Controlled vocabulary for /db_xref qualifier

A new qualifier was introduced in version 1.08 (December 1, 1995) of the Feature table definitions: /db_xref. This new qualifier serves as a vehicle for the linking of DNA sequence records to other external databases.

The text below outlines the format and the present list of allowed database cross references. Inquiries about the addition of other database types should be made to one of the collaborating databases, listed above.

Qualifier:       /db_xref="database:identifier"

Definition:      database cross-reference: pointer to related information in
		 another database	                  
Scope:           all feature keys
Value format:    "database:identifier" where database is the name of the
		 database containing related information, and 
		 identifier is the internal identifier of the related 
		 information according to the naming conventions of the
		 cross-referenced database.

Examples:        
cross reference to GDB identifier:            /db_xref="GDB:39999"   
cross reference to Swiss-Prot entry:          /db_xref="Swiss-Prot:P12345" 

For all databases types 'Case' is important. All databases member of the International Collaboration (DDBJ, EMBL/EBI and GenBank/NCBI) may make recommendations for additions or removal of databases to this list at their convenience, and need not rely on the release cycle of the Feature Table documentation.

Database: Description of database, and type with example(s).

Presently the list includes:

AceView/WormGenes AceView Worm Genome /db_xref="AceView/WormGenes:vha-6"
AFTOL Assembling the Fungal Tree of Life /db_xref="AFTOL:959"
ASAP A Systematic Annotation Package for Community Analysis of Genomes /db_xref="ASAP:ABE-0000006"
ATCC American Type Culture Collection database /db_xref="ATCC:123456"
ApiDB Apicomplexan Database Resources /db_xref="ApiDB:cgd1_1090"
ApiDB_CryptoDB Cryptosporidium Genome Resources /db_xref="ApiDB_CryptoDB:cgd7_20"
ApiDB_PlasmoDB Plasmodium Genome Resources

/db_xref="ApiDB_PlasmoDB: PF11_0344"

ApiDB_ToxoDB Toxoplasma Genome Resources

/db_xref="ApiDB_ToxoDB:49.m00014"

ATCC(in host) American Type Culture Collection database /db_xref="ATCC(in host):123456"
ATCC(dna) American Type Culture Collection database /db_xref="ATCC(dna):123456"
Axeldb A Xenopus laevis database /db_xref="Axeldb:32B3.1"
BDGP_EST Berkeley Drosophila Genome Project EST database /db_xref="BDGP_EST:123456"
BDGP_INS Berkeley Drosophila Genome Project database -- Insertion /db_xref="BDGP_INS:123456"
BOLD  Barcode of Life database /db_xref=Bold:EPAF263 
CDD Conserved Domain Database /db_xref="CDD:02194
dbEST EST database maintained at the NCBI. /db_xref="dbEST:123456"
/db_xref="dbEST:BP535535"
dbProbe NCBI Probe database Public registry of nucleic acid reagents /db_xref="dbProbe:38"
dbSNP Variation database maintained at the NCBI. /db_xref="dbSNP:4647"
/db_xref="dbSNP:rs133073"
dbSTS STS database maintained at the NCBI. /db_xref="dbSTS:456789"
/db_xref="dbSTS:BV210161"
dictyBase Dictyostelium genome database /db_xref="dictyBase:DDB0191090"
EcoGene Database of Escherichia coli Sequence and Function /db_xref="EcoGene:EG11277"
ENSEMBL Database of automatically annotated genomic data /db_xref="ENSEMBL:HUMAN-Clone-AC005612"
/db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102"
ERIC Enteropathogen Resource Integration Center db_xref="ERIC:ABY-0246137"
ESTLIB EBI's EST library identifier /db_xref="ESTLIB:1200"
FANTOM_DB Database of Functional Annotation of Mouse /db_xref="FANTOM_DB:0610005A07"
FLYBASE Database of Genetic and molecular data of Drosophila. /db_xref="FLYBASE:FBgn0000024"
GABI Network of Different Plant Genomic Research Projects /db_xref="GABI:HA05J18"
GDB Human Genome Database accession numbers /db_xref="GDB:G00-128-600"
GeneDB Curated gene database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei /db_xref="GeneDB:SPCC285.16c"
GeneID Entrez Gene Database (replaces NCBI Locus Link) /db_xref="GeneID:3054987"
GI GenInfo identifier, used as a unique sequence identifier for nucleotide and proteins /db_xref="GI:1234567890"
GO Gene Ontology Database identifier /db_xref="GO:123"
GOA Gene Ontology Annotation Database Identifier /db_xref=" GOA :P01100"
GRIN Germplasm Resources Information Network /db_xref="GRIN:1005973"
HGNC Human Gene Nomenclature Database /db_xref="HGNC:2041"
H-InvDB H-Invitational Database /db_xref="H-InvDB:HIT000000001"
/db_xref="H-InvDB:HIX0000001"
HSSP Database of homology-derived secondary structure of proteins /db_xref="HSSP:12GS"
IMGT/GENE-DB Immunogenetics database, immunoglobulin and T-cell receptor genes /db_xref="IMGT/GENE-DB:IGKC"
IMGT/LIGM Immunogenetics database, immunoglobulins and T-cell receptors /db_xref="IMGT/LIGM:U03895"
IMGT/HLA Immunogenetics database, human MHC /db_xref="IMGT/HLA:HLA00031"
Interpro InterPro protein sequence database /db_xref="InterPro:IPR002928"
ISD Influenza Sequence Database /db_xref="ISD:ISDN12345"
ISFinder Insertion sequence elements database /db_xref="ISFinder:ISA1083-2"
JCM Japan Collection of Microorganisms /db_xref="JCM:1339"
LocusID NCBI LocusLink ID **Discontinued March 2005 /db_xref="LocusID:51199"
MaizeGDB Maize Genome Database unique identifiers /db_xref="MaizeGDB:635633 "
MGI Mouse Genome Informatics /db_xref="MGI:1894891"
MIM Mendelian Inheritance in Man numbers /db_xref="MIM:123456"
NBRC NITE Biological Resource Center /db_xref="NBRC:3189"
NextDB Nematode Expression Pattern DataBase /db_xref="NextDB:CELK01662"
niaEST NIA Mouse cDNA Project /db_xref="niaEST:L0304H12-3"
NMPDR National Microbial Pathogen Data Resource /db_xref="NMPDR:fig|306254.1.peg.183"
NRESTdb Natural Rubber EST database /db_xref="NRESTdb:Y01A01"
Pathema Pathema Genome Resource /db_xref="Pathema:BA_4405"
/db_xref="Pathema:191218"
PDB Biological macromolecule three dimensional structure database /dbxref="PDB:12GS"
PFAM Collection of protein families /db_xref="PFAM:PF00003"
PGN Plant Genome Network /db_xref="PGN:aam01-1ms3-a05"
PIR Protein Information Resource accession numbers /db_xref="PIR:S12345"
PSEUDO EMBL pseudo protein identifier /db_xref="PSEUDO:CAC44644.1"
RATMAP Rat Genome Database /db_xref="RATMAP:5"
RFAM RNA families database of alignments and CMs /db_xref="RFAM:RF00230"
RGD Rat Genome Database /db_xref="RGD:620528"
RiceGenes Rice database accession numbers /db_xref="RiceGenes:AA231856"
RZPD Resource Centre Primary Database Clone Identifiers /db_xref="RZPD:IMAGp998I142450Q6"
SEED The SEED Database /db_xref="SEED:fig|83331.1.peg.1"
SGD Saccharomyces Genome Database /db_xref="SGD:L0000470"
SoyBase Glycine max Genome Database /db_xref="SoyBase:Satt005"
SubtiList Bacillus subtilis genome sequencing project /db_xref="SubtiList:BG10001"
taxon NCBI's taxonomic identifier /db_xref="taxon:4932"
UNILIB Unified Library Database, a library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap /db_xref="UNILIB:1002"
UniProtKB/Swiss-Prot section of the UniProt Knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature /db_xref="UniProtKB/Swiss-Prot:P12345"
UniProtKB/TrEMBL section of the UniProt Knowledgebase, containing computationally analysed records waiting for full manual annotation /db_xref=" UniProtKB/TrEMBL:Q00177"
VBASE2 Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse /db_xref="VBASE2:humIGKV165"
VectorBase Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens db_xref="VectorBase:ENSANGG00000007825"
WorfDB C. elegans ORFeome cloning project /db_xref="WorfDB:pos-1"
WormBase Caenorhabditis elegans Genome Database /db_xref="WormBase:R13H7"
Xenbase Xenopus laevis and tropicalis biology and genomics resource /db_xref=Xenbase:XB-GENE-1019547
ZFIN Zebrafish Information Network /db_xref="ZFIN:ZDB-GENE-011205-17"

Revised October 19, 2007