Last updated:2017.1.31.

Controlled vocabulary for /db_xref qualifier

The original site; Controlled vocabulary for /db_xref qualifier 2016.08.28 version
See also db_xref at NCBI.

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.

Definition of /db_xref qualifier

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.

For all [databases] types 'Case' is important. All databases member of the International Collaboration (DDBJ, ENA/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).

Database
Description of database name in /db_xref qualifier
Full name
Full name of the database
Format
Format for /db_xref qualifier
Diff
Flag for any difference with the original site in the line.
Use
Yes: to be described by DDBJ submitters
No: not to be described by DDBJ submitters
Auto: not to be described by DDBJ submitters, described by the database

Presently the list includes:

Database Full name Format Diff Use
AceView/WormGenes AceView Worm Genome /db_xref="AceView/WormGenes:vha-6"   No
AFTOL Assembling the Fungal Tree of Life /db_xref="AFTOL:959" URL removed No
AntWeb   Ant Database   /db_xref="AntWeb:CASENT0058943-D01"   No
APHIDBASE Aphid Genome Database /db_xref="APHIDBASE:ACYPI007424" URL changed No
ApiDB Apicomplexan Database Resources /db_xref="ApiDB:cgd1_1090"   No
ApiDB_CryptoDB Cryptosporidium Genome Resources   /db_xref="ApiDB_CryptoDB:cgd7_20"   No
ApiDB_PlasmoDB   Plasmodium Genome Resources   /db_xref="ApiDB_PlasmoDB: PF11_0344"   No
ApiDB_ToxoDB Toxoplasma Genome Resources /db_xref="ApiDB_ToxoDB:49.m00014"   No
Araport Arabidopsis Information Portal /db_xref="Araport:AT1G01010"   No
ASAP A Systematic Annotation Package for Community Analysis of Genomes /db_xref="ASAP:ABE-0000006" URL changed No
ATCC American Type Culture Collection database /db_xref="ATCC:123456"   No
ATCC(dna) American Type Culture Collection database /db_xref="ATCC(dna):123456”   No
ATCC(in host) American Type Culture Collection database /db_xref="ATCC(in host):123456"   No
Axeldb A Xenopus laevis database /db_xref="Axeldb:32B3.1"   No
BDGP_EST Berkeley Drosophila Genome Project EST database /db_xref="BDGP_EST:123456"   No
BDGP_INS Berkeley Drosophila Genome Project database -- Insertion /db_xref="BDGP_INS:123456"   No
BEEBASE BeeBase /db_xref="BEEBASE:GB55480"   No
BEETLEBASE Tribolium Genome Database -- Insertion /db_xref="BEETLEBASE:TC030551"   No
BEI BEI Resources /db_xref="BEI:NR-50065"   No
BGD Bovine Genome Database /db_xref="BGD:BT10004" URL changed No
BOLD  Barcode of Life database /db_xref="Bold:EPAF263"    Yes
CABRI Common Access to Biological Resources and Information project /db_xref="CABRI: ACC 424"   No
CCAP Culture Collection of algae and protozoa /db_xref="CCAP: 1460/15"   No
CDD Conserved Domain Database /db_xref="CDD:02194" URL changed No
CGD Candida Genome Database /db_xref="CGD:CAL0005934"   No
dbEST EST database maintained at the NCBI. /db_xref="dbEST:123456"
/db_xref="dbEST:BP535535"
URL changed No
dbProbe NCBI Probe database Public registry of nucleic acid reagents /db_xref="dbProbe:38" URL changed No
dbSNP Variation database maintained at the NCBI. /db_xref="dbSNP:4647"
/db_xref="dbSNP:rs133073"
URL changed No
dbSTS STS database maintained at the NCBI. /db_xref="dbSTS:456789"
/db_xref="dbSTS:BV210161"
URL changed No
dictyBase Dictyostelium genome database /db_xref="dictyBase:DDB0191090"   No
ECOCYC E. coli Database /db_xref="ECOCYC:sroC"
/db_xref="ECOCYC:C0343"
  No
EcoGene Database of Escherichia coli Sequence and Function /db_xref="EcoGene:EG11277"   No
ENSEMBL Database of automatically annotated genomic data /db_xref="ENSEMBL:HUMAN-Clone-AC005612"
/db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102"
  No
EnsemblGenomes Extending Ensembl across the taxonomic space /db_xref="EnsemblGenomes:AAC73116"
/db_xref="EnsemblGenomes:b0005"
  No
EnsemblGenomes-Gn EnsemblGenomes Gene /db_xref="EnsemblGenomes-Gn:WBGene00022276" Added No
EnsemblGenomes-Tr EnsemblGenomes Transcript /db_xref="EnsemblGenomes-Tr:MAPG_00606T0" Added No
EPD Eukaryotic Promotor Database /db_xref="EPD: EP00576"   No
ERIC Enteropathogen Resource Integration Center /db_xref="ERIC:ABY-0246137" URL removed No
ESTLIB EBI's EST library identifier /db_xref="ESTLIB:1200"   No
FANTOM_DB Database of Functional Annotation of Mouse /db_xref="FANTOM_DB:0610005A07"   Auto
FBOL International Fungal Working Group Fungal Barcoding /db_xref="FBOL:2224"   Yes
FLYBASE Database of Genetic and molecular data of Drosophila. /db_xref="FLYBASE:FBgn0000024"   No
Fungorum Index Fungorum /db_xref="Fungorum:ID550186"   No
GABI Network of Different Plant Genomic Research Projects /db_xref="GABI:HA05J18" URL changed No
GDB Human Genome Database accession numbers /db_xref="GDB:G00-128-600" URL removed No
GeneDB Curated gene database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei /db_xref="GeneDB:SPCC285.16c"   No
GeneID Entrez Gene Database (replaces NCBI Locus Link) /db_xref="GeneID:3054987" URL changed No
GI GenInfo identifier, used as a unique sequence identifier for nucleotide and proteins /db_xref="GI:1234567890"   No
GO Gene Ontology Database identifier /db_xref="GO:123"   No
GOA Gene Ontology Annotation Database Identifier /db_xref="GOA:P01100"   No
Greengenes 16S rRNA gene database /db_xref="Greengenes:269185"   No
GRIN Germplasm Resources Information Network /db_xref="GRIN:1005973"   No
HGNC Human Gene Nomenclature Database /db_xref="HGNC:2041" URL changed Yes
H-InvDB H-Invitational Database /db_xref="H-InvDB:HIT000000001"
/db_xref="H-InvDB:HIX0000001"
  Auto
HMP Human Microbiome Project /db_xref="HMP:0536"   No
HOMD Human Oral Microbiome Database /db_xref="HOMD:tax_078"
/db_xref="HOMD:seq_1603”
  No
HPM Human Proteome Map /db_xref="HPM:8106"   No
HSSP Database of homology-derived secondary structure of proteins /db_xref="HSSP:12GS" URL removed No
I5KNAL i5k Workspace /db_xref="I5KNAL:OFAS008986" Added No
IKMC International Knockout Mouse Consortium /db_xref="IKMC:66303"   No
IMGT/GENE-DB Immunogenetics database, immunoglobulin and T-cell receptor genes /db_xref="IMGT/GENE-DB:IGKC" URL changed Auto
IMGT/LIGM Immunogenetics database, immunoglobulins and T-cell receptors /db_xref="IMGT/LIGM:U03895" URL changed Auto
IMGT/HLA Immunogenetics database, human MHC /db_xref="IMGT/HLA:HLA00031"   Auto
Interpro InterPro protein sequence database /db_xref="InterPro:IPR002928"   No
IntrepidBio Intrepid BioInformatics /db_xref="ItrepidBio:5259707746"   No
IRD Influenza Research Database /db_xref="IRD:CEIRS-CIP045-123456.2"   No
ISFinder Insertion sequence elements database /db_xref="ISFinder:ISA1083-2"   No
ISHAM-ITS ITS reference database for human and animal pathogenic fungi /db_xref="ISHAM-ITS:MITS310" URL changed Auto
JCM Japan Collection of Microorganisms /db_xref="JCM:1339"   No
JGIDB JGI Genome Portal /db_xref="JGIDB:Chluvu1_81011" URL changed No
JGI Phytozome Comparative genomics of plants /db_xref="Phytozome:Glyma0021s00410"
/db_xref="Phytozome:ppb016588m_2_1.p"
URL changed No
LocusID NCBI LocusLink ID **Discontinued March 2005 /db_xref="LocusID:51199"   No
MaizeGDB Maize Genome Database unique identifiers /db_xref="MaizeGDB:635633"   No
MedGen Human Medical Genetics /db_xref="MedGen:C0010674" URL changed No
MGI Mouse Genome Informatics /db_xref="MGI:1894891"   Auto
MIM Mendelian Inheritance in Man numbers /db_xref="MIM:123456" URL changed No
miRBase The microRNA database /db_xref="miRBase: MI0001857"   No
MycoBank  Fungal Databases, Nomenclature and Species Banks /db_xref="MycoBank:MB519473"   No
NBRC NITE Biological Resource Center /db_xref="NBRC:3189" URL changed No
NextDB Nematode Expression Pattern DataBase /db_xref="NextDB:CELK01662"   No
niaEST NIA Mouse cDNA Project /db_xref="niaEST:L0304H12-3" URL changed No
NMPDR National Microbial Pathogen Data Resource /db_xref="NMPDR:fig|306254.1.peg.183"   No
NRESTdb Natural Rubber EST database /db_xref="NRESTdb:Y01A01" URL changed No
OrthoMCL Ortholog Groups of Protein Sequences /db_xref="OrthoMCL:OG5_130679"   No
Osa1 Rice Genome Annotation Project /db_xref="Osa1:LOC_Os01g12345"   Auto
Pathema Pathema Genome Resource /db_xref="Pathema:BA_4405"
/db_xref="Pathema:191218"
URL changed No
PBmice PiggyBac Mutagenesis Information Center /db_xref="PBmice:38"   No
PDB Biological macromolecule three dimensional structure database /db_xref="PDB:12GS"   Yes
PFAM Collection of protein families /db_xref="PFAM:PF00003" URL changed No
PGN Plant Genome Network /db_xref="PGN:aam01-1ms3-a05" URL removed No
PIR Protein Information Resource accession numbers /db_xref="PIR:S12345"   No
PomBase Database of Structural and Functional Data for Schizosaccaromyces pombe /db_xref="PomBase:SPBC1709.20"   No
PSEUDO EMBL pseudo protein identifier /db_xref="PSEUDO:CAC44644.1"   No
PseudoCap Pseudomonas Genome Database /db_xref="PseudoCap:PA0001"   No
RAP-DB Rice Annotation Project Database /db_xref="RAP-DB:Os01g1234567"   Auto
RATMAP Rat Genome Database /db_xref="RATMAP:5" URL removed No
RBGE_garden Royal Botanic Garden Edinburgh Living Collections /db_xref="RBGE_garden:20021433"   No
RBGE_herbarium Royal Botanic Garden Edinburgh Herbarium /db_xref="RBGE_herbarium:E00217291"   No
RFAM RNA families database of alignments and CMs /db_xref="RFAM:RF00230" URL changed No
RGD Rat Genome Database /db_xref="RGD:620528"   No
RiceGenes Rice database accession numbers /db_xref="RiceGenes:AA231856"   No
RZPD Resource Centre Primary Database Clone Identifiers /db_xref="RZPD:IMAGp998I142450Q6" URL removed No
SEED The SEED Database /db_xref="SEED:fig|83331.1.peg.1"   No
SGD Saccharomyces Genome Database /db_xref="SGD:L0000470"   No
SGN SOL Genomics Network /db_xref="SGN:E553090"   No
SK-FST Saskatoon Arabidopsis T-DNA mutant population - SK Collection /db_xref="SK-FST: FST:SK32219" URL removed No
SoyBase Glycine max Genome Database /db_xref="SoyBase:Satt005" URL changed No
SRPDB Signal Recognition Particle Database /db_xref="SRPDB:Arth.aure._CP000474.fasta"   No
SubtiList Bacillus subtilis genome sequencing project /db_xref="SubtiList:BG10001"   No
TAIR The Arabidopsis Information Resource  /db_xref="TAIR:AT1F51370" Renamed No
taxon NCBI's taxonomic identifier /db_xref="taxon:4932" URL changed Auto
TIGRFAM TIGR protein families /db_xref="TIGRFAM:TIGR00094" URL changed No
TubercuList TubercuList knowledge base /db_xref="TubercuList:Rv3322c"   No
UNILIB Unified Library Database, a library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap /db_xref="UNILIB:1002"   No
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"   Yes
UniProtKB/TrEMBL section of the UniProt Knowledgebase, containing computationally analysed records waiting for full manual annotation /db_xref=" UniProtKB/TrEMBL:Q00177"   No
UniSTS Database of Sequence Tagged Sites /db_xref="UniSTS:486599" URL removed No
UNITE Molecular database for the identification of fungi /db_xref="UNITE:UDB000157"   No
VBASE2 Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse /db_xref="VBASE2:humIGKV165" URL changed No
VectorBase Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens /db_xref="VectorBase:ENSANGG00000007825"   No
VGNC Vertebrate Gene Nomenclature Committee /db_xref="VGNC:VGNC:4927"   No
ViPR Virus Pathogen Resource /db_xref="ViPR:HRV-A34_p1058_sR263_2008"   No
VISTA Vista Enhancer Browser /db_xref="VISTA:hs123" Added No
WorfDB C. elegans ORFeome cloning project /db_xref="WorfDB:pos-1"   No
WormBase Caenorhabditis elegans Genome Database /db_xref="WormBase:R13H7"   No
Xenbase Xenopus laevis and tropicalis biology and genomics resource /db_xref="Xenbase:XB-GENE-1019547" URL changed No
ZFIN Zebrafish Information Network /db_xref="ZFIN:ZDB-GENE-011205-17"   No
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