# Monarch-specific
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

# 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
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]
MAXO: http://purl.obolibrary.org/obo/MAXO_ # MAXO: Medical Action 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 dont 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 : https://www.ncbi.nlm.nih.gov/snp/
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/
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#
