From aa7fc3e728c8bdebc6c3a5176efda5fab0967010 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 24 Apr 2025 19:35:27 -0700 Subject: [PATCH 1/2] Adding matportal ontologies - DEB --- src/semsql/builder/registry/ontologies.yaml | 98 ++++++++++++++------- 1 file changed, 66 insertions(+), 32 deletions(-) diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index 2e35b7b..78deee9 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -34,8 +34,6 @@ ontologies: 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: @@ -62,11 +60,39 @@ ontologies: prefixmap: MSIO: http://purl.obolibrary.org/obo/MSIO_ nmrCV: "http://nmrML.org/nmrCV#NMR:" + chemrof: + url: https://w3id.org/chemrof/chemrof.owl.ttl + prefixmap: + chemrof: https://w3id.org/chemrof/ + deb: + url: "http://rest.matportal.org/ontologies/DEB/submissions/1/download?apikey=66c82e77-ce0d-4385-8056-a95898e47ebb" + prefixmap: + DEB: "http://www.semanticweb.org/osnathakimi/ontologies/deb#" 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_ + sosa: + url: http://www.w3.org/ns/sosa/ + build_command: "robot merge -i $< -o $@" + prefixmap: + sosa: http://www.w3.org/ns/sosa/ + vann: http://purl.org/vocab/vann/ + schema: http://schema.org/ + emi: + url: https://purl.org/emi + build_command: "robot merge -i $< -o $@" + prefixmap: + emi: "https://purl.org/emi#" + genex: http://purl.org/genex# + bibo: http://purl.org/ontology/bibo/ + wgs84_pos: http://www.w3.org/2003/01/geo/wgs84_pos# + npc: + url: https://purl.org/npc + build_command: "robot convert -i $< -o $@" + prefixmap: + npc: "https://purl.org/npc#" modl: url: https://raw.githubusercontent.com/Data-Semantics-Laboratory/modular-ontology-design-library/master/MODL.owl prefixmap: @@ -84,18 +110,6 @@ ontologies: - RO:0002202 prefixmap: biolink: https://w3id.org/biolink/vocab/ - phenio_test: - description: Monarch Phenomics Integrated Ontology (Test) - url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio-test.owl - relation_graph_settings: - properties: - - BFO:0000050 - - BFO:0000051 - - UPHENO:0000001 - - UPHENO:0000003 - - RO:0002202 - prefixmap: - biolink: https://w3id.org/biolink/vocab/ comploinc: url: https://github.com/loinc/comp-loinc/releases/download/v2022-11-05/merged_reasoned_loinc.owl build_command: "robot relax -i $< merge -o $@" @@ -146,22 +160,27 @@ ontologies: url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10who.owl prefixmap: icd10who: https://icd.who.int/browse10/2019/en#/ - #icd11f: - # url: https://github.com/monarch-initiative/icd11/releases/latest/download/icd11foundation.owl - # prefixmap: - # icd11f: http://id.who.int/icd/entity/ + icd11f: + url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd11foundation.owl + prefixmap: + icd11f: http://id.who.int/icd/entity/ ordo: url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/ordo.owl gard: url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/gard.owl prefixmap: GARD: http://purl.obolibrary.org/obo/GARD_ - mondo-ingest: - url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/mondo-ingest.owl + icd10cm: + 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 - CHR: http://purl.obolibrary.org/obo/CHR_ + OMIMPS: https://omim.org/phenotypicSeries/PS + mondo-ingest: + url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/mondo-ingest.owl oeo: url: https://openenergyplatform.org/ontology/oeo/releases/oeo-full.owl prefixmap: @@ -197,6 +216,11 @@ ontologies: build_command: "robot reason -i $< -o $@" prefixmap: KIN: "http://purl.org/ga4gh/kin.owl#KIN_" + metpo: + url: https://raw.githubusercontent.com/berkeleybop/metpo/refs/heads/main/metpo.owl + build_command: "robot reason -i $< -o $@" + prefixmap: + METPO: "http://purl.obolibrary.org/obo/METPO_" biovoices: url: https://zenodo.org/record/5589773/files/ontology.owl?download=1 build_command: "robot relax -i $< merge -o $@" @@ -236,6 +260,19 @@ ontologies: url: http://purl.obolibrary.org/obo/go/extensions/go-amigo.owl neo: url: http://purl.obolibrary.org/obo/go/noctua/neo.owl + prefixmap: + NCBIGene: http://identifiers.org/ncbigene/ + UniProtKB.neo: http://identifiers.org/uniprot/ + XenBase: http://identifiers.org/xenbase/ + RGD: http://identifiers.org/rgd/ + ZFIN: http://identifiers.org/zfin/ + SGD.neo: http://identifiers.org/sgd/ + FB: http://identifiers.org/flybase/ + PomBase: http://identifiers.org/pombase/ + DictyBase: http://identifiers.org/dictybase.gene/ + MGI: "http://identifiers.org/mgi/MGI:" + TAIR.LOCUS: http://arabidopsis.org/servlets/TairObject?type=locus&name= + EcoCyc: "https://ecocyc.org/gene?id=" bao: url: http://www.bioassayontology.org/bao/bao_complete.owl has_imports: true @@ -394,15 +431,6 @@ ontologies: dbpedia: http://dbpedia.org/ uberoncm: url: https://github.com/obophenotype/uberon/releases/latest/download/composite-metazoan.owl - icd10cm: - 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: @@ -462,7 +490,13 @@ ontologies: compression: gzip prefixmap: EC: "https://bioregistry.io/eccode:" - UniProtKB: "https://bioregistry.io/uniprot:" + UniProtKB.br: "https://bioregistry.io/uniprot:" + #eccode: + # url: https://w3id.org/biopragmatics/resources/eccode/eccode.owl.gz + # compression: gzip + # prefixmap: + # EC.legacy: "https://bioregistry.io/eccode:" + # UniProtKB: "https://bioregistry.io/uniprot:" uniprot: url: https://w3id.org/biopragmatics/resources/uniprot/uniprot.owl.gz compression: gzip From 903a26db436ac1afed11866c4b1271e834fbcbda Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 30 Oct 2025 17:33:26 -0700 Subject: [PATCH 2/2] additional sources --- ontologies.Makefile | 244 +++++++++++++++--- src/semsql/builder/prefixes/prefixes.csv | 48 +++- .../builder/prefixes/prefixes_local.csv | 48 +++- src/semsql/builder/registry/ontologies.yaml | 50 +++- 4 files changed, 338 insertions(+), 52 deletions(-) diff --git a/ontologies.Makefile b/ontologies.Makefile index 97d452c..665308c 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -119,6 +119,61 @@ db/msio.owl: download/msio.owl cp $< $@ +download/chemrof.owl: STAMP + curl -L -s https://w3id.org/chemrof/chemrof.owl.ttl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/chemrof.owl + +db/chemrof.owl: download/chemrof.owl + cp $< $@ + + +download/deb.owl: STAMP + curl -L -s http://rest.matportal.org/ontologies/DEB/submissions/1/download?apikey=66c82e77-ce0d-4385-8056-a95898e47ebb > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/deb.owl + +db/deb.owl: download/deb.owl + cp $< $@ + + +download/matpo.owl: STAMP + curl -L -s http://bimerr.iot.linkeddata.es/def/material-properties# > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/matpo.owl + +db/matpo.owl: download/matpo.owl + cp $< $@ + + +download/panet.owl: STAMP + curl -L -s http://purl.org/pan-science/PaNET/PaNET.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/panet.owl + +db/panet.owl: download/panet.owl + cp $< $@ + + +download/phenx.owl: STAMP + curl -L -s https://data.bioontology.org/ontologies/PHENX/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/phenx.owl + +db/phenx.owl: download/phenx.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 @@ -130,6 +185,39 @@ db/pride.owl: download/pride.owl robot relax -i $< merge -o $@ +download/sosa.owl: STAMP + curl -L -s http://www.w3.org/ns/sosa/ > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/sosa.owl + +db/sosa.owl: download/sosa.owl + robot merge -i $< -o $@ + + +download/emi.owl: STAMP + curl -L -s https://purl.org/emi > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/emi.owl + +db/emi.owl: download/emi.owl + robot merge -i $< -o $@ + + +download/npc.owl: STAMP + curl -L -s https://purl.org/npc > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/npc.owl + +db/npc.owl: download/npc.owl + robot convert -i $< -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 @@ -152,17 +240,6 @@ db/phenio.owl: download/phenio.owl cp $< $@ -download/phenio_test.owl: STAMP - curl -L -s https://github.com/monarch-initiative/phenio/releases/latest/download/phenio-test.owl > $@.tmp - sha256sum -b $@.tmp > $@.sha256 - mv $@.tmp $@ - -.PRECIOUS: download/phenio_test.owl - -db/phenio_test.owl: download/phenio_test.owl - cp $< $@ - - download/comploinc.owl: STAMP curl -L -s https://github.com/loinc/comp-loinc/releases/download/v2022-11-05/merged_reasoned_loinc.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -306,6 +383,17 @@ db/icd10who.owl: download/icd10who.owl cp $< $@ +download/icd11f.owl: STAMP + curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd11foundation.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/icd11f.owl + +db/icd11f.owl: download/icd11f.owl + cp $< $@ + + download/ordo.owl: STAMP curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/ordo.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -328,6 +416,28 @@ db/gard.owl: download/gard.owl cp $< $@ +download/icd10cm.owl: STAMP + curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10cm.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/icd10cm.owl + +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/mondo-ingest.owl: STAMP curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/mondo-ingest.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -416,6 +526,28 @@ db/kin.owl: download/kin.owl robot reason -i $< -o $@ +download/metpo.owl: STAMP + curl -L -s https://raw.githubusercontent.com/berkeleybop/metpo/refs/heads/main/metpo.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/metpo.owl + +db/metpo.owl: download/metpo.owl + robot reason -i $< -o $@ + + +download/d3o.owl: STAMP + curl -L -s https://data.bioontology.org/ontologies/D3O/submissions/3/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/d3o.owl + +db/d3o.owl: download/d3o.owl + robot convert -i $< -o $@ + + download/biovoices.owl: STAMP curl -L -s https://zenodo.org/record/5589773/files/ontology.owl?download=1 > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -900,6 +1032,17 @@ db/cosmo.owl: download/cosmo.owl robot merge -i $< -o $@ +download/gist.owl: STAMP + curl -L -s https://w3id.org/semanticarts/ontology/gistCore > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/gist.owl + +db/gist.owl: download/gist.owl + cp $< $@ + + download/fhkb.owl: STAMP curl -L -s None > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -933,28 +1076,6 @@ db/uberoncm.owl: download/uberoncm.owl cp $< $@ -download/icd10cm.owl: STAMP - curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10cm.owl > $@.tmp - sha256sum -b $@.tmp > $@.sha256 - mv $@.tmp $@ - -.PRECIOUS: download/icd10cm.owl - -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 @@ -1252,6 +1373,17 @@ db/enigma_context.owl: download/enigma_context.owl robot merge -i $< -o $@ +download/cbo.owl: STAMP + curl -L -s https://data.bioontology.org/ontologies/CBO/submissions/25/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/cbo.owl + +db/cbo.owl: download/cbo.owl + robot merge -i $< -o $@ + + download/ontie.owl: STAMP curl -L -s https://ontology.iedb.org/file/ontie.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1263,6 +1395,28 @@ db/ontie.owl: download/ontie.owl cp $< $@ +download/pain.owl: STAMP + curl -L -s https://raw.githubusercontent.com/uflcod/pain-ontology/refs/heads/main/pain.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/pain.owl + +db/pain.owl: download/pain.owl + cp $< $@ + + +download/como.owl: STAMP + curl -L -s https://data.bioontology.org/ontologies/COMO/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/como.owl + +db/como.owl: download/como.owl + cp $< $@ + + download/ecosim.owl: STAMP curl -L -s https://data.bioontology.org/ontologies/ECOSIM/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1274,6 +1428,28 @@ db/ecosim.owl: download/ecosim.owl cp $< $@ +download/bervo.owl: STAMP + curl -L -s https://data.bioontology.org/ontologies/BERVO/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/bervo.owl + +db/bervo.owl: download/bervo.owl + cp $< $@ + + +download/valuesets.owl: STAMP + curl -L -s https://w3id.org/valuesets/valuesets.owl.ttl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/valuesets.owl + +db/valuesets.owl: download/valuesets.owl + robot merge -i $< -o $@ + + download/nmdc_schema.owl: STAMP curl -L -s https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/project/owl/nmdc.owl.ttl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1372,4 +1548,4 @@ download/%.owl: STAMP db/%.owl: download/%.owl robot merge -i $< -o $@ -EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio pride modl phenio phenio_test comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio 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 ror 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 pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit 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 +EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio chemrof deb matpo panet phenx pride sosa emi npc modl phenio comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio icd10who icd11f ordo gard icd10cm omim mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin metpo d3o biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid ror 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 gist fhkb dbpendiaont uberoncm co_324 ppeo interpro pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context cbo ontie pain como ecosim bervo valuesets nmdc_schema mixs kgcl 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 fba5e85..9377b7e 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -75,15 +75,28 @@ 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: +chemrof,https://w3id.org/chemrof/ +DEB,http://www.semanticweb.org/osnathakimi/ontologies/deb# +matpo,http://bimerr.iot.linkeddata.es/def/material-properties# +building,http://bimerr.iot.linkeddata.es/def/building# +saref,https://saref.etsi.org/core/ +PANET,http://purl.org/pan-science/PaNET/PaNET +PHENX,http://purl.bioontology.org/ontology/phenX/ PRIDE,http://purl.obolibrary.org/obo/PRIDE_ +sosa,http://www.w3.org/ns/sosa/ +vann,http://purl.org/vocab/vann/ +schema,http://schema.org/ +emi,https://purl.org/emi# +genex,http://purl.org/genex# +bibo,http://purl.org/ontology/bibo/ +wgs84_pos,http://www.w3.org/2003/01/geo/wgs84_pos# +npc,https://purl.org/npc# 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/ HBA,https://purl.brain-bican.org/ontology/hbao/HBA_ MBA,https://purl.brain-bican.org/ontology/mbao/MBA_ @@ -95,10 +108,11 @@ BCIO,http://humanbehaviourchange.org/ontology/BCIO_ BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_ SIO,http://semanticscience.org/resource/SIO_ icd10who,https://icd.who.int/browse10/2019/en#/ +icd11f,http://id.who.int/icd/entity/ GARD,http://purl.obolibrary.org/obo/GARD_ +ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/ OMIM,https://omim.org/entry/ -OMIMPS,https://www.omim.org/phenotypicSeries/PS -CHR,http://purl.obolibrary.org/obo/CHR_ +OMIMPS,https://omim.org/phenotypicSeries/PS OEO,http://openenergy-platform.org/ontology/oeo/OEO_ OEOX,http://openenergy-platform.org/ontology/oeo/OEOX_ envthes,http://vocabs.lter-europe.net/EnvThes/ @@ -110,6 +124,8 @@ GOLDTERMS,https://w3id.org/gold.path/ GOLDVOCAB,https://w3id.org/gold.vocab/ SDGIO,http://purl.unep.org/sdg/SDGIO_ KIN,http://purl.org/ga4gh/kin.owl#KIN_ +METPO,https://w3id.org/metpo/ +D3O,https://purl.dsmz.de/schema/ ontorion,http://ontorion.com/namespace# omop,https://athena.ohdsi.org/search-terms/terms/ comet,https://w3id.org/linkml-common/ @@ -117,6 +133,18 @@ CCO,http://www.ontologyrepository.com/CommonCoreOntologies/ OccO,http://purl.obolibrary.org/obo/OccO_ IOFcore,https://spec.industrialontologies.org/ontology/ UPa,http://purl.obolibrary.org/obo/UPa_ +NCBIGene,http://identifiers.org/ncbigene/ +UniProtKB.neo,http://identifiers.org/uniprot/ +XenBase,http://identifiers.org/xenbase/ +RGD,http://identifiers.org/rgd/ +ZFIN,http://identifiers.org/zfin/ +SGD.neo,http://identifiers.org/sgd/ +FB,http://identifiers.org/flybase/ +PomBase,http://identifiers.org/pombase/ +DictyBase,http://identifiers.org/dictybase.gene/ +MGI,http://identifiers.org/mgi/MGI: +TAIR.LOCUS,http://arabidopsis.org/servlets/TairObject?type=locus&name= +EcoCyc,https://ecocyc.org/gene?id= orcid,https://orcid.org/ ror,https://ror.org/ evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# @@ -143,12 +171,11 @@ 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_ +gist,https://w3id.org/semanticarts/ns/ontology/gist/ +gistd,https://w3id.org/semanticarts/ns/data/gist/ 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_ @@ -159,7 +186,7 @@ hgnc,http://purl.obolibrary.org/obo/hgnc_ SGD,https://www.yeastgenome.org/locus/ gtdb,https://gtdb.ecogenomic.org/tree?r= EC,https://bioregistry.io/eccode: -UniProtKB,https://bioregistry.io/uniprot: +UniProtKB.br,https://bioregistry.io/uniprot: UniProtKB,https://bioregistry.io/uniprot: RESID,https://proteininformationresource.org/cgi-bin/resid?id= UNIMOD,http://www.unimod.org/modifications_view.php?editid1= @@ -179,9 +206,14 @@ VCCF,http://purl.obolibrary.org/obo/VCCF_ OBT,http://purl.obolibrary.org/obo/OBT_ NANDO,http://nanbyodata.jp/ontology/NANDO_ ECSO,http://purl.dataone.org/odo/ECSO_ +CBO,http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_1_2.owl# ONTIE,https://ontology.iedb.org/ontology/ONTIE_ +PAIN,http://purl.obolibrary.org/obo/PAIN_ +COMO,http://purl.obolibrary.org/obo/COMO_ ECOSIM,http://purl.obolibrary.org/obo/ECOSIM_ ECOSIMCONCEPT,http://purl.obolibrary.org/obo/ECOSIMCONCEPT_ +BERVO,https://w3id.org/bervo/BERVO_ +VALUESETS,https://w3id.org/valuesets/ nmdc,https://w3id.org/nmdc/ linkml,https://w3id.org/linkml/ mixs,https://w3id.org/mixs/ diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index 2450ca2..e0b328e 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -12,15 +12,28 @@ 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: +chemrof,https://w3id.org/chemrof/ +DEB,http://www.semanticweb.org/osnathakimi/ontologies/deb# +matpo,http://bimerr.iot.linkeddata.es/def/material-properties# +building,http://bimerr.iot.linkeddata.es/def/building# +saref,https://saref.etsi.org/core/ +PANET,http://purl.org/pan-science/PaNET/PaNET +PHENX,http://purl.bioontology.org/ontology/phenX/ PRIDE,http://purl.obolibrary.org/obo/PRIDE_ +sosa,http://www.w3.org/ns/sosa/ +vann,http://purl.org/vocab/vann/ +schema,http://schema.org/ +emi,https://purl.org/emi# +genex,http://purl.org/genex# +bibo,http://purl.org/ontology/bibo/ +wgs84_pos,http://www.w3.org/2003/01/geo/wgs84_pos# +npc,https://purl.org/npc# 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/ HBA,https://purl.brain-bican.org/ontology/hbao/HBA_ MBA,https://purl.brain-bican.org/ontology/mbao/MBA_ @@ -32,10 +45,11 @@ BCIO,http://humanbehaviourchange.org/ontology/BCIO_ BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_ SIO,http://semanticscience.org/resource/SIO_ icd10who,https://icd.who.int/browse10/2019/en#/ +icd11f,http://id.who.int/icd/entity/ GARD,http://purl.obolibrary.org/obo/GARD_ +ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/ OMIM,https://omim.org/entry/ -OMIMPS,https://www.omim.org/phenotypicSeries/PS -CHR,http://purl.obolibrary.org/obo/CHR_ +OMIMPS,https://omim.org/phenotypicSeries/PS OEO,http://openenergy-platform.org/ontology/oeo/OEO_ OEOX,http://openenergy-platform.org/ontology/oeo/OEOX_ envthes,http://vocabs.lter-europe.net/EnvThes/ @@ -47,6 +61,8 @@ GOLDTERMS,https://w3id.org/gold.path/ GOLDVOCAB,https://w3id.org/gold.vocab/ SDGIO,http://purl.unep.org/sdg/SDGIO_ KIN,http://purl.org/ga4gh/kin.owl#KIN_ +METPO,https://w3id.org/metpo/ +D3O,https://purl.dsmz.de/schema/ ontorion,http://ontorion.com/namespace# omop,https://athena.ohdsi.org/search-terms/terms/ comet,https://w3id.org/linkml-common/ @@ -54,6 +70,18 @@ CCO,http://www.ontologyrepository.com/CommonCoreOntologies/ OccO,http://purl.obolibrary.org/obo/OccO_ IOFcore,https://spec.industrialontologies.org/ontology/ UPa,http://purl.obolibrary.org/obo/UPa_ +NCBIGene,http://identifiers.org/ncbigene/ +UniProtKB.neo,http://identifiers.org/uniprot/ +XenBase,http://identifiers.org/xenbase/ +RGD,http://identifiers.org/rgd/ +ZFIN,http://identifiers.org/zfin/ +SGD.neo,http://identifiers.org/sgd/ +FB,http://identifiers.org/flybase/ +PomBase,http://identifiers.org/pombase/ +DictyBase,http://identifiers.org/dictybase.gene/ +MGI,http://identifiers.org/mgi/MGI: +TAIR.LOCUS,http://arabidopsis.org/servlets/TairObject?type=locus&name= +EcoCyc,https://ecocyc.org/gene?id= orcid,https://orcid.org/ ror,https://ror.org/ evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# @@ -80,12 +108,11 @@ 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_ +gist,https://w3id.org/semanticarts/ns/ontology/gist/ +gistd,https://w3id.org/semanticarts/ns/data/gist/ 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_ @@ -96,7 +123,7 @@ hgnc,http://purl.obolibrary.org/obo/hgnc_ SGD,https://www.yeastgenome.org/locus/ gtdb,https://gtdb.ecogenomic.org/tree?r= EC,https://bioregistry.io/eccode: -UniProtKB,https://bioregistry.io/uniprot: +UniProtKB.br,https://bioregistry.io/uniprot: UniProtKB,https://bioregistry.io/uniprot: RESID,https://proteininformationresource.org/cgi-bin/resid?id= UNIMOD,http://www.unimod.org/modifications_view.php?editid1= @@ -116,9 +143,14 @@ VCCF,http://purl.obolibrary.org/obo/VCCF_ OBT,http://purl.obolibrary.org/obo/OBT_ NANDO,http://nanbyodata.jp/ontology/NANDO_ ECSO,http://purl.dataone.org/odo/ECSO_ +CBO,http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_1_2.owl# ONTIE,https://ontology.iedb.org/ontology/ONTIE_ +PAIN,http://purl.obolibrary.org/obo/PAIN_ +COMO,http://purl.obolibrary.org/obo/COMO_ ECOSIM,http://purl.obolibrary.org/obo/ECOSIM_ ECOSIMCONCEPT,http://purl.obolibrary.org/obo/ECOSIMCONCEPT_ +BERVO,https://w3id.org/bervo/BERVO_ +VALUESETS,https://w3id.org/valuesets/ nmdc,https://w3id.org/nmdc/ linkml,https://w3id.org/linkml/ mixs,https://w3id.org/mixs/ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index 78deee9..908bc3c 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -68,6 +68,20 @@ ontologies: url: "http://rest.matportal.org/ontologies/DEB/submissions/1/download?apikey=66c82e77-ce0d-4385-8056-a95898e47ebb" prefixmap: DEB: "http://www.semanticweb.org/osnathakimi/ontologies/deb#" + matpo: + url: http://bimerr.iot.linkeddata.es/def/material-properties# + prefixmap: + matpo: http://bimerr.iot.linkeddata.es/def/material-properties# + building: http://bimerr.iot.linkeddata.es/def/building# + saref: https://saref.etsi.org/core/ + panet: + url: http://purl.org/pan-science/PaNET/PaNET.owl + prefixmap: + PANET: http://purl.org/pan-science/PaNET/PaNET + phenx: + url: "https://data.bioontology.org/ontologies/PHENX/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb" + prefixmap: + PHENX: http://purl.bioontology.org/ontology/phenX/ pride: url: https://raw.githubusercontent.com/PRIDE-Archive/pride-ontology/master/pride_cv.obo build_command: "robot relax -i $< merge -o $@" @@ -220,7 +234,12 @@ ontologies: url: https://raw.githubusercontent.com/berkeleybop/metpo/refs/heads/main/metpo.owl build_command: "robot reason -i $< -o $@" prefixmap: - METPO: "http://purl.obolibrary.org/obo/METPO_" + METPO: "https://w3id.org/metpo/" + d3o: + url: https://data.bioontology.org/ontologies/D3O/submissions/3/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb + build_command: "robot convert -i $< -o $@" + prefixmap: + D3O: https://purl.dsmz.de/schema/ biovoices: url: https://zenodo.org/record/5589773/files/ontology.owl?download=1 build_command: "robot relax -i $< merge -o $@" @@ -421,6 +440,11 @@ ontologies: cosmo: url: https://micra.com/COSMO/COSMO.owl has_imports: true + gist: + url: https://w3id.org/semanticarts/ontology/gistCore + prefixmap: + gist: https://w3id.org/semanticarts/ns/ontology/gist/ + gistd: https://w3id.org/semanticarts/ns/data/gist/ fhkb: prefixmap: fhkb: http://owl.cs.manchester.ac.uk/tutorials/fhkb# @@ -578,7 +602,12 @@ ontologies: ECSO: http://purl.dataone.org/odo/ECSO_ enigma_context: url: https://raw.githubusercontent.com/jmchandonia/CORAL/main/example/enigma/ontologies/context_measurement_ontology.obo - build_command: "robot merge -i $< -o $@" + build_command: "robot merge -i $< -o $@" + cbo: + build_command: "robot merge -i $< -o $@" + url: https://data.bioontology.org/ontologies/CBO/submissions/25/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb + prefixmap: + CBO: "http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_1_2.owl#" #meo: # url: "'https://data.bioontology.org/ontologies/MEO/submissions/9/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'" # prefixmap: @@ -587,11 +616,28 @@ ontologies: url: https://ontology.iedb.org/file/ontie.owl prefixmap: ONTIE: https://ontology.iedb.org/ontology/ONTIE_ + pain: + url: "https://raw.githubusercontent.com/uflcod/pain-ontology/refs/heads/main/pain.owl" + prefixmap: + PAIN: http://purl.obolibrary.org/obo/PAIN_ + como: + url: "https://data.bioontology.org/ontologies/COMO/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb" + prefixmap: + COMO: http://purl.obolibrary.org/obo/COMO_ ecosim: url: "https://data.bioontology.org/ontologies/ECOSIM/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb" prefixmap: ECOSIM: http://purl.obolibrary.org/obo/ECOSIM_ ECOSIMCONCEPT: http://purl.obolibrary.org/obo/ECOSIMCONCEPT_ + bervo: + url: "https://data.bioontology.org/ontologies/BERVO/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb" + prefixmap: + BERVO: https://w3id.org/bervo/BERVO_ + valuesets: + build_command: "robot merge -i $< -o $@" + url: https://w3id.org/valuesets/valuesets.owl.ttl + prefixmap: + VALUESETS: https://w3id.org/valuesets/ #monarch: # url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.db.gz # format: kgxdb