From 61b51661a8c90fdb540f0d55a575db884a263182 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 13 Aug 2024 18:25:03 -0700 Subject: [PATCH 1/2] Adding overrides for SWO prefixes. See https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2307#issuecomment-2287584654 --- ontologies.Makefile | 13 ++++++++++++- src/semsql/builder/prefixes/prefixes.csv | 14 +++++++++++++- src/semsql/builder/prefixes/prefixes_local.csv | 12 ++++++++++++ src/semsql/builder/registry/ontologies.yaml | 16 ++++++++++++++++ 4 files changed, 53 insertions(+), 2 deletions(-) diff --git a/ontologies.Makefile b/ontologies.Makefile index 4ff13ee..ef0c223 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -9,6 +9,17 @@ db/upheno.owl: download/upheno.owl robot merge -i $< -o $@ +download/swo.owl: STAMP + curl -L -s http://purl.obolibrary.org/obo/swo.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/swo.owl + +db/swo.owl: download/swo.owl + robot merge -i $< -o $@ + + download/chiro.owl: STAMP curl -L -s http://purl.obolibrary.org/obo/chiro.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1086,4 +1097,4 @@ 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 = upheno swo 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 diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index 95054a6..6707b19 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -62,6 +62,17 @@ semapv,https://w3id.org/semapv/vocab/ sssom,https://w3id.org/sssom/ CLINGEN,https://www.clinicalgenome.org/affiliation/ prefix,base +SWO,http://www.ebi.ac.uk/swo/SWO_ +SWO.organization,http://www.ebi.ac.uk/swo/organization/SWO_ +SWO.maturity,http://www.ebi.ac.uk/swo/maturity/SWO_ +SWO.objective,http://www.ebi.ac.uk/swo/objective/SWO_ +SWO.license,http://www.ebi.ac.uk/swo/license/SWO_ +SWO.version,http://www.ebi.ac.uk/swo/version/SWO_ +SWO.data,http://www.ebi.ac.uk/swo/data/SWO_ +SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_ +SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_ +OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_ +OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD FMA,http://purl.org/sig/ont/fma/fma MSIO,http://purl.obolibrary.org/obo/MSIO_ nmrCV,http://nmrML.org/nmrCV#NMR: @@ -100,11 +111,12 @@ cyc,http://sw.cyc.com/concept OBIws,http://purl.obolibrary.org/obo/OBIws_ chr,http://purl.obolibrary.org/obo/CHR_ prov,http://www.w3.org/ns/prov# -voag,http://voag.linkedmodel.org/voag# dtype,http://www.linkedmodel.org/schema/dtype# +voag,http://voag.linkedmodel.org/voag# vaem,http://www.linkedmodel.org/schema/vaem# qudtschema,http://qudt.org/schema/qudt/ qudtunit,http://qudt.org/vocab/unit/ +si-quantity,https://si-digital-framework.org/SI/quantities/ quantitykind,http://qudt.org/vocab/quantitykind/ cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_ fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb# diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index ca8188c..05f2935 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -1,4 +1,15 @@ prefix,base +SWO,http://www.ebi.ac.uk/swo/SWO_ +SWO.organization,http://www.ebi.ac.uk/swo/organization/SWO_ +SWO.maturity,http://www.ebi.ac.uk/swo/maturity/SWO_ +SWO.objective,http://www.ebi.ac.uk/swo/objective/SWO_ +SWO.license,http://www.ebi.ac.uk/swo/license/SWO_ +SWO.version,http://www.ebi.ac.uk/swo/version/SWO_ +SWO.data,http://www.ebi.ac.uk/swo/data/SWO_ +SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_ +SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_ +OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_ +OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD FMA,http://purl.org/sig/ont/fma/fma MSIO,http://purl.obolibrary.org/obo/MSIO_ nmrCV,http://nmrML.org/nmrCV#NMR: @@ -42,6 +53,7 @@ voag,http://voag.linkedmodel.org/voag# vaem,http://www.linkedmodel.org/schema/vaem# qudtschema,http://qudt.org/schema/qudt/ qudtunit,http://qudt.org/vocab/unit/ +si-quantity,https://si-digital-framework.org/SI/quantities/ quantitykind,http://qudt.org/vocab/quantitykind/ cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_ fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb# diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index a9a1e67..22d08de 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -5,6 +5,22 @@ ontologies: upheno: url: http://purl.obolibrary.org/obo/upheno.owl build_command: "robot merge -i $< -o $@" + swo: + url: http://purl.obolibrary.org/obo/swo.owl + build_command: "robot merge -i $< -o $@" + # runoak -i sqlite:obo:swo + prefixmap: + SWO: http://www.ebi.ac.uk/swo/SWO_ + SWO.organization: http://www.ebi.ac.uk/swo/organization/SWO_ + SWO.maturity: http://www.ebi.ac.uk/swo/maturity/SWO_ + SWO.objective: http://www.ebi.ac.uk/swo/objective/SWO_ + SWO.license: http://www.ebi.ac.uk/swo/license/SWO_ + SWO.version: http://www.ebi.ac.uk/swo/version/SWO_ + SWO.data: http://www.ebi.ac.uk/swo/data/SWO_ + SWO.interface: http://www.ebi.ac.uk/swo/interface/SWO_ + SWO.algorithm: http://www.ebi.ac.uk/swo/algorithm/SWO_ + OntoDM: http://www.ontodm.com/OntoDM-core/OntoDM_ + OntoDM.kdd: "http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD" chiro: url: http://purl.obolibrary.org/obo/chiro.owl build_command: "robot relax -i $< merge -o $@" From f25ac945bc3da1ef24ade40ed7dd9cedd6bfd6da Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Wed, 29 Jan 2025 19:28:11 -0800 Subject: [PATCH 2/2] new sources --- ontologies.Makefile | 199 ++++++++++++++++-- sparql/skos-to-owl.ru | 61 ++++++ src/semsql/builder/prefixes/prefixes.csv | 22 ++ .../builder/prefixes/prefixes_local.csv | 22 ++ src/semsql/builder/registry/ontologies.yaml | 98 ++++++++- 5 files changed, 378 insertions(+), 24 deletions(-) create mode 100644 sparql/skos-to-owl.ru diff --git a/ontologies.Makefile b/ontologies.Makefile index ef0c223..f96c11d 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -1,14 +1,3 @@ -download/upheno.owl: STAMP - curl -L -s http://purl.obolibrary.org/obo/upheno.owl > $@.tmp - sha256sum -b $@.tmp > $@.sha256 - mv $@.tmp $@ - -.PRECIOUS: download/upheno.owl - -db/upheno.owl: download/upheno.owl - robot merge -i $< -o $@ - - download/swo.owl: STAMP curl -L -s http://purl.obolibrary.org/obo/swo.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -31,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -97,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -109,7 +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 > $@.tmp + curl -L -s https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl.gz | gzip -dc > $@.tmp sha256sum -b $@.tmp > $@.sha256 mv $@.tmp $@ @@ -174,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/xsmo.owl + +db/xsmo.owl: download/xsmo.owl + cp $< $@ + + download/bcio.owl: STAMP curl -L -s http://humanbehaviourchange.org/ontology/bcio.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -240,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -417,7 +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 > $@.tmp + curl -L -s https://w3id.org/orcidio/orcidio.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 mv $@.tmp $@ @@ -493,6 +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 > $@.zip.tmp && unzip -p $@.zip.tmp ChemOnt_2_1.obo > $@.tmp && rm $@.zip.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.zip.tmp && unzip -p $@.zip.tmp CSO.3.3.owl > $@.tmp && rm $@.zip.tmp sha256sum -b $@.tmp > $@.sha256 @@ -515,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.zip.tmp && unzip -p $@.zip.tmp Homo_sapiens.owl > $@.tmp && rm $@.zip.tmp sha256sum -b $@.tmp > $@.sha256 @@ -603,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -746,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -835,7 +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 > $@.tmp + curl -L -s https://w3id.org/biopragmatics/resources/uniprot/2022_02/uniprot.owl.gz | gzip -dc > $@.tmp sha256sum -b $@.tmp > $@.sha256 mv $@.tmp $@ @@ -846,14 +978,14 @@ db/uniprot.owl: download/uniprot.owl download/rhea.owl: STAMP - curl -L -s https://w3id.org/biopragmatics/resources/rhea/rhea.owl > $@.tmp + curl -L -s https://w3id.org/biopragmatics/resources/rhea/rhea.obo > $@.tmp sha256sum -b $@.tmp > $@.sha256 mv $@.tmp $@ .PRECIOUS: download/rhea.owl db/rhea.owl: download/rhea.owl - cp $< $@ + robot merge -i $< -o $@ download/swisslipid.owl: STAMP @@ -911,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/kegg.genome.owl + +db/kegg.genome.owl: download/kegg.genome.owl + cp $< $@ + + download/drugmechdb.owl: STAMP curl -L -s None > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1032,6 +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 > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.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/ > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1097,4 +1262,4 @@ download/%.owl: STAMP db/%.owl: download/%.owl robot merge -i $< -o $@ -EXTRA_ONTOLOGIES = upheno swo 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 diff --git a/sparql/skos-to-owl.ru b/sparql/skos-to-owl.ru new file mode 100644 index 0000000..f78b10d --- /dev/null +++ b/sparql/skos-to-owl.ru @@ -0,0 +1,61 @@ +PREFIX skos: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX 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 . +}; + + diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index 6707b19..9fa4fa5 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -73,13 +73,19 @@ SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_ SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_ OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_ OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD +PCL,http://purl.obolibrary.org/obo/PCL_ +ENSEMBL,http://identifiers.org/ensembl/ +chemrof,https://w3id.org/chemrof/ +OGCO,http://purl.obolibrary.org/obo/OGCO_ FMA,http://purl.org/sig/ont/fma/fma MSIO,http://purl.obolibrary.org/obo/MSIO_ nmrCV,http://nmrML.org/nmrCV#NMR: +PRIDE,http://purl.obolibrary.org/obo/PRIDE_ modl,https://archive.org/services/purl/purl/modular_ontology_design_library# biolink,https://w3id.org/biolink/vocab/ biolink,https://w3id.org/biolink/vocab/ loinc,https://loinc.org/ +XSMO,http://purl.obolibrary.org/obo/XSMO_ BCIO,http://humanbehaviourchange.org/ontology/BCIO_ BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_ icd10who,https://icd.who.int/browse10/2019/en#/ @@ -88,6 +94,12 @@ OMIM,https://omim.org/entry/ OMIMPS,https://www.omim.org/phenotypicSeries/PS CHR,http://purl.obolibrary.org/obo/CHR_ OEO,http://openenergy-platform.org/ontology/oeo/OEO_ +OEOX,http://openenergy-platform.org/ontology/oeo/OEOX_ +envthes,http://vocabs.lter-europe.net/EnvThes/ +omv,http://omv.ontoware.org/2005/05/ +iadopt,https://w3id.org/iadopt/ont/ +lternet.tema,https://vocab.lternet.edu/vocab/vocab/?tema= +webprotege,http://webprotege.stanford.edu/ GOLDTERMS,https://w3id.org/gold.path/ GOLDVOCAB,https://w3id.org/gold.vocab/ SDGIO,http://purl.unep.org/sdg/SDGIO_ @@ -104,12 +116,17 @@ evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# old.fix,http://purl.org/obo/owl/FIX# mlo,http://www.a2rd.net.br/mlo# ito,https://identifiers.org/ito: +CHEMONTID,http://purl.obolibrary.org/obo/CHEMONTID_ cso,https://cso.kmi.open.ac.uk/topics/ freebase,http://rdf.freebase.com/ns/ yago,http://yago-knowledge.org/resource/ cyc,http://sw.cyc.com/concept OBIws,http://purl.obolibrary.org/obo/OBIws_ +reactome.obo,http://purl.obolibrary.org/obo/reactome_ +reactome.biopax,http://www.reactome.org/biopax/77/48887# chr,http://purl.obolibrary.org/obo/CHR_ +oboe-core,http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# +oboe-standards,http://ecoinformatics.org/oboe/oboe.1.0/oboe-standards.owl# prov,http://www.w3.org/ns/prov# dtype,http://www.linkedmodel.org/schema/dtype# voag,http://voag.linkedmodel.org/voag# @@ -123,6 +140,8 @@ fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb# dbpediaont,http://dbpedia.org/ontology/ dbpedia,http://dbpedia.org/ ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/ +OMIM,https://omim.org/entry/ +OMIMPS,https://www.omim.org/phenotypicSeries/PS co_324,https://cropontology.org/rdf/CO_324: PPEO,http://purl.org/ppeo/PPEO.owl# InterPro,http://purl.obolibrary.org/obo/InterPro_ @@ -140,6 +159,8 @@ drugbank,http://purl.obolibrary.org/obo/drugbank_ drugbank,http://purl.obolibrary.org/obo/drugcentral_ complexportal,http://purl.obolibrary.org/obo/complexportal_ complexportal,http://purl.obolibrary.org/obo/wikipathways_ +pathbank,http://purl.obolibrary.org/obo/pathbank_ +pathbank,http://purl.obolibrary.org/obo/kegg.genome_ MESH,http://id.nlm.nih.gov/mesh/ RXNORM,http://purl.bioontology.org/ontology/RXNORM/ OBT,http://purl.obolibrary.org/obo/OBT_ @@ -152,6 +173,7 @@ nmdc,https://w3id.org/nmdc/ linkml,https://w3id.org/linkml/ mixs,https://w3id.org/mixs/ mixs,https://w3id.org/mixs/ +kgcl,https://w3id.org/kgcl/ fibo,https://spec.edmcouncil.org/fibo/ontology/ cmnsav,https://www.omg.org/spec/Commons/AnnotationVocabulary/ RBO,http://purl.obolibrary.org/obo/RBO_ diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index 05f2935..b0fb225 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -10,13 +10,19 @@ SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_ SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_ OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_ OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD +PCL,http://purl.obolibrary.org/obo/PCL_ +ENSEMBL,http://identifiers.org/ensembl/ +chemrof,https://w3id.org/chemrof/ +OGCO,http://purl.obolibrary.org/obo/OGCO_ FMA,http://purl.org/sig/ont/fma/fma MSIO,http://purl.obolibrary.org/obo/MSIO_ nmrCV,http://nmrML.org/nmrCV#NMR: +PRIDE,http://purl.obolibrary.org/obo/PRIDE_ modl,https://archive.org/services/purl/purl/modular_ontology_design_library# biolink,https://w3id.org/biolink/vocab/ biolink,https://w3id.org/biolink/vocab/ loinc,https://loinc.org/ +XSMO,http://purl.obolibrary.org/obo/XSMO_ BCIO,http://humanbehaviourchange.org/ontology/BCIO_ BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_ icd10who,https://icd.who.int/browse10/2019/en#/ @@ -25,6 +31,12 @@ OMIM,https://omim.org/entry/ OMIMPS,https://www.omim.org/phenotypicSeries/PS CHR,http://purl.obolibrary.org/obo/CHR_ OEO,http://openenergy-platform.org/ontology/oeo/OEO_ +OEOX,http://openenergy-platform.org/ontology/oeo/OEOX_ +envthes,http://vocabs.lter-europe.net/EnvThes/ +omv,http://omv.ontoware.org/2005/05/ +iadopt,https://w3id.org/iadopt/ont/ +lternet.tema,https://vocab.lternet.edu/vocab/vocab/?tema= +webprotege,http://webprotege.stanford.edu/ GOLDTERMS,https://w3id.org/gold.path/ GOLDVOCAB,https://w3id.org/gold.vocab/ SDGIO,http://purl.unep.org/sdg/SDGIO_ @@ -41,12 +53,17 @@ evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# old.fix,http://purl.org/obo/owl/FIX# mlo,http://www.a2rd.net.br/mlo# ito,https://identifiers.org/ito: +CHEMONTID,http://purl.obolibrary.org/obo/CHEMONTID_ cso,https://cso.kmi.open.ac.uk/topics/ freebase,http://rdf.freebase.com/ns/ yago,http://yago-knowledge.org/resource/ cyc,http://sw.cyc.com/concept OBIws,http://purl.obolibrary.org/obo/OBIws_ +reactome.obo,http://purl.obolibrary.org/obo/reactome_ +reactome.biopax,http://www.reactome.org/biopax/77/48887# chr,http://purl.obolibrary.org/obo/CHR_ +oboe-core,http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# +oboe-standards,http://ecoinformatics.org/oboe/oboe.1.0/oboe-standards.owl# prov,http://www.w3.org/ns/prov# dtype,http://www.linkedmodel.org/schema/dtype# voag,http://voag.linkedmodel.org/voag# @@ -60,6 +77,8 @@ fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb# dbpediaont,http://dbpedia.org/ontology/ dbpedia,http://dbpedia.org/ ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/ +OMIM,https://omim.org/entry/ +OMIMPS,https://www.omim.org/phenotypicSeries/PS co_324,https://cropontology.org/rdf/CO_324: PPEO,http://purl.org/ppeo/PPEO.owl# InterPro,http://purl.obolibrary.org/obo/InterPro_ @@ -77,6 +96,8 @@ drugbank,http://purl.obolibrary.org/obo/drugbank_ drugbank,http://purl.obolibrary.org/obo/drugcentral_ complexportal,http://purl.obolibrary.org/obo/complexportal_ complexportal,http://purl.obolibrary.org/obo/wikipathways_ +pathbank,http://purl.obolibrary.org/obo/pathbank_ +pathbank,http://purl.obolibrary.org/obo/kegg.genome_ MESH,http://id.nlm.nih.gov/mesh/ RXNORM,http://purl.bioontology.org/ontology/RXNORM/ OBT,http://purl.obolibrary.org/obo/OBT_ @@ -89,5 +110,6 @@ nmdc,https://w3id.org/nmdc/ linkml,https://w3id.org/linkml/ mixs,https://w3id.org/mixs/ mixs,https://w3id.org/mixs/ +kgcl,https://w3id.org/kgcl/ fibo,https://spec.edmcouncil.org/fibo/ontology/ cmnsav,https://www.omg.org/spec/Commons/AnnotationVocabulary/ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index 22d08de..6a05b48 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -2,9 +2,12 @@ id: semantic-sql-registry description: Registry overlap for Semantic-SQL designed to supplement OBO vocabularies license: CC0 ontologies: - upheno: - url: http://purl.obolibrary.org/obo/upheno.owl - build_command: "robot merge -i $< -o $@" + #upheno: + # url: http://purl.obolibrary.org/obo/upheno/v2/upheno.owl + # build_command: "robot merge -i $< -o $@" + #upheno1: + # url: http://purl.obolibrary.org/obo/upheno.owl + # build_command: "robot merge -i $< -o $@" swo: url: http://purl.obolibrary.org/obo/swo.owl build_command: "robot merge -i $< -o $@" @@ -24,6 +27,19 @@ ontologies: chiro: url: http://purl.obolibrary.org/obo/chiro.owl build_command: "robot relax -i $< merge -o $@" + pcl: + url: http://purl.obolibrary.org/obo/pcl.owl + prefixmap: + PCL: http://purl.obolibrary.org/obo/PCL_ + ENSEMBL: http://identifiers.org/ensembl/ + chemessence: + url: https://github.com/cmungall/chemessence/releases/latest/download/chemessence.owl + prefixmap: + chemrof: https://w3id.org/chemrof/ + ogco: + url: https://raw.githubusercontent.com/cmungall/chemessence/refs/heads/main/src/ontology/components/ogco.owl + prefixmap: + OGCO: http://purl.obolibrary.org/obo/OGCO_ ncit: url: http://purl.obolibrary.org/obo/ncit.owl build_command: "robot relax -i $< merge -o $@" @@ -46,13 +62,19 @@ ontologies: prefixmap: MSIO: http://purl.obolibrary.org/obo/MSIO_ nmrCV: "http://nmrML.org/nmrCV#NMR:" + pride: + url: https://raw.githubusercontent.com/PRIDE-Archive/pride-ontology/master/pride_cv.obo + build_command: "robot relax -i $< merge -o $@" + prefixmap: + PRIDE: http://purl.obolibrary.org/obo/PRIDE_ modl: url: https://raw.githubusercontent.com/Data-Semantics-Laboratory/modular-ontology-design-library/master/MODL.owl prefixmap: modl: "https://archive.org/services/purl/purl/modular_ontology_design_library#" phenio: description: Monarch Phenomics Integrated Ontology - url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl + url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl.gz + compression: gzip relation_graph_settings: properties: - BFO:0000050 @@ -85,6 +107,10 @@ ontologies: url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl reacto: url: http://purl.obolibrary.org/obo/go/extensions/reacto.owl + xsmo: + url: https://download.xenbase.org/xenbase/Ontologies/XSMO/XSMO_1.1/XSMO_1.1.owl + prefixmap: + XSMO: http://purl.obolibrary.org/obo/XSMO_ bcio: url: http://humanbehaviourchange.org/ontology/bcio.owl prefixmap: @@ -114,6 +140,19 @@ ontologies: url: https://openenergyplatform.org/ontology/oeo/releases/oeo-full.owl prefixmap: OEO: http://openenergy-platform.org/ontology/oeo/OEO_ + OEOX: http://openenergy-platform.org/ontology/oeo/OEOX_ + envthes: + url: https://vocabs.lter-europe.net/rest/v1/envthes/data?format=text/turtle + build_command: "robot query -i $< --update sparql/skos-to-owl.ru -o $@" + prefixmap: + envthes: http://vocabs.lter-europe.net/EnvThes/ + omv: http://omv.ontoware.org/2005/05/ + iadopt: https://w3id.org/iadopt/ont/ + lternet.tema: "https://vocab.lternet.edu/vocab/vocab/?tema=" + wifire: + url: https://raw.githubusercontent.com/WIFIRE-Lab/WIFIRE-commons-ontology/master/WIFIRE-commons-ontology-V1.owl + prefixmap: + webprotege: http://webprotege.stanford.edu/ taxslim: url: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.obo build_command: "robot convert -i $< -o $@" @@ -175,7 +214,7 @@ ontologies: url: http://www.bioassayontology.org/bao/bao_complete.owl has_imports: true orcid: - url: https://raw.githubusercontent.com/cthoyt/wikidata-orcid-ontology/main/orcid.owl + url: https://w3id.org/orcidio/orcidio.owl prefixmap: orcid: https://orcid.org/ cpont: @@ -203,6 +242,15 @@ ontologies: zip_extract_file: ITO.owl prefixmap: ito: "https://identifiers.org/ito:" + chemont: + url: http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip + zip_extract_file: ChemOnt_2_1.obo + build_command: "robot convert -i $< -o $@" + prefixmap: + CHEMONTID: "http://purl.obolibrary.org/obo/CHEMONTID_" + molgenie: + url: https://github.com/MolGenie/ontology/blob/main/mol_classes_ext_2024-11-20.obo + build_command: "robot convert -i $< -o $@" cso: url: https://cso.kmi.open.ac.uk/download/version-3.3/CSO.3.3.owl.zip zip_extract_file: CSO.3.3.owl @@ -215,9 +263,17 @@ ontologies: url: https://data.bioontology.org/ontologies/OBIWS/submissions/2/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb prefixmap: OBIws: http://purl.obolibrary.org/obo/OBIws_ + biopragmatics-reactome: + url: https://w3id.org/biopragmatics/resources/reactome/reactome.obo + prefixmap: + reactome.obo: http://purl.obolibrary.org/obo/reactome_ + #post_processing_steps: + # - "sqlite3 {db} < views/reactome.sql" reactome-hs: url: https://reactome.org/download/current/biopax.zip zip_extract_file: Homo_sapiens.owl + prefixmap: + reactome.biopax: "http://www.reactome.org/biopax/77/48887#" #post_processing_steps: # - "sqlite3 {db} < views/reactome.sql" reactome-mm: @@ -244,6 +300,14 @@ ontologies: named_prefixmaps: - sweet - prefixcc + oboe-core: + url: http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl + prefixmap: + oboe-core: http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# + oboe-standards: + url: http://ecoinformatics.org/oboe/oboe.1.0/oboe-standards.owl + prefixmap: + oboe-standards: http://ecoinformatics.org/oboe/oboe.1.0/oboe-standards.owl# lov: url: https://lov.linkeddata.es/lov.n3.gz format: n3 @@ -302,6 +366,11 @@ ontologies: url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10cm.owl prefixmap: ICD10CM: http://purl.bioontology.org/ontology/ICD10CM/ + omim: + url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/omim.owl + prefixmap: + OMIM: https://omim.org/entry/ + OMIMPS: https://www.omim.org/phenotypicSeries/PS #sdtm: # url: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/SDTM%20Terminology.OWL.zip #empathi: @@ -359,12 +428,13 @@ ontologies: EC: http://purl.obolibrary.org/obo/eccode_ uniprot.obo: http://purl.obolibrary.org/obo/uniprot_ uniprot: - url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/uniprot/2022_02/uniprot.owl.gz + url: https://w3id.org/biopragmatics/resources/uniprot/2022_02/uniprot.owl.gz compression: gzip prefixmap: uniprot.obo: http://purl.obolibrary.org/obo/uniprot_ rhea: - url: https://w3id.org/biopragmatics/resources/rhea/rhea.owl + url: https://w3id.org/biopragmatics/resources/rhea/rhea.obo + build_command: "robot merge -i $< -o $@" prefixmap: RHEA: http://purl.obolibrary.org/obo/rhea_ uniprot.obo: http://purl.obolibrary.org/obo/uniprot_ @@ -393,6 +463,15 @@ ontologies: url: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.owl prefixmap: complexportal: http://purl.obolibrary.org/obo/wikipathways_ + pathbank: + url: https://w3id.org/biopragmatics/resources/pathbank/pathbank.obo.gz + compression: gzip + prefixmap: + pathbank: http://purl.obolibrary.org/obo/pathbank_ + kegg.genome: + url: https://w3id.org/biopragmatics/resources/kegg.genome/kegg.genome.obo + prefixmap: + pathbank: http://purl.obolibrary.org/obo/kegg.genome_ drugmechdb: prefixmap: MESH: http://id.nlm.nih.gov/mesh/ @@ -446,6 +525,11 @@ ontologies: build_command: "robot merge -i $< reason -o $@" prefixmap: mixs: https://w3id.org/mixs/ + kgcl: + url: https://w3id.org/kgcl/kgcl.owl.ttl + build_command: "robot merge -i $< reason -o $@" + prefixmap: + kgcl: https://w3id.org/kgcl/ fibo: url: https://spec.edmcouncil.org/fibo/ontology/AboutFIBOProd/ build_command: "robot merge -i $< -o $@"