From 69841d0af92e2fc51ca3a324abf85fab487681e7 Mon Sep 17 00:00:00 2001 From: cmungall Date: Tue, 3 Jan 2023 17:10:33 -0800 Subject: [PATCH 1/2] Hacky short term solution for https://github.com/INCATools/ontology-access-kit/issues/427 --- utils/ncbo2owl.pl | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100755 utils/ncbo2owl.pl diff --git a/utils/ncbo2owl.pl b/utils/ncbo2owl.pl new file mode 100755 index 0000000..2f4c0d7 --- /dev/null +++ b/utils/ncbo2owl.pl @@ -0,0 +1,7 @@ +#!/usr/bin/perl -np +# See: https://github.com/INCATools/ontology-access-kit/issues/427 +s@skos:prefLabel @rdfs:label @; +s@ @rdfs:subClassOf @; +s@umls:cui """(\w+)"""\^\^xsd:string@skos:exactMatch umls:$1@; +s@umls:cui """(\w+)"""\^\^xsd:string@skos:exactMatch umls:$1@; +s@() ()@rdfs:subClassOf [a owl:Restriction; owl:onProperty $1; owl:someValuesFrom $3]@; From 25f52d66ca86a37d6fb8a21fb222c1ec16d3c943 Mon Sep 17 00:00:00 2001 From: cmungall Date: Tue, 3 Jan 2023 17:11:12 -0800 Subject: [PATCH 2/2] regen --- Makefile | 8 ++++---- ontologies.Makefile | 13 ++++++++++++- src/semsql/builder/prefixes/prefixes.csv | 1 + src/semsql/builder/prefixes/prefixes_local.csv | 1 + src/semsql/builder/registry/ontologies.yaml | 3 +++ 5 files changed, 21 insertions(+), 5 deletions(-) diff --git a/Makefile b/Makefile index 2062528..c884839 100644 --- a/Makefile +++ b/Makefile @@ -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: diff --git a/ontologies.Makefile b/ontologies.Makefile index a0c1c0c..a9b27b1 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -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 @@ -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 diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index 88de6c2..98da06e 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -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_ diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index 8038244..0901583 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -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/ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index c4dde36..e32cea0 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -164,3 +164,6 @@ ontologies: compression: gzip prefixmap: complexportal: http://purl.obolibrary.org/obo/complexportal_ + drugmechdb: + prefixmap: + MESH: http://id.nlm.nih.gov/mesh/