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Adding overrides for SWO prefixes. #91

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Jan 30, 2025
Merged

Adding overrides for SWO prefixes. #91

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Adding overrides for SWO prefixes.
cmungall Aug 14, 2024
f25ac94
new sources
cmungall Jan 30, 2025
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196 changes: 186 additions & 10 deletions ontologies.Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
download/upheno.owl: STAMP
curl -L -s http://purl.obolibrary.org/obo/upheno.owl > [email protected]
download/swo.owl: STAMP
curl -L -s http://purl.obolibrary.org/obo/swo.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/upheno.owl
.PRECIOUS: download/swo.owl

db/upheno.owl: download/upheno.owl
db/swo.owl: download/swo.owl
robot merge -i $< -o $@


Expand All @@ -20,6 +20,39 @@ db/chiro.owl: download/chiro.owl
robot relax -i $< merge -o $@


download/pcl.owl: STAMP
curl -L -s http://purl.obolibrary.org/obo/pcl.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/pcl.owl

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


download/chemessence.owl: STAMP
curl -L -s https://github.com/cmungall/chemessence/releases/latest/download/chemessence.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/chemessence.owl

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


download/ogco.owl: STAMP
curl -L -s https://raw.githubusercontent.com/cmungall/chemessence/refs/heads/main/src/ontology/components/ogco.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/ogco.owl

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


download/ncit.owl: STAMP
curl -L -s http://purl.obolibrary.org/obo/ncit.owl > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -86,6 +119,17 @@ db/msio.owl: download/msio.owl
cp $< $@


download/pride.owl: STAMP
curl -L -s https://raw.githubusercontent.com/PRIDE-Archive/pride-ontology/master/pride_cv.obo > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/pride.owl

db/pride.owl: download/pride.owl
robot relax -i $< merge -o $@


download/modl.owl: STAMP
curl -L -s https://raw.githubusercontent.com/Data-Semantics-Laboratory/modular-ontology-design-library/master/MODL.owl > [email protected]
sha256sum -b [email protected] > [email protected]
Expand All @@ -98,7 +142,7 @@ db/modl.owl: download/modl.owl


download/phenio.owl: STAMP
curl -L -s https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl > [email protected]
curl -L -s https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl.gz | gzip -dc > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

Expand Down Expand Up @@ -163,6 +207,17 @@ db/reacto.owl: download/reacto.owl
cp $< $@


download/xsmo.owl: STAMP
curl -L -s https://download.xenbase.org/xenbase/Ontologies/XSMO/XSMO_1.1/XSMO_1.1.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/xsmo.owl

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


download/bcio.owl: STAMP
curl -L -s http://humanbehaviourchange.org/ontology/bcio.owl > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -229,6 +284,28 @@ db/oeo.owl: download/oeo.owl
cp $< $@


download/envthes.owl: STAMP
curl -L -s https://vocabs.lter-europe.net/rest/v1/envthes/data?format=text/turtle > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/envthes.owl

db/envthes.owl: download/envthes.owl
robot query -i $< --update sparql/skos-to-owl.ru -o $@


download/wifire.owl: STAMP
curl -L -s https://raw.githubusercontent.com/WIFIRE-Lab/WIFIRE-commons-ontology/master/WIFIRE-commons-ontology-V1.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/wifire.owl

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


download/taxslim.owl: STAMP
curl -L -s http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.obo > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -406,7 +483,7 @@ db/bao.owl: download/bao.owl


download/orcid.owl: STAMP
curl -L -s https://raw.githubusercontent.com/cthoyt/wikidata-orcid-ontology/main/orcid.owl > [email protected]
curl -L -s https://w3id.org/orcidio/orcidio.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

Expand Down Expand Up @@ -482,6 +559,28 @@ db/ito.owl: download/ito.owl
cp $< $@


download/chemont.owl: STAMP
curl -L -s http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip > [email protected] && unzip -p [email protected] ChemOnt_2_1.obo > [email protected] && rm [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/chemont.owl

db/chemont.owl: download/chemont.owl
robot convert -i $< -o $@


download/molgenie.owl: STAMP
curl -L -s https://github.com/MolGenie/ontology/blob/main/mol_classes_ext_2024-11-20.obo > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/molgenie.owl

db/molgenie.owl: download/molgenie.owl
robot convert -i $< -o $@


download/cso.owl: STAMP
curl -L -s https://cso.kmi.open.ac.uk/download/version-3.3/CSO.3.3.owl.zip > [email protected] && unzip -p [email protected] CSO.3.3.owl > [email protected] && rm [email protected]
sha256sum -b [email protected] > [email protected]
Expand All @@ -504,6 +603,17 @@ db/obiws.owl: download/obiws.owl
cp $< $@


download/biopragmatics-reactome.owl: STAMP
curl -L -s https://w3id.org/biopragmatics/resources/reactome/reactome.obo > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/biopragmatics-reactome.owl

db/biopragmatics-reactome.owl: download/biopragmatics-reactome.owl
cp $< $@


download/reactome-hs.owl: STAMP
curl -L -s https://reactome.org/download/current/biopax.zip > [email protected] && unzip -p [email protected] Homo_sapiens.owl > [email protected] && rm [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -592,6 +702,28 @@ db/sweetAll.owl: download/sweetAll.owl
robot merge -i $< -o $@


download/oboe-core.owl: STAMP
curl -L -s http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/oboe-core.owl

db/oboe-core.owl: download/oboe-core.owl
cp $< $@


download/oboe-standards.owl: STAMP
curl -L -s http://ecoinformatics.org/oboe/oboe.1.0/oboe-standards.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/oboe-standards.owl

db/oboe-standards.owl: download/oboe-standards.owl
cp $< $@


download/lov.owl: STAMP
curl -L -s https://lov.linkeddata.es/lov.n3.gz | gzip -dc > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -735,6 +867,17 @@ db/icd10cm.owl: download/icd10cm.owl
cp $< $@


download/omim.owl: STAMP
curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/omim.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/omim.owl

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


download/co_324.owl: STAMP
curl -L -s https://cropontology.org/ontology/CO_324/rdf > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -824,7 +967,7 @@ db/eccode.owl: download/eccode.owl


download/uniprot.owl: STAMP
curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/uniprot/2022_02/uniprot.owl.gz | gzip -dc > [email protected]
curl -L -s https://w3id.org/biopragmatics/resources/uniprot/2022_02/uniprot.owl.gz | gzip -dc > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

Expand All @@ -835,14 +978,14 @@ db/uniprot.owl: download/uniprot.owl


download/rhea.owl: STAMP
curl -L -s https://w3id.org/biopragmatics/resources/rhea/rhea.owl > [email protected]
curl -L -s https://w3id.org/biopragmatics/resources/rhea/rhea.obo > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/rhea.owl

db/rhea.owl: download/rhea.owl
cp $< $@
robot merge -i $< -o $@


download/swisslipid.owl: STAMP
Expand Down Expand Up @@ -900,6 +1043,28 @@ db/wikipathways.owl: download/wikipathways.owl
cp $< $@


download/pathbank.owl: STAMP
curl -L -s https://w3id.org/biopragmatics/resources/pathbank/pathbank.obo.gz | gzip -dc > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/pathbank.owl

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


download/kegg.genome.owl: STAMP
curl -L -s https://w3id.org/biopragmatics/resources/kegg.genome/kegg.genome.obo > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/kegg.genome.owl

db/kegg.genome.owl: download/kegg.genome.owl
cp $< $@


download/drugmechdb.owl: STAMP
curl -L -s None > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -1021,6 +1186,17 @@ db/mixs.owl: download/mixs.owl
robot merge -i $< reason -o $@


download/kgcl.owl: STAMP
curl -L -s https://w3id.org/kgcl/kgcl.owl.ttl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/kgcl.owl

db/kgcl.owl: download/kgcl.owl
robot merge -i $< reason -o $@


download/fibo.owl: STAMP
curl -L -s https://spec.edmcouncil.org/fibo/ontology/AboutFIBOProd/ > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -1086,4 +1262,4 @@ download/%.owl: STAMP
db/%.owl: download/%.owl
robot merge -i $< -o $@

EXTRA_ONTOLOGIES = upheno chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo taxslim goldterms sdgio kin biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito cso obiws reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio pride modl phenio phenio_test comploinc bero aio reacto xsmo bcio icd10who ordo gard mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito chemont molgenie cso obiws biopragmatics-reactome reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll oboe-core oboe-standards lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm omim co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context ontie ecosim nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
61 changes: 61 additions & 0 deletions sparql/skos-to-owl.ru
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX IAO: <http://purl.obolibrary.org/obo/IAO_>

# Transform broader to subClassOf
DELETE {
?concept skos:broader ?broaderConcept .
}
INSERT {
?concept rdf:type owl:Class .
?broaderConcept rdf:type owl:Class .
?concept rdfs:subClassOf ?broaderConcept .
}
WHERE {
?concept skos:broader ?broaderConcept .
};

# Transform prefLabel to rdfs:label
DELETE {
?concept skos:prefLabel ?label .
}
INSERT {
?concept rdfs:label ?label .
}
WHERE {
?concept skos:prefLabel ?label .
};

# Transform SKOS definition to IAO definition
DELETE {
?concept skos:definition ?definition .
}
INSERT {
?concept IAO:0000115 ?definition .
}
WHERE {
?concept skos:definition ?definition .
};


DELETE {
?concept rdf:type skos:Concept .
}
INSERT {
?concept rdf:type owl:Class .
}
WHERE {
?concept rdf:type skos:Concept .
};


DELETE {
?concept rdf:type owl:NamedIndividual .
}
WHERE {
?concept rdf:type owl:Class .
};


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