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@ktym ktym/rs_id.json
Last active Oct 13, 2015

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RefSeq db_xref to Identifiers.org mapping
{
/*
* NCBI RefSeq
*/
"RefSeq": {
"label": "NCBI RefSeq", // custom
"class": "RefSeq",
"prefix": "http://identifiers.org/refseq/"
},
"BioProject": {
"label": "NCBI BioProject", // custom
"class": "BioProject",
"prefix": "http://identifiers.org/bioproject/"
},
"PubMed": {
"label": "NCBI PubMed", // custom
"class": "PubMed",
"prefix": "http://identifiers.org/pubmed/"
},
"GeneID": {
"label": "NCBI Gene",
"class": "Gene",
"prefix": "http://identifiers.org/ncbigene/"
},
"Protein": {
"label": "NCBI Protein",
"class": "Protein",
"prefix": "http://identifiers.org/ncbiprotein/"
},
"taxon": {
"label": "NCBI Taxonomy", // custom
"class": "Taxonomy",
"prefix": "http://identifiers.org/taxonomy/"
},
"UniSTS": {
"label": "UniSTS",
"class": "UniSTS",
"prefix": "http://identifiers.org/unists/"
},
/*
* NCBI RefSeq xref human
*/
"CCDS": {
"label": "Consensus CDS",
"class": "CCDS",
"prefix": "http://identifiers.org/ccds/"
},
"HGNC": {
"label": "HUGO Gene Nomenclature Committee",
"class": "HGNC",
"prefix": "http://identifiers.org/hgnc/"
},
"HPRD": {
"label": "Human Protein Reference Database",
"class": "HPRD",
"prefix": "http://identifiers.org/hprd/"
},
"MIM": {
"label": "Online Mendelian Inheritance in Man",
"class": "OMIM",
"prefix": "http://identifiers.org/omim/"
},
"miRBase": {
"label": "miRBase Sequence Database",
"class": "miRBase",
"prefix": "http://identifiers.org/mirbase/"
},
/*
* NCBI RefSeq xref
*/
"ASAP": {
"label": "A Systematic Annotation Package", // definition
"class": "ASAP",
"prefix": "http://identifiers.org/asap/"
},
"ATCC": {
"label": "American Type Culture Collection", // synonym
"class": "ATCC",
"prefix": "http://identifiers.org/atcc/"
},
"CDD": {
"label": "Conserved Domain Database",
"class": "CDD",
"prefix": "http://identifiers.org/cdd/"
},
"EcoGene": {
"label": "EcoGene",
"class": "EcoGene",
"prefix": "http://identifiers.org/ecogene/"
},
"GO": {
"label": "Gene Ontology",
"class": "GO",
"prefix": "http://identifiers.org/obo.go/"
},
"GOA": {
"label": "Gene Ontology Annotation", // synonym
"class": "GOA",
"prefix": "http://identifiers.org/goa/"
},
"Greengenes": {
"label": "GreenGenes",
"class": "Greengenes",
"prefix": "http://identifiers.org/greengenes/"
},
"HSSP": {
"label": "Homology-derived Structure of Proteins",
"class": "HSSP",
"prefix": "http://identifiers.org/hssp/"
},
"ISFinder": {
"label": "ISFinder",
"class": "ISFinder",
"prefix": "http://identifiers.org/isfinder/"
},
"InterPro": {
"label": "InterPro",
"class": "InterPro",
"prefix": "http://identifiers.org/interpro/"
},
"NBRC": {
"label": "NITE Biological Research Center Catalogue",
"class": "NBRC",
"prefix": "http://identifiers.org/nbrc/"
},
"PDB": {
"label": "Protein Data Bank",
"class": "PDB",
"prefix": "http://identifiers.org/pdb/"
},
"PFAM": {
"label": "Protein Family Database", // synonym
"class": "Pfam",
"prefix": "http://identifiers.org/pfam/"
},
"REBASE": {
"label": "Restriction Enzyme Database", // synonym
"class": "REBASE",
"prefix": "http://identifiers.org/rebase/"
},
"TIGRFAM": {
"label": "TIGRFAMS",
"class": "TIGRFAM",
"prefix": "http://identifiers.org/tigrfam/"
},
"UniProtKB/Swiss-Prot": {
"label": "UniProt/SwissProt",
"class": "UniProt",
"prefix": "http://identifiers.org/uniprot/"
},
"UniProtKB/TrEMBL": {
"label": "UniProt/TrEMBL",
"class": "UniProt",
"prefix": "http://identifiers.org/uniprot/"
},
/*
* NEED SOME HACK
*/
// remove "tax_" prefix from ID
"HOMD": {
"label": "Human Oral Microbiome Database Taxonomy", // custom
"class": "HomdTaxon",
"prefix": "http://identifiers.org/homd.taxon/"
},
// add "ECOCYC:" prefix to ID
"ECOCYC": {
"label": "BioCyc/EcoCyc",
"class": "EcoCyc",
"prefix": "http://identifiers.org/biocyc/ECOCYC:"
},
/*
* NOT AVAILABLE IN Identifiers.org FOR NOW
*/
// http://www.ericbrc.org/portal/eric/
"ERIC": {
"label": "Euteropathogen Resource Integration Center", // custom
"class": "ERIC",
"prefix": "http://identifiers.org/eric/"
},
"GI": {
"label": "NCBI GenInfo Identifier", // custom
"class": "GI",
"prefix": "http://identifiers.org/ncbigi/"
},
// http://www.hmpdacc.org/
// http://www.hmpdacc-resources.org/cgi-bin/hmp_catalog/main.cgi?section=HmpSummary&page=displayHmpProject&hmp_id=
"HMP": {
"label": "Human Microbiome Project", // custom
"class": "HMP",
"prefix": "http://identifiers.org/hmp/"
},
"PSEUDO": {
"label": "EMBL pseudo protein identifier", // custom
"class": "PSEUDO",
"prefix": "http://identifiers.org/pseudo/"
},
// http://pathema.jcvi.org/
"Pathema": {
"label": "Pathema Genome Resource", // custom
"class": "Pathema",
"prefix": "http://identifiers.org/pathema/"
},
// http://www.pseudomonas.com/
// http://www.pseudomonas.com/getAnnotation.do?locusID=
"PseudoCap": {
"label": "Pseudomonas Genome Database", // custom
"class": "PseudoCap",
"prefix": "http://identifiers.org/pseudocap/"
}
}
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