Controlled vocabulary for /db_xref qualifier

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



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″  
AntWeb   Ant Database   /db_xref=”AntWeb:CASENT0058943-D01″  
APHIDBASE Aphid Genome Database /db_xref=”APHIDBASE:ACYPI007424″  
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″  
Araport Arabidopsis Information Portal /db_xref=”Araport:AT1G01010″  
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″  
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″  
BEEBASE BeeBase db_xref= BEEBASE:GB55480  
BEETLEBASE Tribolium Genome Database — Insertion /db_xref=”BEETLEBASE:TC030551″  
BEI BEI Resources /db_xref=”BEI:NR-50065″  
BGD Bovine Genome Database /db_xref=”BGD:BT10004″  
BOLD  Barcode of Life database /db_xref=”Bold:EPAF263″   
CABRI Common Access to Biological Resources and Information project /db_xref=”CABRI: ACC 424″  
CCAP Culture Collection of algae and protozoa /db_xref=”CCAP: 1460/15″  
CDD Conserved Domain Database /db_xref=”CDD:02194  
CGD Candida Genome Database /db_xref=”CGD:CAL0005934  
dbEST EST database maintained at the NCBI. /db_xref=”dbEST:123456″
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″
dbSTS STS database maintained at the NCBI. /db_xref=”dbSTS:456789″
dictyBase Dictyostelium genome database /db_xref=”dictyBase:DDB0191090″  
EcoGene Database of Escherichia coli Sequence and Function /db_xref=”EcoGene:EG11277″  
ECOCYC EcoCyc E. coli database /db_xref=”ECOCYC:sroC”
ENSEMBL Database of automatically annotated genomic data /db_xref=”ENSEMBL:HUMAN-Clone-AC005612″
EnsemblGenomes Extending Ensembl across the taxonomic space /db_xref=”EnsemblGenomes:AAC73116″/db_xref=”EnsemblGenomes:b0005″  
EPD Eukaryotic Promotor Database /db_xref=”EPD:EP00576″  
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″  
FBOL International Fungal Working Group Fungal Barcoding /db_xref=”FBOL:2224″  
FLYBASE Database of Genetic and molecular data of Drosophila. /db_xref=”FLYBASE:FBgn0000024″  
Fungorum Index Fungorum /db_xref=”Fungorum:ID550186″  
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″  
Greengenes 16S rRNA gene database /db_xref=”Greengenes:269185″  
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″
HMP Human Microbiome Project /db_xref=”HMP:0536″  
HOMD Human Oral Microbiome Database /db_xref=”HOMD:tax_078″


HPM Human Proteome Map /db_xref=”HPM:8106″  
HSSP Database of homology-derived secondary structure of proteins /db_xref=”HSSP:12GS”  
IKMC International Knockout Mouse Consortium /db_xref=”IKMC:66303  
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″  
IntrepidBio Intrepid BioInformatics /db_xref=”IntrepidBio:5259707746″  
IRD Influenza Research Database /db_xref=”IRD:CEIRS-CIP045-123456.2″  
ISFinder Insertion sequence elements database /db_xref=”ISFinder:ISA1083-2″  

ITS reference database for pathogenic fungi

JCM Japan Collection of Microorganisms /db_xref=”JCM:1339″  
JGIDB JGI Genome Portal /db_xref=”JGIDB:Chluvu1_81011″  
JGI’s Phytozome Comparative genomics of plants /db_xref=”Phytozome:Glyma0021s00410″


LocusID NCBI LocusLink ID **Discontinued March 2005 /db_xref=”LocusID:51199″  
MaizeGDB Maize Genome Database unique identifiers /db_xref=”MaizeGDB:635633″  
MarpolBase Genome Database for Marchantia polymorpha /db_xref=”MarpolBase:Mp1g00010.1″  
MedGen Human Medical Genetics /db_xref=”MedGen:C0010674″  
MGI Mouse Genome Informatics /db_xref=”MGI:1894891″  
MIM Mendelian Inheritance in Man numbers /db_xref=”MIM:123456″  
miRBase The microRNA database /db_xref=”miRBase: MI0001857″  
MycoBank Fungal Databases, Nomenclature and Species Banks /db_xref=”MycoBank:MB519473″  
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″  
OrthoMCL Ortholog Groups of Protein Sequences /db_xref=”OrthoMCL:OG5_130679″  
Osa1 Rice Genome Annotation Project /db_xref=”Osa1:LOC_Os01g12345″  
Pathema Pathema Genome Resource /db_xref=”Pathema:BA_4405″
PBmice PiggyBac Mutagenesis Information Center /db_xref=”PBmice:38″  
PDB Biological macromolecule three dimensional structure database /db_xref=”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″  
PomBase Database of Structural and Functional Data for Schizosaccaromyces pombe /db_xref=”PomBase:SPBC1709.20″  
PSEUDO EMBL pseudo protein identifier /db_xref=”PSEUDO:CAC44644.1″  
PseudoCap Pseudomonas Genome Database /db_xref=”PseudoCap:PA0001″  
RAP-DB Rice Annotation Project Database /db_xref=”RAP-DB:Os01g1234567″  
RATMAP Rat Genome Database /db_xref=”RATMAP:5″  
RBGE_garden Royal Botanic Garden Edinburgh Living Collections /db_xref=”RBGE_garden:20021433″  
RBGE_herbarium Royal Botanic Garden Edinburgh Herbarium /db_xref=”RBGE_herbarium:E00217291″  
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″  
RNAcentral The non-coding RNA sequence database /db_xref=”RNAcentral:URS00001B9622″  
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″  
SGN SOL Genomics Network /db_xref=”SGN:E553090″  
SK-FST Saskatoon Arabidopsis T-DNA mutant population – SK Collection /db_xref=”SK-FST: FST:SK32219″  
SoyBase Glycine max Genome Database /db_xref=”SoyBase:Satt005″  
SRPDB Signal Recognition Particle Database /db_xref=”SRPDB:Arth.aure._CP000474.fasta  
SubtiList Bacillus subtilis genome sequencing project /db_xref=”SubtiList:BG10001″  
taxon NCBI’s taxonomic identifier /db_xref=”taxon:4932″  
The Arabidopsis IR The Arabidopsis Information Resource  /db_xref=”TAIR:AT1F51370″  
TIGRFAM TIGR protein families /db_xref=”TIGRFAM:TIGR00094″  
TubercuList TubercuList knowledge base /db_xref=”TubercuList:Rv3322c”  
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″  
UniSTS Database of Sequence Tagged Sites /db_xref=” UniSTS:486599″  
UNITE Molecular database for the identification of fungi /db_xref=” UNITE:UDB000157″  
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″  
VGNC Vertebrate Gene Nomenclature Committee /db_xref= “VGNC:VGNC:4927”  
ViPR Virus Pathogen Resource /db_xref=”ViPR:HRV-A34_p1058_sR263_2008″  
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 30, 2014