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phenol-io contains the generic I/O functionality for ontologies

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# Monarch-specific
'': 'https://monarchinitiative.org/'
'MONARCH': 'https://monarchinitiative.org/MONARCH_'

'MonarchData': 'https://data.monarchinitiative.org/ttl/'
'MonarchArchive': 'https://archive.monarchinitiative.org/201710/'

# other semantic-web items
'rdf': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
'rdfs': 'http://www.w3.org/2000/01/rdf-schema#'
'dc': 'http://purl.org/dc/elements/1.1/'
'foaf': 'http://xmlns.com/foaf/0.1/'
'xml': 'http://www.w3.org/XML/1998/namespace'
'xsd': 'http://www.w3.org/2001/XMLSchema#'
'owl': 'http://www.w3.org/2002/07/owl#'
'skos': 'https://www.w3.org/TR/skos-reference/#'
'Annotation': 'http://www.w3.org/ns/oa#Annotation'  # FIXME - i don't think we're using this

# dataset description
'dcat': 'http://www.w3.org/ns/dcat#'
'dct': 'http://purl.org/dc/terms/'
'dctypes': 'http://purl.org/dc/dcmitype/'
'pav': 'http://purl.org/pav/'

# ontologies
# [y] indicates those that the monarch team contributes to
'AQTLTrait': 'http://identifiers.org/animalqtltrait/'  # FIXME - should get integrated into Upheno
'MONDO': 'http://purl.obolibrary.org/obo/MONDO_' # MONDO
'BFO': 'http://purl.obolibrary.org/obo/BFO_' # BFO: Basic Formal Ontology
'CARO': 'http://purl.obolibrary.org/obo/CARO_'
'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]
'ECTO': 'http://purl.obolibrary.org/obo/ECTO_' # ECTO: Environmental Exposure 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
# till we get a purl? `FBgn': 'http://flybase.org/reports/'           # flybase gene?
'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]
'NCIT': 'http://purl.obolibrary.org/obo/NCIT_'  # NCIT
'Thesaurus': 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#' # NCIT Thesarus
'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: RelationshipI 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='
'RGDRef': 'http://rgd.mcw.edu/rgdweb/report/reference/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#'




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