# 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

# 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/elements/1.1/'                            # Dublin Core (metadata)
'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': 'https://www.w3.org/TR/skos-reference/#'                    # Simple Knowledge Organization System
# 'Annotation': 'http://www.w3.org/ns/oa#Annotation'                # Web annotation
'schemaorg': '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)
'dcterms': 'http://purl.org/dc/terms/'                              # Dublin Core (addtional terms)
'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://purl.obolibrary.org/obo/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)
'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=RBRC'            # 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='

'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/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': 'http://www.mousephenotype.org/data/genes/'                             # International Mouse Phenotyping Consortium (MGI:nnn)
'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
'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

#                                                           # International Mouse Phenotyping Resource of Standardised Screens
'IMPRESS-procedure': 'https://www.mousephenotype.org/impress/procedures/'
'IMPRESS-protocol': 'https://www.mousephenotype.org/impress/protocol/'
'IMPRESS-parameter': 'https://www.mousephenotype.org/impress/parameterontologies/'

#                                                                                   # 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
