ontologies.yaml

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/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 $@"
    # 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 $@"
  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
  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 $@"
  fma:
    url: http://sig.biostr.washington.edu/share/downloads/fma/release/latest/fma.owl
    prefixmap:
      FMA: http://purl.org/sig/ont/fma/fma
  maxo:
    url: http://purl.obolibrary.org/obo/maxo.owl
    # https://github.com/monarch-initiative/MAxO/issues/367
    build_command: "robot relax -i $< merge reason -r structural -o $@"
  foodon:
    url: http://purl.obolibrary.org/obo/foodon.owl
    build_command: "robot merge -i $< relax reduce -c true -o $@"
  chebiplus:
    url: http://purl.obolibrary.org/obo/chebi.owl
    build_command: "robot merge -i $< -I http://purl.obolibrary.org/obo/chiro.owl relax -o $@"
  msio:
    url: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl
    prefixmap:
      MSIO: http://purl.obolibrary.org/obo/MSIO_
      nmrCV: "http://nmrML.org/nmrCV#NMR:"
  chemrof:
    url: https://w3id.org/chemrof/chemrof.owl.ttl
    build_command: "robot merge -i $< -o $@"
    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#"
  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 $@"
    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:
      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.gz
    compression: gzip
    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 $@"
    prefixmap:
      loinc: https://loinc.org/
  # See https://github.com/obophenotype/uberon/issues/3267
  hba:
    url: https://github.com/brain-bican/human_brain_atlas_ontology/raw/main/hbao-base.owl
    prefixmap:
      HBA: https://purl.brain-bican.org/ontology/hbao/HBA_
  mba:
    url: https://github.com/brain-bican/mouse_brain_atlas_ontology/raw/main/mbao-base.owl
    prefixmap:
      MBA: https://purl.brain-bican.org/ontology/mbao/MBA_
  dmba:
    url: https://github.com/brain-bican/developing_mouse_brain_atlas_ontology/raw/main/dmbao-base.owl
    prefixmap:
      DMBA: https://purl.brain-bican.org/ontology/dmbao/DMBA_
  dhba:
    url: https://github.com/brain-bican/developing_human_brain_atlas_ontology/raw/main/dhbao-base.owl
    prefixmap:
      DHBA: https://purl.brain-bican.org/ontology/dhbao/DHBA_
  pba:
    url: https://github.com/brain-bican/primate_brain_atlas_ontology/raw/main/pbao-base.owl
    prefixmap:
      PBA: https://purl.brain-bican.org/ontology/pbao/PBA_
  bero:
    url: https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl
  aio:
    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:
      BCIO: http://humanbehaviourchange.org/ontology/BCIO_
      BCIOR: http://humanbehaviourchange.org/ontology/BCIOR_
  sio:
    url: http://semanticscience.org/ontology/sio.owl
    # TBD: see https://github.com/biopragmatics/bioregistry/issues/1394
    prefixmap:
      SIO: http://semanticscience.org/resource/SIO_
  icd10who:
    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/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_
  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://omim.org/phenotypicSeries/PS
  mondo-ingest:
    url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/mondo-ingest.owl
  # ENERO Foundry / Open Energy Family ontologies
  oeo:
    url: https://openenergyplatform.org/ontology/oeo/releases/oeo-full.owl
    prefixmap:
      # note: they recently switched to https AND removed a hyphen
      # https://github.com/OpenEnergyPlatform/ontology/pull/2050
      OEO: https://openenergyplatform.org/ontology/oeo/OEO_
      OEOX: https://openenergyplatform.org/ontology/oeo/OEOX_
      OEO.CCO: http://www.ontologyrepository.com/CommonCoreOntologies/
  cepo:
    url: https://raw.githubusercontent.com/OpenEnergyPlatform/ClimateEnergyPolicyOntology/production/src/ontology/cepo.owl
    has_imports: true
    prefixmap:
      CEPO: http://purl.org/cepo/ontology#cepo_
  oto:
    url: https://raw.githubusercontent.com/OpenEnergyPlatform/OpenTransportOntology/production/src/ontology/oto.ttl
    has_imports: true
    format: turtle
    # Temporary workaround: the published import target `http://w3id.org/oto/develop/oto-shared.ttl`
    # currently resolves to HTML docs instead of RDF/Turtle.
    # Upstream issue: https://github.com/OpenEnergyPlatform/OpenTransportOntology/issues/46
    build_command: "perl -0pe 's@http://w3id.org/oto/develop/oto-shared.ttl@https://raw.githubusercontent.com/OpenEnergyPlatform/OpenTransportOntology/production/src/ontology/edits/oto-shared.ttl@g' $< > $@.tmp.ttl && robot merge -i $@.tmp.ttl -o $@ && rm $@.tmp.ttl"
    prefixmap:
      OTO: http://w3id.org/oto/OTO_
  meno:
    url: https://raw.githubusercontent.com/stap-m/midlevel-energy-ontology/main/ontology/src/midlevel-energy.owl
    has_imports: true
    prefixmap:
      MENO: https://raw.githubusercontent.com/stap-m/midlevel-energy-ontology/main/ontology/src/midlevel-energy.owl/MENO_
  muno:
    url: https://raw.githubusercontent.com/stap-m/muno/main/src/muno.owl
    has_imports: true
    # Temporary workaround: the published OWL imports two placeholder
    # `semanticweb.org/.../untitled-ontology-*` IRIs that are only resolved via
    # the repo-local Protégé catalog. Rewrite them to the raw extracted imports.
    # Upstream issue: https://github.com/stap-m/muno/issues/6
    build_command: "perl -0pe 's@http://www.semanticweb.org/abc/ontologies/2025/2/untitled-ontology-46/@https://raw.githubusercontent.com/stap-m/muno/main/src/ro-extracted.owl@g; s@http://www.semanticweb.org/abc/ontologies/2025/2/untitled-ontology-47/@https://raw.githubusercontent.com/stap-m/muno/main/src/iao-extracted.owl@g' $< > $@.tmp.owl && robot merge -i $@.tmp.owl -o $@ && rm $@.tmp.owl"
    prefixmap:
      MUNO: https://raw.githubusercontent.com/stap-m/muno/main/src/muno.owl/MUNO_
  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 $@"
  goldterms:
    url: https://raw.githubusercontent.com/cmungall/gold-ontology/main/gold.owl
    build_command: "robot relax -i $< reason -o $@"
    prefixmap:
      GOLDTERMS: https://w3id.org/gold.path/
      GOLDVOCAB: https://w3id.org/gold.vocab/
  sdgio:
    url: https://raw.githubusercontent.com/SDG-InterfaceOntology/sdgio/master/sdgio.owl
    prefixmap:
      SDGIO: http://purl.unep.org/sdg/SDGIO_
  kin:
    url: http://purl.org/ga4gh/kin.owl
    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: "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 $@"
    prefixmap:
      ontorion: http://ontorion.com/namespace#
  omop:
    prefixmap:
      omop: https://athena.ohdsi.org/search-terms/terms/
  comet:
    url: https://raw.githubusercontent.com/linkml/linkml-common/main/project/owl/linkml_common.owl.ttl
    build_command: "robot relax -i $< merge -o $@"    
    prefixmap:
      comet: https://w3id.org/linkml-common/
  cco:
    url: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AllCoreOntology
    build_command: "robot merge -i $< relax -o $@"
    prefixmap:
      CCO: http://www.ontologyrepository.com/CommonCoreOntologies/
  occo:
    url: https://raw.githubusercontent.com/Occupation-Ontology/OccO/main/src/ontology/occo-merged.owl
    prefixmap:
      OccO: http://purl.obolibrary.org/obo/OccO_
  iof:
    url: https://spec.industrialontologies.org/ontology/AboutIOFProd/
    build_command: "robot relax -i $< merge -o $@"
    prefixmap:
      IOFcore: https://spec.industrialontologies.org/ontology/
  upa:
    url: http://purl.obolibrary.org/obo/upa.owl
    prefixmap:
      UPa: http://purl.obolibrary.org/obo/UPa_
  go:
    url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
  go-lego:
    url: http://purl.obolibrary.org/obo/go/extensions/go-lego.owl
  go-amigo:
    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
  orcid:
    url: https://w3id.org/orcidio/orcidio.owl
    prefixmap:
      orcid: https://orcid.org/
      geonames: https://www.geonames.org/
  ror:
    url: https://w3id.org/biopragmatics/resources/ror/ror.owl.gz
    compression: gzip
    prefixmap:
      ror: https://ror.org/
  cpont:
    url: https://w3id.org/cpont/cpont.owl
  biolink:
    url: https://w3id.org/biolink/biolink-model.owl.ttl
    jsonld_context: https://biolink.github.io/biolink-model/context.jsonld
    format: turtle
    #
  biopax:
    url: http://www.biopax.org/release/biopax-level3.owl
  enanomapper:
    url: http://enanomapper.github.io/ontologies/enanomapper.owl
    has_imports: true
    prefixmap:
      evs.ncit: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
      old.fix: http://purl.org/obo/owl/FIX#
  mlo:
    url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2023-09-11/external/ml-ontology-202010021305.owl
    has_imports: true
    prefixmap:
      mlo: http://www.a2rd.net.br/mlo#
  ito:
    url: https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip
    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
    prefixmap:
      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:
    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:
    url: https://reactome.org/download/current/biopax.zip
    zip_extract_file: Mus_musculus.owl
    post_processing_steps:
      - "sqlite3 {db} < views/reactome.sql"
  
  efo:
    url: http://www.ebi.ac.uk/efo/efo.owl
    has_imports: true
  hcao:
    url: https://raw.githubusercontent.com/HumanCellAtlas/ontology/master/hcao.owl
  hpinternational:
    url:  http://purl.obolibrary.org/obo/hp/hp-international.owl
  edam:
    url: http://edamontology.org/EDAM.owl
  chr:
    url: https://raw.githubusercontent.com/monarch-initiative/monochrom/master/chr.owl
    prefixmap:
      chr: http://purl.obolibrary.org/obo/CHR_
  sweetAll:
    url: http://sweetontology.net/sweetAll
    has_imports: true
    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
    compression: gzip
  schema-dot-org:
    url: https://schema.org/version/latest/schemaorg-current-https.rdf
  prov:
    url: http://www.w3.org/ns/prov.owl
    prefixmap:
      prov: "http://www.w3.org/ns/prov#"
  #voag:
  #  url: http://voag.linkedmodel.org/voag
  #  build_command: "robot merge -i $<  -o $@"
  #  prefixmap:
  #    voag: http://voag.linkedmodel.org/voag#
  dtype:
    url: http://www.linkedmodel.org/schema/dtype
    prefixmap:
      dtype: http://www.linkedmodel.org/schema/dtype#
      voag: http://voag.linkedmodel.org/voag#      
  vaem:
    url: http://www.linkedmodel.org/schema/vaem
    prefixmap:
      vaem: http://www.linkedmodel.org/schema/vaem#
  qudtunit:
    url: http://qudt.org/vocab/unit
    build_command: "robot merge -i $<  -o $@"
    prefixmap:
      qudtschema: http://qudt.org/schema/qudt/
      qudtunit: http://qudt.org/vocab/unit/
      si-quantity: https://si-digital-framework.org/SI/quantities/
  quantitykind:
    url: http://qudt.org/vocab/quantitykind
    build_command: "robot merge -i $<  -o $@"
    prefixmap:
      quantitykind: http://qudt.org/vocab/quantitykind/
  cellosaurus:
    url: https://raw.githubusercontent.com/calipho-sib/cellosaurus/master/cellosaurus.obo
    format: obo
    prefixmap:
      cellosaurus: http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
  cosmo:
    url: https://micra.com/COSMO/COSMO.owl
    has_imports: true
  gist:
    url: https://w3id.org/semanticarts/ontology/gistCore
    # gist.owl contains DTD elements, rdftab doesn't like this
    build_command: "robot merge -i $< -o $@"
    prefixmap:
      gist: https://w3id.org/semanticarts/ns/ontology/gist/
      gistd: https://w3id.org/semanticarts/ns/data/gist/
  gistBFO:
    url: https://w3id.org/semanticarts/ontology/gistBFO
    # merge import closure
    build_command: "robot merge -i $< -o $@"
    prefixmap:
      gist: https://w3id.org/semanticarts/ns/ontology/gist/    
  fhkb:
    prefixmap:
      fhkb: http://owl.cs.manchester.ac.uk/tutorials/fhkb#
  dbpendiaont:
    url: "https://databus.dbpedia.org/ontologies/dbpedia.org/ontology--DEV/2023.01.03-072003/ontology--DEV_type=parsed.owl"
    prefixmap:
      dbpediaont: http://dbpedia.org/ontology/
      dbpedia: http://dbpedia.org/
  uberoncm:
    url: https://github.com/obophenotype/uberon/releases/latest/download/composite-metazoan.owl
  #sdtm:
  #  url: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/SDTM%20Terminology.OWL.zip
  #empathi:
  #  url: https://raw.githubusercontent.com/shekarpour/empathi.io/master/empathi.owl
  #  format: owlx
  #  named_prefixmaps:
  #    - prefixcc
  #  prefixmap:
  #    empathi: https://w3id.org/empathi/

## CROP ONTOLOGIES
  co_324:
    url: https://cropontology.org/ontology/CO_324/rdf
    prefixmap:
      co_324: "https://cropontology.org/rdf/CO_324:"

  ppeo:
    url: http://purl.org/ppeo/PPEO.owl
    prefixmap:
      PPEO: http://purl.org/ppeo/PPEO.owl#

## PyOBO products      
## See https://github.com/INCATools/semantic-sql/issues/45
  interpro:
    url: https://w3id.org/biopragmatics/resources/interpro/interpro.obo
    build_command: "perl -npe 's@ go:@ GO:@g;s@ ro:@ RO:@g;s@ interpro:@ InterPro:@g' $< > $@.tmp && robot convert -i $@.tmp -o $@"
    format: obo
    prefixmap:
      InterPro: http://purl.obolibrary.org/obo/InterPro_
  pfam:
    url: https://w3id.org/biopragmatics/resources/pfam/pfam.owl
    prefixmap:
      PFAM: https://www.ebi.ac.uk/interpro/entry/pfam/
      PFAM.CLAN: https://www.ebi.ac.uk/interpro/set/pfam/
  hgnc.genegroup:
    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc.genegroup/hgnc.genegroup.owl.gz
    compression: gzip
    prefixmap:
      hgnc.genegroup: http://purl.obolibrary.org/obo/hgnc.genegroup_
  hgnc:
    # note: owl is no longer produced
    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc/2022-06-01/hgnc.owl.gz
    compression: gzip
    prefixmap:
      hgnc: http://purl.obolibrary.org/obo/hgnc_
  sgd:
    url: https://w3id.org/biopragmatics/resources/sgd/sgd.obo
    format: obo
    prefixmap:
      SGD: https://www.yeastgenome.org/locus/
  gtdb:
    url: https://w3id.org/biopragmatics/resources/gtdb/gtdb.owl
    prefixmap:
      gtdb: https://gtdb.ecogenomic.org/tree?r=
  eccode:
    url: https://w3id.org/biopragmatics/resources/eccode/eccode.owl.gz
    compression: gzip
    prefixmap:
      EC: "https://bioregistry.io/eccode:"
      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
    prefixmap:
      UniProtKB: "https://bioregistry.io/uniprot:"
  uniprot.ptm:
    url: https://w3id.org/biopragmatics/resources/uniprot.ptm/uniprot.ptm.owl
    prefixmap:
      RESID: https://proteininformationresource.org/cgi-bin/resid?id=
      UNIMOD: http://www.unimod.org/modifications_view.php?editid1=
      uniprot.ptm: https://biopragmatics.github.io/providers/uniprot.ptm/
  credit:
    url: https://raw.githubusercontent.com/biopragmatics/obo-db-ingest/main/export/credit/credit.owl
    prefixmap:
      credit: https://credit.niso.org/contributor-roles/
  rhea:
    url: https://w3id.org/biopragmatics/resources/rhea/rhea.owl.gz
    # https://github.com/biopragmatics/obo-db-ingest/issues/15
    build_command: "perl -npe 's@https://www.ebi.ac.uk/.*ec=@https://bioregistry.io/eccode:@g' $< > $@.tmp && robot convert -i $@.tmp -o $@"
    compression: gzip
    # build_command: "robot merge -i $<  -o $@"
    prefixmap:
      RHEA: https://www.rhea-db.org/rhea/
  swisslipid:
    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/swisslipid/2023-02-03/swisslipid.obo.gz
    format: obo
    compression: gzip
    prefixmap:
      swisslipid: http://purl.obolibrary.org/obo/swisslipid_
  drugbank:
    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugbank/5.1.9/drugbank.owl.gz
    compression: gzip
    prefixmap:
      drugbank: http://purl.obolibrary.org/obo/drugbank_
  drugcentral:
    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugcentral.owl.gz
    compression: gzip
    prefixmap:
      drugbank: http://purl.obolibrary.org/obo/drugcentral_
  complexportal:
    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/complexportal/2022-02-03/complexportal.owl.gz
    compression: gzip
    prefixmap:
      complexportal: http://purl.obolibrary.org/obo/complexportal_
  wikipathways:
    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/
  rxnorm:
    prefixmap:
      RXNORM: http://purl.bioontology.org/ontology/RXNORM/
  vccf:
    url: https://raw.githubusercontent.com/obophenotype/vccf-ontology/main/vccf.owl
    prefixmap:
      VCCF: http://purl.obolibrary.org/obo/VCCF_
  ontobiotope:
    url: "'https://data.agroportal.lirmm.fr/ontologies/ONTOBIOTOPE/download?apikey=1de0a270-29c5-4dda-b043-7c3580628cd5&download_format=rdf'"
    prefixmap:
      OBT: http://purl.obolibrary.org/obo/OBT_
  nando:
    url: "'https://data.bioontology.org/ontologies/NANDO/submissions/15/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'"
    prefixmap:
      NANDO: http://nanbyodata.jp/ontology/NANDO_
  ecso:
    url: "'https://data.bioontology.org/ontologies/ECSO/submissions/64/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'"
    prefixmap:
      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 $@"
  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:
  #    MEO: http://purl.jp/bio/11/meo/MEO_
  ontie:
    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"
    build_command: "robot merge -i $<  -o $@"
    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/
  micront:
    url: https://raw.githubusercontent.com/grp-schmidt/microntology/refs/heads/main/micront.owl
    prefixmap:
      MICRONT: "http://purl.obolibrary.org/obo/micront.owl#MICRONT_"
  #monarch:
  #  url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.db.gz
  #  format: kgxdb

  # LinkML Schemas
  nmdc_schema:
    url: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/project/owl/nmdc.owl.ttl
    build_command: "robot merge -i $<  -o $@"
    prefixmap:
      nmdc: https://w3id.org/nmdc/
      linkml: https://w3id.org/linkml/
      mixs: https://w3id.org/mixs/
  mixs:
    url: https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/main/project/owl/mixs.owl.ttl
    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 $@"
    prefixmap:
      fibo: https://spec.edmcouncil.org/fibo/ontology/
      cmnsav: https://www.omg.org/spec/Commons/AnnotationVocabulary/

  # BFO variant products
  bfo2020:
    url: http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
    #post_processing_steps:
    #  - "echo hello {db}"
    #  - "echo goodbye {db}"
  bfo2020_core:
    url: http://purl.obolibrary.org/obo/bfo/2020/bfo-core.owl
  bfo2020_notime:
    url: http://purl.obolibrary.org/obo/bfo/2020/notime/bfo.owl
  bfo2020_time:
    url: https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/src/owl/profiles/temporal%20extensions/temporalized%20relations/owl/bfo-temporalized-relations.owl

## SAREF and Building Ontologies
  saref4ener:
    description: ETSI SAREF extension for the energy domain (smart energy, demand response)
    url: https://saref.etsi.org/saref4ener/
    # Needs content negotiation - curl -H "Accept: text/turtle"
    build_command: "curl -sL -H 'Accept: text/turtle' https://saref.etsi.org/saref4ener/ > $@.ttl && robot convert -i $@.ttl -o $@ && rm $@.ttl"
    prefixmap:
      saref4ener: https://saref.etsi.org/saref4ener/
      saref: https://saref.etsi.org/core/
      s4ener: https://saref.etsi.org/saref4ener/
  saref4bldg:
    description: ETSI SAREF extension for building automation (IFC4-based)
    url: https://saref.etsi.org/saref4bldg/
    # Needs content negotiation - curl -H "Accept: text/turtle"
    build_command: "curl -sL -H 'Accept: text/turtle' https://saref.etsi.org/saref4bldg/ > $@.ttl && robot convert -i $@.ttl -o $@ && rm $@.ttl"
    prefixmap:
      saref4bldg: https://saref.etsi.org/saref4bldg/
      saref: https://saref.etsi.org/core/
      s4bldg: https://saref.etsi.org/saref4bldg/
  hhearvs:
    description: HHEAR Value Sets - value sets for the Human Health Exposure Analysis Resource
    url: "https://data.bioontology.org/ontologies/HHEARVS/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb"
    build_command: "perl -npe 's@<owl:imports.*/>@@g; s@skos:broader@rdfs:subClassOf@g; s@skos:prefLabel@rdfs:label@g; s@owl:NamedIndividual@owl:Class@g' $< > $@.tmp && robot convert -i $@.tmp -o $@ && rm $@.tmp"
    prefixmap:
      HHEAR: http://purl.org/twc/HHEAR_
      HHEARVS: http://purl.org/twc/HHEARVS_
      HHEARVS.nihreporter: https://reporter.nih.gov/search/2NC9YrDMM0SiuN8TnuRgKg/project-details/
  sdoho:
    description: Social Determinants of Health Ontology
    url: "https://data.bioontology.org/ontologies/SDOHO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb"
    build_command: "perl -npe 's@<owl:imports.*/>@@g' $< > $@.tmp && robot convert -i $@.tmp -o $@ && rm $@.tmp"
    prefixmap:
      SDOHO: "https://sbmi.uth.edu/bsdi/SDoHO#"
  pathgo:
    description: Pathogenesis Gene Ontology - mechanisms through which pathogens cause cellular damage
    url: https://raw.githubusercontent.com/jhuapl-bio/pathogenesis-gene-ontology/refs/heads/master/pathgo.owl
    prefixmap:
      PATHGO: http://purl.obolibrary.org/obo/PATHGO_
  brick:
    description: Brick schema for building operations (HVAC, sensors, equipment, zones)
    url: https://github.com/BrickSchema/Brick/releases/download/v1.4.0/Brick.ttl
    format: turtle
    # Has unresolvable imports (BACnet) - strip imports and convert to OWL/XML
    build_command: "sed '48061,48072d' $< > $@.tmp && robot convert -i $@.tmp -f owl -o $@ && rm $@.tmp"
    prefixmap:
      brick: "https://brickschema.org/schema/Brick#"
      bsh: "https://brickschema.org/schema/BrickShape#"
      tag: "https://brickschema.org/schema/BrickTag#"
      ref: "https://brickschema.org/schema/Brick/ref#"
      rec: "https://w3id.org/rec#"
      bacnet: "http://data.ashrae.org/bacnet/2020#"
      s223: "http://data.ashrae.org/standard223#"
      qudt: "http://qudt.org/schema/qudt/"
      qudtqk: "http://qudt.org/vocab/quantitykind/"
      unit: "http://qudt.org/vocab/unit/"
      sosa: "http://www.w3.org/ns/sosa/"
      sh: "http://www.w3.org/ns/shacl#"
      vcard: "http://www.w3.org/2006/vcard/ns#"
  minsysont:
    description: Critical Minerals Ontology (Mineral System Ontology)
    url: https://raw.githubusercontent.com/adavarpa/CMO-Critical-Minerals-Ontology-/refs/heads/main/CMO.owl
    build_command: "robot merge -i $< -o $@.tmp.owl && perl -npe 's/\\[HSiO4\\]/%5BHSiO4%5D/g' $@.tmp.owl > $@ && rm $@.tmp.owl"
    prefixmap:
      MinSysOnt: "http://www.semanticweb.org/hbabaie/ontologies/2021/5/MinSysOnt#"
      CMO.minerals: "http://www.semanticweb.org/Davarpanah-Babaie/Ontologies/2022/CMO#"
  sulo:
    description: Simplified Upper Level Ontology
    url: https://w3id.org/sulo/sulo.ttl
    format: turtle
    prefixmap:
      sulo: https://w3id.org/sulo/