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| ontologyUris: | |
| - /data/all.owl | |
| ontologyDataUris: [] | |
| dataTsvs: [] | |
| curies: | |
| # Skolemize Blank Nodes | |
| # overwrite iri fragment with '' for unresovable bnodes | |
| '_': 'https://monarchinitiative.org/.well-known/genid/' | |
| # Monarch-specific | |
| '': 'https://monarchinitiative.org/' | |
| 'MONARCH': 'https://monarchinitiative.org/MONARCH_' | |
| 'MonarchData': 'http://data.monarchinitiative.org/ttl/' | |
| 'MonarchArchive': 'http://archive.monarchinitiative.org/ttl/' | |
| # other semantic-web items | |
| 'Annotation': 'http://www.w3.org/ns/oa#Annotation' # FIXME - i don't think we're using this | |
| 'dc': 'http://purl.org/dc/elements/1.1/' | |
| 'foaf': 'http://xmlns.com/foaf/0.1/' | |
| # ontologies | |
| # [y] indicates those that the monarch team contributes to | |
| 'AQTLTrait': 'http://identifiers.org/animalqtltrait/' # FIXME - should get integrated into Upheno | |
| 'BFO': 'http://purl.obolibrary.org/obo/BFO_' # BFO: Basic Formal Ontology | |
| 'CHEBI' : 'http://purl.obolibrary.org/obo/CHEBI_' # ChEBI: Chemicals of Biological Interest | |
| 'CHR' : 'http://purl.obolibrary.org/obo/CHR_' # CHR: Chromosome Ontology | |
| 'CL' : 'http://purl.obolibrary.org/obo/CL_' # CL: Cell Ontology (cell types) [y] | |
| 'CLO' : 'http://purl.obolibrary.org/obo/CLO_' # CLO: Cell Line Ontology [y] | |
| 'CMO' : 'http://purl.obolibrary.org/obo/CMO_' # CMO: Clinical Measurements Ontology | |
| 'DATA' : 'http://edamontology.org/data_' # EDAM: Data and Methods Ontology (data artifacts) | |
| 'DC' : 'http://purl.obolibrary.org/obo/DC_' # TODO | |
| 'DECIPHER' : 'http://purl.obolibrary.org/obo/DECIPHER_' # DECIPHER: Deciphering Developmental Disease | |
| 'DOID': 'http://purl.obolibrary.org/obo/DOID_' # DOID: Human Disease Ontology [y] | |
| 'ECO': 'http://purl.obolibrary.org/obo/ECO_' # ECO: Evidence Code Ontology [y] | |
| 'EFO' : 'http://www.ebi.ac.uk/efo/EFO_' # EFO: Experimental Factor Ontology (all kinds of stuff) [y] | |
| 'ENVO' : 'http://purl.obolibrary.org/obo/ENVO_' # ENVO: Environment Ontology | |
| 'EOM' : 'http://purl.obolibrary.org/obo/EOM_' # elements of morphology phentoypes | |
| 'ERO' : 'http://purl.obolibrary.org/obo/ERO_' # ERO: eagle-i resource ontology [y] | |
| 'faldo' : 'http://biohackathon.org/resource/faldo#' # FALDO: Feature Annotation Location Description Ontology (genomic feature properties) [y] | |
| 'FBcv' : 'http://purl.obolibrary.org/obo/FBcv_' # FBcv: flybase CV (includes phenotypes) | |
| 'FBbt': 'http://purl.obolibrary.org/obo/FBbt_' # FBbt: flybase anatomy | |
| 'FBdv': 'http://purl.obolibrary.org/obo/FBdv_' # FBdv: flybase developmental stages | |
| 'GENO': 'http://purl.obolibrary.org/obo/GENO_' # GENO: Genotype Partonomy Ontology [y] | |
| 'GO' : 'http://purl.obolibrary.org/obo/GO_' # GO: Gene Ontology [y] | |
| 'HP': 'http://purl.obolibrary.org/obo/HP_' # HP: Human Phenotype Ontology [y] | |
| 'IAO': 'http://purl.obolibrary.org/obo/IAO_' # IAO: Information Artifact Ontology [y] | |
| 'KEGG-ds' : 'http://purl.obolibrary.org/KEGG-ds_' # KEGG-ds: KEGG Disease Ontology | |
| 'LPT': 'http://purl.obolibrary.org/obo/LPT_' # LPT: Livestock Phenotypic Trait Ontology | |
| 'MA': 'http://purl.obolibrary.org/obo/MA_' # MA: Mouse Anatomy Ontology [y] | |
| 'MedGen' : 'http://www.ncbi.nlm.nih.gov/medgen/' # a vocabulary - should this be in purl? | |
| 'MESH': 'http://purl.obolibrary.org/obo/MESH_' # MeSH: Medical Subject Headings (medical diseases, phenotypes, and drugs) | |
| 'MP': 'http://purl.obolibrary.org/obo/MP_' # MP: Mammalian Phenotype Ontology [y] | |
| 'MPATH': 'http://purl.obolibrary.org/obo/MPATH_' # MPATH: Mammalian Pathology Ontology | |
| 'NBO': 'http://purl.obolibrary.org/obo/NBO_' # NBO: NeuroBehavior Ontology [y] | |
| 'OBA': 'http://purl.obolibrary.org/obo/OBA_' # OBA: Ontology of Biological Attributes (traits) | |
| 'OBAN': 'http://purl.org/oban/' # OBAN: Open Biomedical Annotation Model [y] | |
| 'OBI': 'http://purl.obolibrary.org/obo/OBI_' # OBI: Ontology of Biomedical Investigations [y] | |
| 'OBO': 'http://purl.obolibrary.org/obo/' # all ontologies in the OBO namespace (this is not itself an ontology) | |
| 'OIO': 'http://www.geneontology.org/formats/oboInOwl#' # oboInOwl: obo-specific annotation properties, like synonym types | |
| 'OMIA' : 'http://purl.obolibrary.org/obo/OMIA_' # OMIA: Online Mendelian Inheritance in Animals (animal diseases) | |
| 'OMIM' : 'http://purl.obolibrary.org/obo/OMIM_' # OMIM: Online Mendelian Inheritance in Man (human disease and variants) | |
| 'Orphanet' : 'http://www.orpha.net/ORDO/Orphanet_' # Orphanet: rare diseases and orphan drugs | |
| 'PATO': 'http://purl.obolibrary.org/obo/PATO_' # PATO: Phenotypic Quality Ontology [y] | |
| 'PCO': 'http://purl.obolibrary.org/obo/PCO_' # PCO: Population and Community Ontology [y] | |
| 'PR': 'http://purl.obolibrary.org/obo/PR_' # PRO: protein ontology | |
| 'PW' : 'http://purl.obolibrary.org/obo/PW_' # PW: pathway ontology | |
| 'RO': 'http://purl.obolibrary.org/obo/RO_' # RO: Relationship Ontology [y] | |
| 'SIO' : 'http://semanticscience.org/resource/SIO_' # SIO: SemanticScience Integrated Ontology (information artifacts) | |
| 'SNOMED' : 'http://purl.obolibrary.org/obo/SNOMED_' # SNOMED:diseases and phenotypes | |
| 'SO' : 'http://purl.obolibrary.org/obo/SO_' # SO: Sequence Ontology [y] | |
| 'STATO': 'http://purl.obolibrary.org/obo/STATO_' # Statistics Ontology | |
| 'UBERON' : 'http://purl.obolibrary.org/obo/UBERON_' # UBERON: integrated anatomy ontology (metazoans, mostly) [y] | |
| 'UPHENO' : 'http://purl.obolibrary.org/obo/UPHENO_' # UPHENO: integrated phenotype ontology, and normal traits [y] | |
| 'UMLS' : 'http://purl.obolibrary.org/obo/UMLS_' # UMLS: unified medical language system | |
| 'UO' : 'http://purl.obolibrary.org/obo/UO_' # UO: units of measurements | |
| 'VT' : 'http://purl.obolibrary.org/obo/VT_' # VT: Vertebrate Trait Ontology | |
| 'WBPhenotype': 'http://purl.obolibrary.org/obo/WBPhenotype_' # WBPhenotype: WormBase phenotypes (nematode) [y] | |
| 'XCO' : 'http://purl.obolibrary.org/obo/XCO_' # XCO: Experimental Conditions Ontology | |
| 'ZFA': 'http://purl.obolibrary.org/obo/ZFA_' # ZFA: Zebrafish Anatomy Ontology [y] | |
| 'ZFS': 'http://purl.obolibrary.org/obo/ZFS_' # ZFS: Zebrafish Staging [y] | |
| 'ZP': 'http://purl.obolibrary.org/obo/ZP_' # ZP: Zebrafish Phenotype Ontology [y] | |
| 'WBbt': 'http://purl.obolibrary.org/obo/WBbt_' #WBbt: C. elegans gross anatomy | |
| 'EMAPA': 'http://purl.obolibrary.org/obo/EMAPA_' # EMAPA: Mouse gross anatomy and development, timed | |
| 'XAO': 'http://purl.obolibrary.org/obo/XAO_' # XAO: Xenopus anatomy and development | |
| # publication/reference sources | |
| 'DOI' : 'http://dx.doi.org/' | |
| 'GeneReviews' : 'http://www.ncbi.nlm.nih.gov/books/' # diseases too | |
| 'ISBN': 'https://monarchinitiative.org/ISBN_' | |
| 'ISBN-10': 'https://monarchinitiative.org/ISBN10_' | |
| 'ISBN-13': 'https://monarchinitiative.org/ISBN13_' | |
| 'ISBN-15': 'https://monarchinitiative.org/ISBN15_' | |
| 'J' : 'http://www.informatics.jax.org/reference/J:' # MGI-internal identifiers for pubs | |
| 'MPD': 'http://phenome.jax.org/' | |
| 'MPD-assay': 'http://phenome.jax.org/db/qp?rtn=views/catlines&keymeas=' | |
| 'PMID': 'http://www.ncbi.nlm.nih.gov/pubmed/' | |
| 'PMCID' : 'http://www.ncbi.nlm.nih.gov/pmc/' | |
| 'AQTLPub' : 'http://www.animalgenome.org/cgi-bin/QTLdb/BT/qabstract?PUBMED_ID=' | |
| 'GO_REF' : 'http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:' | |
| 'HPO' : 'http://human-phenotype-ontology.org/' # to be used for persons, though they don't resolve with this | |
| # strains, lines, or organismal reagents | |
| 'APB': 'http://pb.apf.edu.au/phenbank/strain.html?id=' | |
| 'CMMR': 'http://www.cmmr.ca/order.php?t=m&id=' | |
| 'Coriell' : 'https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=' | |
| 'CoriellCollection' : 'https://catalog.coriell.org/1/' | |
| 'CoriellFamily' : 'https://catalog.coriell.org/0/Sections/BrowseCatalog/FamilyTypeSubDetail.aspx?fam=' | |
| 'CoriellIndividual' : 'https://catalog.coriell.org/Search?q=' | |
| 'dbSNPIndividual' : 'http://www.ncbi.nlm.nih.gov/SNP/snp_ind.cgi?ind_id=' # FIXME | |
| 'EMMA' : 'https://www.infrafrontier.eu/search?keyword=EM:' | |
| 'JAX' : 'http://jaxmice.jax.org/strain/' | |
| 'MMRRC' : 'https://www.mmrrc.org/catalog/sds.php?mmrrc_id=' | |
| 'MPD-strain': 'http://phenome.jax.org/db/q?rtn=strains/details&strainid=' | |
| 'MUGEN': 'http://bioit.fleming.gr/mugen/Controller?workflow=ViewModel&expand_all=true&name_begins=model.block&eid=' | |
| 'NCIMR': 'https://mouse.ncifcrf.gov/available_details.asp?ID=' | |
| 'RBRC': 'http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=RBRC' | |
| # organisms and genome builds (also NCBITaxon) | |
| 'NCBIAssembly': 'http://www.ncbi.nlm.nih.gov/assembly/' | |
| 'NCBIGenome' : 'http://www.ncbi.nlm.nih.gov/genome/' | |
| 'NCBITaxon' : 'http://purl.obolibrary.org/obo/NCBITaxon_' | |
| 'OMIA-breed': 'https://monarchinitiative.org/model/OMIA-breed:' | |
| 'UCSC' : 'ftp://hgdownload.cse.ucsc.edu/goldenPath/' | |
| # homology | |
| 'HOMOLOGENE' : 'http://www.ncbi.nlm.nih.gov/homologene/' | |
| 'KEGG-ko' : 'http://www.kegg.jp/dbget-bin/www_bget?ko:' | |
| 'PANTHER' : 'http://www.pantherdb.org/panther/family.do?clsAccession=' # protein/orthologous families | |
| # variants | |
| 'AQTL' : 'http://identifiers.org/animalqtl/' # FIXME temporary # traits | |
| 'CGD' : 'http://ohsu.edu/cgd/' # diseases, variant instances | |
| 'ClinVar' : 'http://www.ncbi.nlm.nih.gov/clinvar/' # variant+condition | |
| 'ClinVarVariant' : 'http://www.ncbi.nlm.nih.gov/clinvar/variation/' | |
| 'ClinVarSubmitters' : 'http://www.ncbi.nlm.nih.gov/clinvar/submitters/' | |
| 'COSMIC' : 'http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=' | |
| 'HGMD' : 'http://identifiers.org/hgmd/' | |
| 'dbSNP' : 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=' | |
| 'dbVar' : 'http://www.ncbi.nlm.nih.gov/dbvar/' | |
| # pathways | |
| 'KEGG-path' : 'http://www.kegg.jp/dbget-bin/www_bget?path:' | |
| 'REACT' : 'http://www.reactome.org/PathwayBrowser/#/' | |
| # genes (and RNAs and transcripts) | |
| 'BIOGRID' : 'http://thebiogrid.org/' # also interactions | |
| 'CCDS' : 'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=' # transcripty things | |
| 'dictyBase' : 'http://dictybase.org/gene/' | |
| 'EcoGene' : 'http://ecogene.org/gene/' | |
| 'ENSEMBL' : 'http://identifiers.org/ensembl/' | |
| 'FlyBase' : 'http://flybase.org/reports/' # also variants, pubs, genotypes, strains | |
| 'GenBank' : 'http://www.ncbi.nlm.nih.gov/nuccore/' | |
| 'HGNC' : 'http://identifiers.org/hgnc/HGNC:' | |
| 'IMPC' : 'http://www.mousephenotype.org/data/genes/' # FIXME | |
| 'KEGG-hsa' : 'http://www.kegg.jp/dbget-bin/www_bget?hsa:' | |
| 'MGI': 'http://www.informatics.jax.org/accession/MGI:' # also variants, pubs, genotypes | |
| 'miRBase' : 'http://identifiers.org/mirbase/' # microRNA genes | |
| 'NCBIGene' : 'http://www.ncbi.nlm.nih.gov/gene/' | |
| 'PomBase' : 'http://identifiers.org/PomBase:' | |
| 'RefSeq' : 'http://www.ncbi.nlm.nih.gov/refseq/?term=' | |
| 'RGD' : 'http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=' | |
| 'SGD' : 'http://identifiers.org/SGD:' | |
| 'TAIR' : 'http://identifiers.org/TAIR:' | |
| 'WormBase' : 'http://identifiers.org/wormbase/' # also variants, pubs, genotypes | |
| 'Xenbase' : 'http://identifiers.org/xenbase/' | |
| 'ZFIN' : 'http://zfin.org/' # also variants, pubs, genotypes | |
| # proteins | |
| 'EC' : 'http://identifiers.org/ec-code/' | |
| 'HPRD' : 'http://www.hprd.org/protein/' | |
| 'NCBIProtein' : 'http://www.ncbi.nlm.nih.gov/protein/' | |
| 'PDB' : 'http://identifiers.org/PDB:' | |
| 'SwissProt' : 'http://identifiers.org/SwissProt:' | |
| 'TrEMBL' : 'http://www.uniprot.org/uniprot/' | |
| 'UniProtKB' : 'http://identifiers.org/uniprot/' | |
| # SEPIO: Scientific Evidence and Provenance Information Ontology | |
| 'SEPIO': 'http://purl.obolibrary.org/obo/SEPIO_' | |
| 'VIVO': 'http://vivoweb.org/ontology/core#' | |
| #Procedures/protocols | |
| 'IMPRESS-procedure' : 'https://www.mousephenotype.org/impress/procedures/' | |
| 'IMPRESS-protocol' : 'https://www.mousephenotype.org/impress/protocol/' | |
| 'IMPRESS-parameter' : 'https://www.mousephenotype.org/impress/parameterontologies/' | |
| #Drugs, chemicals, compounds | |
| 'CID' : 'http://pubchem.ncbi.nlm.nih.gov/compound/' | |
| 'DrugBank' : 'http://www.drugbank.ca/drugs/' | |
| 'SIO': 'http://semanticscience.org/resource/SIO_' | |
| 'OAE': 'http://purl.obolibrary.org/obo/OAE_' | |
| 'RXCUI': 'http://purl.bioontology.org/ontology/RXNORM/' | |
| 'MEDDRA': 'http://purl.bioontology.org/ontology/MEDDRA/' | |
| 'FDADrug': 'http://www.fda.gov/Drugs/InformationOnDrugs/' | |
| 'BT': 'http://c.biothings.io/#' | |
| 'UNII': 'http://fdasis.nlm.nih.gov/srs/unii/' | |
| 'GINAS' : 'http://tripod.nih.gov/ginas/app/substance#' |