Open jnguyenx opened 7 years ago
http://localhost:8080/api/match/jaccard?id=HP:0007280
ontologyUris: - http://purl.obolibrary.org/obo/hp.owl ontologyDataUris: [] dataTsvs: - ./Hs_disease_phenotype.txt 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#'
@damiansm was trying to make that work.
http://localhost:8080/api/match/jaccard?id=HP:0007280