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Unified Medical Language System (UMLS)

HGNC (HUGO Gene Nomenclature Committee) - Source Representation


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VSAB: HGNC2017_05

General Notes/Comments:

The HUGO Gene Nomenclature Committee (HGNC) is an international organization whose primary ethos is to promote and sustain collaboration in the field of human genetics.

Data is supplied in a single, tab-delimited, text file (UTF-8).

Summary of Changes

New data field and corresponding new ATN:

  • field: rna_central_ids; ATN = RNA_CENTRAL_ID

Summary of Source-Provided Files

Documentation and Reference

http://www.genenames.org/help/statistics-downloads
www.hugo-international.org

File NameDescription
hgnc_complete_set_05042017.txtTab-delimited text file.

Source-Provided File Details

Field NumberField NameDescriptionRepresentation
1hgnc_idA unique ID for every approved symbolMRCONSO.CODE; MRCONSO.SCUI
2symbolApproved gene symbolMRCONSO.STR; MRSAT.ATN=GENESYMBOL
3nameApproved name for the geneMRCONSO.STR
4locus_groupA group name for a set of related locus typesMRSAT.ATN=LOCUS_GROUP
5locus_typeSpecifies type as defined by HGNC (e.g., RNA, transfer)MRSAT.ATN=LOCUS_TYPE
6statusStatus of the symbol (e.g., Approved or Entry Withdrawn)Not Processed
7locationCytogenetic location of the geneMRSAT.ATN=CYTOGENETIC_LOCATION
8location_sortableSame as "location" but single digit chromosomes are prefixed with a 0 enabling them to be sorted in correct number order (e.g., 02q34)Not Processed
9alias_symbolOther symbols used to refer to the geneMRCONSO.STR
10alias_nameOther names used to refer to the geneMRCONSO.STR
11prev_symbolSymbols previously approved for this geneMRSAT.ATN=PREV_SYMBOL
12prev_nameGene names previously approved for this geneMRSAT.ATN=PREV_NAME
13gene_familyName given to a gene family or group the gene has been assigned toMRSAT.ATN=GENE_FAM_DESC
14gene_family_idID used to designate a gene family or group the gene has been assigned toMRSAT.ATN=GENE_FAM_ID
15date_approved_reservedThe date the entry was first approvedMRSAT.ATN=DATE_CREATED
16date_symbol_changedThe date the gene symbol was last changedMRSAT.ATN=DATE_SYMBOL_CHANGED
17date_name_changedThe date the gene name was last changedMRSAT.ATN=DATE_NAME_CHANGED
18date_modifiedDate the entry was last modifiedMRSAT.ATN=DATE_LAST_MODIFIED
19entrez_idEntrez gene IDMRSAT.ATN=ENTREZGENE_ID
20ensembl_gene_idEnsembl gene IDMRSAT.ATN=ENSEMBLGENE_ID
21vega_idVega gene IDMRSAT.ATN=VEGA_ID
22ucsc_idUCSC gene IDMRSAT.ATN=MAPPED_UCSC_ID
23enaInternational Nucleotide Sequence Database Collaboration accession number(s)MRSAT.ATN=ENA
24refseq_accessionRefSeq nucleotide accession(s)MRSAT.ATN=REFSEQ_ID
25ccds_idConsensus CDS IDMRSAT.ATN=CCDS_ID
26uniprot_idsUniProt protein accessionMRSAT.ATN=SWP
27pubmed_idPubmed and Europe Pubmed Cental PMID(s)MRSAT.ATN=PMID
28mgd_idMouse genome informatics database IDMRSAT.ATN=MGD_ID
29rgd_idRat genome database gene IDMRSAT.ATN=RGD_ID
30lsdbThe name of the Locus specific Mutation Database and URL for the gene separated by a | characterMRSAT.ATN=LOCUS_SPECIFIC_DB_XR
31cosmicSymbol used within the Catalogue of somatic mutations in cancer for the geneMRSAT.ATN=DB_XR_ID|COSMIC:
32omim_idOnline Mendelian Inheritance in Man (OMIM) IDMRSAT.ATN=OMIM_ID
33mirbasemiRBase IDMRSAT.ATN=DB_XR_ID|MiRBase:
34homeodbHomeobox Database IDMRSAT.ATN=DB_XR_ID|HomeoDB:
35snornabaseSnoRNABase IDMRSAT.ATN=DB_XR_ID|snoRNABase:
36bioparadigms_slcSymbol used to link to the SLC tables database at bioparadigms.org for the geneMRSAT.ATN=DB_XR_ID|BioParadigms:
37orphanetOrphanet IDMRSAT.ATN=Orphanet:
38pseudogene.orgPseudogene.org IDMRSAT.ATN=DB_XR_ID|Pseudogene.org:
39horde_idSymbol used within HORDE for the geneMRSAT.ATN=DB_XR_ID|HORDE_ID:
40meropsID used to link to the MEROPS peptidase databaseMRSAT.ATN=DB_XR_ID|MEROPS:
41imgtSymbol used within the international ImMunoGeneTics information systemMRSAT.ATN=DB_XR_ID|IMGT/GENE-DB:
42iupharThe objectID used to link to the IUPHAR/BPS Guide to PHAMACOLOGY database.MRSAT.ATN=DB_XR_ID|IUPHAR:
43kznf_gene_catalogID used to link to the Human KZNF Gene CatalogMRSAT.ATN=DB_XR_ID|KZNF Gene Catalog:
44mamit-trnadbID to link to the Mamit-tRNA databaseMRSAT.ATN=DB_XR_ID|Mamit-tRNAdb:
45cdSymbol used within the Human Cell Differentiation Molecule database for the geneMRSAT.ATN=DB_XR_ID|CD:
46lncrnadblncRNA Database IDMRSAT.ATN=DB_XR_ID|lncRNAdb:
47enzyme_idENZYME EC accession numberMRSAT.ATN=EZ
48intermediate_filament_dbID used to link to the Human Intermediate filament DatabaseMRSAT.ATN=DB_XR_ID|Intermediate Filament DB:
49rna_central_idsRNA Central IDMRSAT.ATN=RNA_CENTRAL_ID