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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