst %,all-%,$(SELECTED_ONTS))

all-%: db/%.db
sqlite3 $< "SELECT COUNT(*) FROM statements"
#stage/%.db.gz: db/%.db
# gzip -c $< > $@.tmp && mv $@.tmp $@
stage/%.db.gz:
gzip -c db/$*.db > $@.tmp && mv $@.tmp $@
stage/%.db.gz: db/%.db
gzip -c $< > $@.tmp && mv $@.tmp $@
#stage/%.db.gz:
# gzip -c db/$*.db > $@.tmp && mv $@.tmp $@
.PRECIOUS: stage/%.db.gz

list-onts:
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13 changes: 12 additions & 1 deletion ontologies.Makefile
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Expand Up @@ -416,6 +416,17 @@ db/complexportal.owl: download/complexportal.owl
cp $< $@


download/drugmechdb.owl: STAMP
curl -L -s None > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/drugmechdb.owl

db/drugmechdb.owl: download/drugmechdb.owl
cp $< $@


download/%.owl: STAMP
curl -L -s http://purl.obolibrary.org/obo/$*.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand All @@ -426,4 +437,4 @@ download/%.owl: STAMP
db/%.owl: download/%.owl
robot merge -i $< -o $@

EXTRA_ONTOLOGIES = chiro ncit maxo foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot rhea drugbank drugcentral complexportal
EXTRA_ONTOLOGIES = chiro ncit maxo foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot rhea drugbank drugcentral complexportal drugmechdb
1 change: 1 addition & 0 deletions src/semsql/builder/prefixes/prefixes.csv
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Expand Up @@ -70,6 +70,7 @@ uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
drugbank,http://purl.obolibrary.org/obo/drugbank_
drugbank,http://purl.obolibrary.org/obo/drugcentral_
complexportal,http://purl.obolibrary.org/obo/complexportal_
MESH,http://id.nlm.nih.gov/mesh/
RBO,http://purl.obolibrary.org/obo/RBO_
RBO,http://purl.obolibrary.org/obo/RBO_
CLYH,http://purl.obolibrary.org/obo/CLYH_
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1 change: 1 addition & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
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Expand Up @@ -18,3 +18,4 @@ uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
drugbank,http://purl.obolibrary.org/obo/drugbank_
drugbank,http://purl.obolibrary.org/obo/drugcentral_
complexportal,http://purl.obolibrary.org/obo/complexportal_
MESH,http://id.nlm.nih.gov/mesh/
3 changes: 3 additions & 0 deletions src/semsql/builder/registry/ontologies.yaml
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Expand Up @@ -164,3 +164,6 @@ ontologies:
compression: gzip
prefixmap:
complexportal: http://purl.obolibrary.org/obo/complexportal_
drugmechdb:
prefixmap:
MESH: http://id.nlm.nih.gov/mesh/
7 changes: 7 additions & 0 deletions utils/ncbo2owl.pl
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@@ -0,0 +1,7 @@
#!/usr/bin/perl -np
# See: https://github.com/INCATools/ontology-access-kit/issues/427
s@skos:prefLabel @rdfs:label @;
s@<http://purl.bioontology.org/ontology/\w+/isa> @rdfs:subClassOf @;
s@umls:cui """(\w+)"""\^\^xsd:string@skos:exactMatch umls:$1@;
s@umls:cui """(\w+)"""\^\^xsd:string@skos:exactMatch umls:$1@;
s@(<http://purl.bioontology.org/ontology/RXNORM/(has_ingredient|consists_of|has_dose_form|tradename_of)>) (<http://purl.bioontology.org/ontology/RXNORM/\d+>)@rdfs:subClassOf [a owl:Restriction; owl:onProperty $1; owl:someValuesFrom $3]@;