# Monarch-specific '': 'https://monarchinitiative.org/' # local BASE IRI 'MONARCH': 'https://monarchinitiative.org/MONARCH_' # local BOGUS IRI effectivly bnodes but less 'BNODE': 'https://monarchinitiative.org/.well-known/genid/' # local RDF Skolemized Blank Node 'MonarchData': 'https://data.monarchinitiative.org/ttl/' # Bleeding edge RDF data 'MonarchArchive': 'https://archive.monarchinitiative.org/' # Release RDF data 'MonarchLogoRepo': 'https://github.com/monarch-initiative/monarch-ui/blob/master/public/img/sources/' # Monarch's stash of logos for sources we ingest - this is used to set schemalogo in Dataset.py 'biolink': 'https://w3id.org/biolink/vocab/' # Biolink model # other semantic-web items 'rdf': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' # Resource Description Framework 'rdfs': 'http://www.w3.org/2000/01/rdf-schema#' # Resource Description Framework Schema 'dc': 'http://purl.org/dc/terms/' # Dublin Core (metadata) (terms is superset of elements) 'foaf': 'http://xmlns.com/foaf/0.1/' # Friend Of A Friend (social) 'xml': 'http://www.w3.org/XML/1998/namespace' # Extensible Markup Language 'xsd': 'http://www.w3.org/2001/XMLSchema#' # XML Schema Definition 'owl': 'http://www.w3.org/2002/07/owl#' # Web Ontology Language 'skos': 'http://www.w3.org/2004/02/skos/core#' # Simple Knowledge Organization System # 'Annotation': 'http://www.w3.org/ns/oa#Annotation' # Web annotation 'schema': 'http://schema.org/' # Schema.org "provides schemas for structured data on the Internet" # dataset description 'dcat': 'http://www.w3.org/ns/dcat#' # Data Catalog Vocabulary 'dctypes': 'http://purl.org/dc/dcmitype/' # Dublin Core Metadata Initiative (types) 'pav': 'http://purl.org/pav/' # Provenance, Authoring and Versioning 'cito': 'http://purl.org/spar/cito/' # Citation Typing Ontology 'void': 'http://rdfs.org/ns/void#' # Vocabulary of Interlinked Datasets (VOID) # ontologies 'AQTLTrait': 'http://identifiers.org/animalqtltrait/' # Animal Quantitative Trait Loci Database # FIXME - should get integrated into Upheno 'BFO': 'http://purl.obolibrary.org/obo/BFO_' # Basic Formal Ontology 'COHD': 'http://purl.obolibrary.org/obo/COHD_' # Columbia Open Health Data 'CHEBI': 'http://purl.obolibrary.org/obo/CHEBI_' # Chemicals of Biological Interest 'CHR': 'http://purl.obolibrary.org/obo/CHR_' # Chromosome Ontology 'CL': 'http://purl.obolibrary.org/obo/CL_' # Cell Ontology (cell types) 'CLO': 'http://purl.obolibrary.org/obo/CLO_' # Cell Line Ontology 'CMO': 'http://purl.obolibrary.org/obo/CMO_' # Clinical Measurements Ontology 'EDAM-DATA': 'http://edamontology.org/data_' # Data and Methods Ontology (data artifacts) 'DC_CL': 'http://purl.obolibrary.org/obo/DC_CL' # *** seeing it fixed in github but not yet live was `DC` 'DECIPHER': 'https://decipher.sanger.ac.uk/syndrome/' # Deciphering Developmental Disease 'DOID': 'http://purl.obolibrary.org/obo/DOID_' # Human Disease Ontology 'ECO': 'http://purl.obolibrary.org/obo/ECO_' # Evidence Code Ontology 'EFO': 'http://www.ebi.ac.uk/efo/EFO_' # Experimental Factor Ontology (all kinds of stuff) 'ENVO': 'http://purl.obolibrary.org/obo/ENVO_' # Environment Ontology 'ERO': 'http://purl.obolibrary.org/obo/ERO_' # Eeagle-i Resource Ontology 'faldo': 'http://biohackathon.org/resource/faldo#' # Feature Annotation Location Description Ontology 'FBcv': 'http://purl.obolibrary.org/obo/FBcv_' # FlyBase Controled Vocabulary (includes phenotypes) 'FBbt': 'http://purl.obolibrary.org/obo/FBbt_' # FlyBase anatomy 'FBdv': 'http://purl.obolibrary.org/obo/FBdv_' # Flybase developmental stages # till we get a purl? `FBgn': 'http://flybase.org/reports/' # flybase gene? 'GARD': 'http://purl.obolibrary.org/obo/GARD_' # Genetic and Rare Diseases (GARD) Information Center 'GENO': 'http://purl.obolibrary.org/obo/GENO_' # Genotype Partonomy Ontology 'GO': 'http://purl.obolibrary.org/obo/GO_' # Gene Ontology 'HP': 'http://purl.obolibrary.org/obo/HP_' # Human Phenotype Ontology 'IAO': 'http://purl.obolibrary.org/obo/IAO_' # Information Artifact Ontology 'ICD9': 'http://purl.obolibrary.org/obo/ICD9_' # International Classification of Disease 9th Rev 'KEGG-ds': 'http://purl.obolibrary.org/KEGG-ds_' # Kyoto Encyclopedia of Genes and Genomes Disease Ontology 'LPT': 'http://purl.obolibrary.org/obo/LPT_' # Livestock Phenotypic Trait Ontology 'MA': 'http://purl.obolibrary.org/obo/MA_' # Mouse Anatomy Ontology 'MedGen': 'http://www.ncbi.nlm.nih.gov/medgen/' # Human Medical Genetics vocabulary 'MESH': 'http://id.nlm.nih.gov/mesh/' # Medical Subject Headings (medical diseases, phenotypes, and drugs) 'MP': 'http://purl.obolibrary.org/obo/MP_' # Mammalian Phenotype Ontology 'MPATH': 'http://purl.obolibrary.org/obo/MPATH_' # Mammalian Pathology Ontology 'NBO': 'http://purl.obolibrary.org/obo/NBO_' # NeuroBehavior Ontology 'OBA': 'http://purl.obolibrary.org/obo/OBA_' # Ontology of Biological Attributes (traits) 'OBAN': 'http://purl.org/oban/' # Open Biomedical Annotation Model 'OBI': 'http://purl.obolibrary.org/obo/OBI_' # Ontology of Biomedical Investigations 'OBO': 'http://purl.obolibrary.org/obo/' # Biological Ontology namespace (this is not itself an ontology) 'oboInOwl': 'http://www.geneontology.org/formats/oboInOwl#' # obo-specific annotation properties, like synonym types # 'OMIA' was http://omia.angis.org.au/ IS https://omia.org/ # (see about helping to update original data) 'OMIA': 'https://omia.org/OMIA' # Online Mendelian Inheritance in Animals (disease/species) # LIDIA seems retired. so these are not resovable # Also: http://www.vetsci.usyd.edu.au/lida/ 'LIDA': 'http://sydney.edu.au/vetscience/lida/dogs/search/disorder/' # Listing of Inherited Disorders in Animals (defunct?) 'OMIM': 'http://omim.org/entry/' # Online Mendelian Inheritance in Man (human disease and variants) 'OMIMPS': 'http://www.omim.org/phenotypicSeries/' # Online Mendelian Inheritance in Man (phenotypes) 'ORPHA': 'http://www.orpha.net/ORDO/Orphanet_' # Rare diseases and Orphan drugs 'PATO': 'http://purl.obolibrary.org/obo/PATO_' # Phenotypic Quality Ontology 'PCO': 'http://purl.obolibrary.org/obo/PCO_' # Population and Community Ontology 'PR': 'http://purl.obolibrary.org/obo/PR_' # Protein ontology 'PW': 'http://purl.obolibrary.org/obo/PW_' # PathWay ontology 'RO': 'http://purl.obolibrary.org/obo/RO_' # Relationship Ontology 'SCTID': 'http://purl.obolibrary.org/obo/SCTID_' # SNOMED 'SIO': 'http://semanticscience.org/resource/SIO_' # SemanticScience Integrated Ontology (information artifacts) 'SNOMED': 'http://purl.obolibrary.org/obo/SNOMED_' # Diseases and Phenotypes 'SO': 'http://purl.obolibrary.org/obo/SO_' # Sequence Ontology 'STATO': 'http://purl.obolibrary.org/obo/STATO_' # Statistics Ontology 'UBERON': 'http://purl.obolibrary.org/obo/UBERON_' # Integrated anatomy ontology (metazoans, mostly) 'UPHENO': 'http://purl.obolibrary.org/obo/UPHENO_' # Integrated phenotype ontology, and normal traits 'UMLS': 'http://linkedlifedata.com/resource/umls/id/' # Unified Medical Language system 'UO': 'http://purl.obolibrary.org/obo/UO_' # Units of measurements 'VT': 'http://purl.obolibrary.org/obo/VT_' # Vertebrate Trait Ontology 'WBPhenotype': 'http://purl.obolibrary.org/obo/WBPhenotype_' # WormBase Phenotypes (nematode) 'XCO': 'http://purl.obolibrary.org/obo/XCO_' # Experimental Conditions Ontology 'ZFA': 'http://purl.obolibrary.org/obo/ZFA_' # Zebrafish Anatomy Ontology 'ZFS': 'http://purl.obolibrary.org/obo/ZFS_' # Zebrafish Staging 'ZP': 'http://purl.obolibrary.org/obo/ZP_' # Zebrafish Phenotype Ontology 'WBbt': 'http://purl.obolibrary.org/obo/WBbt_' # C. elegans gross anatomy 'EMAPA': 'http://purl.obolibrary.org/obo/EMAPA_' # Mouse gross anatomy and development, timed 'XAO': 'http://purl.obolibrary.org/obo/XAO_' # Xenopus Anatomy and development 'MONDO': 'http://purl.obolibrary.org/obo/MONDO_' # Monarch Disease Ontology 'NCIT': 'http://purl.obolibrary.org/obo/NCIT_' # National Cancer Institute Thesaurus 'SEPIO': 'http://purl.obolibrary.org/obo/SEPIO_' # Scientific Evidence and Provenance Information Ontology 'VIVO': 'http://vivoweb.org/ontology/core#' # ontology for representing scholarship 'vfb': 'http://virtualflybrain.org/reports/' # Drosophila neuroanatomy # phenotype 'EOM': 'https://elementsofmorphology.nih.gov/index.cgi?tid=' # Elements of Morphology phentoypes 'EOM_IMG': 'https://elementsofmorphology.nih.gov/images/terms/' # publication/reference sources 'DOI': 'http://dx.doi.org/' # Digital Object identifier 'GeneReviews': 'http://www.ncbi.nlm.nih.gov/books/' # NCBI gene and diseases # more bogus IRIs 'ISBN': 'https://monarchinitiative.org/ISBN_' # International Standard Book Number 'ISBN-10': 'https://monarchinitiative.org/ISBN10_' # Same as ISBN has 10 digits pre 2007 'ISBN-13': 'https://monarchinitiative.org/ISBN13_' # International Standard Book Number with 13 digits starts w/ 978 or 979 # 'ISBN-15': 'https://monarchinitiative.org/ISBN15_' # I would like to think it is a typo blindly propagated *** 'J': 'http://www.informatics.jax.org/reference/J:' # MGI-internal identifiers for pubs (Journals) 'MPD': 'https://phenome.jax.org/' # Mouse Phenome Database 'MPD-assay': 'https://phenome.jax.org/db/qp?rtn=views/catlines&keymeas=' # Mouse Phenome Database assay 'PMID': 'http://www.ncbi.nlm.nih.gov/pubmed/' # PubMed Identifier 'PMCID': 'http://www.ncbi.nlm.nih.gov/pmc/' # PubMed Central Identifier 'AspGD_REF': 'http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=' # Aspergillus DB citation 'AQTLPub': 'https://www.animalgenome.org/cgi-bin/QTLdb/BT/qabstract?PUBMED_ID=' # Animal Quantitative Trait Locus Publication 'GO_REF': 'http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:' # GO Reference Collection 'PAINT_REF': 'http://www.geneontology.org/gene-associations/submission/paint/' # Phylogenetic Annotation INference Tool 'HPO': 'http://human-phenotype-ontology.org/' # Human Phenotype Ontology 'APO': 'http://purl.obolibrary.org/obo/APO_' # Ascomycete phenotype ontolog # strains, lines, or organismal reagents 'APB': 'http://pb.apf.edu.au/phenbank/strain.html?id=' # Australian Phenome Bank 'CMMR': 'http://www.cmmr.ca/order.php?t=m&id=' # Canadian Mouse Mutant Repository 'Coriell': 'https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=' # Coriell Institute for Medical Research '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 (form only has 'sub_id') # https://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2018q2/000186.html 'EMMA': 'https://www.infrafrontier.eu/search?keyword=EM:' # European Mouse Mutant Archive 'JAX': 'http://jaxmice.jax.org/strain/' # The Jackson Laboratory 'MMRRC': 'https://www.mmrrc.org/catalog/sds.php?mmrrc_id=' # Mutant Mouse Resource & Research Centers 'MPD-strain': 'http://phenome.jax.org/db/q?rtn=strains/details&strainid=' # Mouse Phenome Database 'MUGEN': 'http://bioit.fleming.gr/mugen/Controller?workflow=ViewModel&expand_all=true&name_begins=model.block&eid=' # Mouse Genetics 'NCIMR': 'https://mouse.ncifcrf.gov/available_details.asp?ID=' # link rot? 'RBRC': 'http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=' # RIKEN BioResource Research Center # organisms and genome builds # # National Center for Biotechnology Information 'NCBIAssembly': 'https://www.ncbi.nlm.nih.gov/assembly?term=' # Assembly e.g. GRCh38 'NCBIGenome': 'https://www.ncbi.nlm.nih.gov/genome/' # Genome e.g. 51 (for human) 'NCBITaxon': 'http://purl.obolibrary.org/obo/NCBITaxon_' # Taxon e.g. 9606 'OMIA-breed': 'https://monarchinitiative.org/model/OMIA-breed:' # Local IRI for Online Inheritance In Animal breeds 'UCSC': 'ftp://hgdownload.cse.ucsc.edu/goldenPath/' # University of California, Santa Cruz golden path 'UCSCBuild': 'http://genome.ucsc.edu/cgi-bin/hgGateway?db=' # University of California, Santa Cruz genome build # homology 'HOMOLOGENE': 'http://www.ncbi.nlm.nih.gov/homologene/' # Putative Homology Groups 'KEGG-ko': 'http://www.kegg.jp/dbget-bin/www_bget?ko:' # Kyoto Encyclopedia of Genes and Genomes (KEGG Orthology) 'PANTHER': 'http://www.pantherdb.org/panther/family.do?clsAccession=' # Protein ANalysis THrough Evolutionary Relationships # variants / traits # 'AnimalQTLdb': 'previously' 'horseQTL': 'https://www.animalgenome.org/cgi-bin/QTLdb/EC/qdetails?QTL_ID=' 'cattleQTL': 'https://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=' 'catfishQTL': 'https://www.animalgenome.org/cgi-bin/QTLdb/IP/qdetails?QTL_ID=' 'chickenQTL': 'https://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=' 'pigQTL': 'https://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=' 'rainbow_troutQTL': 'https://www.animalgenome.org/cgi-bin/QTLdb/OM/qdetails?QTL_ID=' 'sheepQTL': 'https://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=' 'BGD': 'http://bovinegenome.org/genepages/btau40/genes/' # The Bovine Genome Database (no direct link) # # 'http://128.206.116.13:8080/bovinemine/report.do?id=' 'ClinVar': 'http://www.ncbi.nlm.nih.gov/clinvar/' # Clinical Variation in Human 'ClinVarVariant': 'http://www.ncbi.nlm.nih.gov/clinvar/variation/' # ClinVar cooked variants 'ClinVarSubmitters': 'http://www.ncbi.nlm.nih.gov/clinvar/submitters/' # ClinVar raw variants 'COSMIC': 'http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=' # Catalogue Of Somatic Mutations In Cancer 'HGMD': 'http://www.hgmd.cf.ac.uk/ac/gene.php?gene=' # Human Gene Mutation Database 'dbSNP': 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=' # Small Variation 'dbVar': 'http://www.ncbi.nlm.nih.gov/dbvar/' # Large Variation 'GWAS': 'https://www.ebi.ac.uk/gwas/variants/' # Genome Wide Association Study Catalog # pathways 'KEGG-path': 'http://www.kegg.jp/dbget-bin/www_bget?path:' # Kyoto Encyclopedia of Genes and Genomes (pathways) 'KEGG-img': 'http://www.genome.jp/kegg/pathway/map/' # Pathway Visualization 'REACT': 'http://www.reactome.org/PathwayBrowser/#/' # Manually curated pathway database 'SMPDB': 'http://smpdb.ca/view/' # Small Molecule Pathway Database # genes (and RNAs and transcripts) 'AspGD': 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=' # Aspergillus Genome Database 'BIOGRID': 'http://thebiogrid.org/' # Biological General Repository for Interaction Datasets 'CCDS': 'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=' # Consensus CDS (CoDing Sequence) 'CGNC': 'http://birdgenenames.org/cgnc/GeneReport?id=' # Chicken Gene Nomenclature Consortium 'dictyBase': 'http://dictybase.org/gene/' # Dictyostelium discoideum database (social amoebae) 'EcoGene': 'http://ecogene.org/gene/' # Escherichia coli K-1 'ENSEMBL': 'http://ensembl.org/id/' # joint EMBL, EBI, Sanger Institute central resource 'EnsemblGenome': 'http://www.ensemblgenomes.org/id/' # The Ensembl genome annotation system 'FlyBase': 'http://flybase.org/reports/' # Fruitfly database 'Genatlas': 'http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=' # gene mapping and genetic diseases (Human) 'GenBank': 'http://www.ncbi.nlm.nih.gov/nuccore/' # NCBI nucleotide sequences # 'HGNC': 'http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=' # *** pre drupal site 'HGNC': 'https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:' # HUGO Gene Nomenclature Committee (Human) 'IMPC': 'https://www.mousephenotype.org/data/genes/' # International Mouse Phenotyping Consortium (MGI:nnn) 'IMPC-pipe': 'https://www.mousephenotype.org/impress/PipelineInfo?id=' # 'IMPC-proc': 'https://www.mousephenotype.org/impress/ProcedureInfo?action=list&procID=' # [&pipeID=] 'IMPC-param': 'https://www.mousephenotype.org/impress/OntologyInfo?action=list&procID=' # # 'KEGG-hsa': 'http://www.kegg.jp/dbget-bin/www_bget?hsa:' # Kyoto Encyclopedia of Genes and Genomes (Human) 'MGI': 'http://www.informatics.jax.org/accession/MGI:' # Mouse Genome Informatics 'miRBase': 'http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=' # microRNA nomenclature, sequences & annotation 'NCBIGene': 'https://www.ncbi.nlm.nih.gov/gene/' # National Center for Biotechnology Information (Genes) 'PomBase': 'https://www.pombase.org/spombe/result/' # Database for fission yeast Schizosaccharomyces pombe *** 'RefSeq': 'http://www.ncbi.nlm.nih.gov/refseq/?term=' # NCBI Reference Sequence Database 'RGD': 'http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=' # Rat Genome Database 'RGDRef': 'http://rgd.mcw.edu/rgdweb/report/reference/main.html?id=' # Rat Genome Database Reference publications 'SGD': 'https://www.yeastgenome.org/locus/' # Saccharomyces Genome Database 'SGD_REF': 'https://www.yeastgenome.org/reference/' # Saccharomyces Genome Database Reference publications 'TAIR': 'https://www.arabidopsis.org/servlets/TairObject?type=locus&id=' # The Arabidopsis Information Resource 'VGNC': 'https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/' # Vertebrate Gene Nomenclature Committee 'WormBase': 'https://www.wormbase.org/get?name=' # Caenorhabditis elegans Database (nematodes) ie WBGene00000001 'Xenbase': 'http://www.xenbase.org/gene/showgene.do?method=display&geneId=' # Xenopus Database (frog) 'ZFIN': 'http://zfin.org/' # Zebrafish Information Network # proteins (and protein/macromolecular complexes) 'ComplexPortal': 'https://www.ebi.ac.uk/complexportal/complex/' # Manually curated, encyclopaedic resource of macromolecular complexes 'EC': 'https://www.enzyme-database.org/query.php?ec=' # Enzyme Commission (nomenclature) 'HPRD': 'http://www.hprd.org/protein/' # Human Protein Reference Database 'NCBIProtein': 'http://www.ncbi.nlm.nih.gov/protein/' # NCBI amino acid sequences 'PDB': 'http://www.ebi.ac.uk/pdbsum/' # Protein Data Bank 'SwissProt': 'http://identifiers.org/SwissProt:' # UniProt Knowledgebase UniProtKB Manual 'TrEMBL': 'http://purl.uniprot.org/uniprot/' # UniProt Knowledgebase UniProtKB Automated 'UniProtKB': 'http://identifiers.org/uniprot/' # UniProt Knowledgebase UniProtKB Both 'InterPro': 'https://www.ebi.ac.uk/interpro/entry/InterPro/' # Classification of protein families # # may become "GtoPdb" 'IUPHAR': 'http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=' # Omnibus pharmacological information portal # Drugs, chemicals, compounds 'CID': 'http://pubchem.ncbi.nlm.nih.gov/compound/' # NCBI PubChem Compound 'DrugBank': 'http://www.drugbank.ca/drugs/' # DrugBank database (drugs and drug targets) 'OAE': 'http://purl.obolibrary.org/obo/OAE_' # Ontology of Adverse Events 'RXCUI': 'http://purl.bioontology.org/ontology/RXNORM/' # Normalized names for clinical drugs (from Unified Medical Language System) 'MEDDRA': 'http://purl.bioontology.org/ontology/MEDDRA/' # Medical Dictionary for Regulatory Activities 'FDADrug': 'http://www.fda.gov/Drugs/InformationOnDrugs/' # U.S. Food & Drug Administration Drug (*** what uses? seems useless) 'BT': 'http://c.biothings.io/#' # MyChem (BioThings) 'UNII': 'http://fdasis.nlm.nih.gov/srs/unii/' # Unique Ingredient Identifier (from FDA Substance Registration System) 'GINAS': 'http://tripod.nih.gov/ginas/app/substance#' # Global Ingredient Archival System (National Institute of Health) 'HMDB': 'http://www.hmdb.ca/metabolites/' # Human Metabolome Database 'WD_Prop': 'https://www.wikidata.org/wiki/Property:' # Wikidata Property 'WD_Entity': 'https://www.wikidata.org/wiki/' # Wikidata