Controlled vocabulary for /db_xref qualifier

The original site; Controlled vocabulary for /db_xref qualifier 2012.08.09 version

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.
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:

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

Database

Full name

Format

Diff

Use

AceView/WormGenes

AceView Worm Genome

/db_xref="AceView/WormGenes:vha-6"

 

Yes

AFTOL

Assembling the Fungal Tree of Life

/db_xref="AFTOL:959"

 

Yes

AntWeb  

Ant Database  

/db_xref="AntWeb:CASENT0058943-D01"

 

Yes

APHIDBASE

Aphid Genome Database

/db_xref="APHIDBASE:ACYPI007424"

 

Yes

ApiDB

Apicomplexan Database Resources

/db_xref="ApiDB:cgd1_1090"

 

Yes

ApiDB_CryptoDB

Cryptosporidium Genome Resources  

/db_xref="ApiDB_CryptoDB:cgd7_20"

 

Yes

ApiDB_PlasmoDB  

Plasmodium Genome Resources  

/db_xref="ApiDB_PlasmoDB: PF11_0344"

 

Yes

ApiDB_ToxoDB

Toxoplasma Genome Resources

/db_xref="ApiDB_ToxoDB:49.m00014"

 

Yes

ASAP

A Systematic Annotation Package for Community Analysis of Genomes

/db_xref="ASAP:ABE-0000006"

 

Yes

ATCC

American Type Culture Collection database

/db_xref="ATCC:123456"

 

Yes

ATCC(dna)

American Type Culture Collection database

/db_xref="ATCC(dna):123456”

 

Yes

ATCC(in host)

American Type Culture Collection database

/db_xref="ATCC(in host):123456"

 

Yes

Axeldb

A Xenopus laevis database

/db_xref="Axeldb:32B3.1"

 

Yes

BDGP_EST

Berkeley Drosophila Genome Project EST database

/db_xref="BDGP_EST:123456"

 

Yes

BDGP_INS

Berkeley Drosophila Genome Project database -- Insertion

/db_xref="BDGP_INS:123456"

 

Yes

BEETLEBASE

Tribolium Genome Database -- Insertion

/db_xref="BEETLEBASE:TC030551"

 

Yes

BGD

Bovine Genome Database

/db_xref="BGD:BT10004"

new

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

 

Yes

dbEST

EST database maintained at the NCBI.

/db_xref="dbEST:123456"
/db_xref="dbEST:BP535535"

 

Yes

dbProbe

NCBI Probe database Public registry of nucleic acid reagents

/db_xref="dbProbe:38"

 

Yes

dbSNP

Variation database maintained at the NCBI.

/db_xref="dbSNP:4647"
/db_xref="dbSNP:rs133073"

 

Yes

dbSTS

STS database maintained at the NCBI.

/db_xref="dbSTS:456789"
/db_xref="dbSTS:BV210161"

 

Yes

dictyBase

Dictyostelium genome database

/db_xref="dictyBase:DDB0191090"

 

Yes

EcoGene

Database of Escherichia coli Sequence and Function

/db_xref="EcoGene:EG11277"

 

Yes

ENSEMBL

Database of automatically annotated genomic data

/db_xref="ENSEMBL:HUMAN-Clone-AC005612"
/db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102"

 

Yes

EnsemblGenomes

Extending Ensembl across the taxonomic space

/db_xref="EnsemblGenomes:AAC73116"/db_xref="EnsemblGenomes:b0005"

 

No

EPD

Eukaryotic Promotor Database

/db_xref="EPD: EP00576"

 

No

ERIC

Enteropathogen Resource Integration Center

/db_xref="ERIC:ABY-0246137"

 

Yes

ESTLIB

EBI's EST library identifier

/db_xref="ESTLIB:1200"

 

Yes

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"

 

Yes

GABI

Network of Different Plant Genomic Research Projects

/db_xref="GABI:HA05J18"

 

Yes

GDB

Human Genome Database accession numbers

/db_xref="GDB:G00-128-600"

 

Yes

GeneDB

Curated gene database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei

/db_xref="GeneDB:SPCC285.16c"

 

Yes

GeneID

Entrez Gene Database (replaces NCBI Locus Link)

/db_xref="GeneID:3054987"

 

Yes

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"

 

Yes

GOA

Gene Ontology Annotation Database Identifier

/db_xref=" GOA :P01100"

 

Yes

Greengenes

16S rRNA gene database

/db_xref="Greengenes:269185"

 

Yes

GRIN

Germplasm Resources Information Network

/db_xref="GRIN:1005973"

 

Yes

HGNC

Human Gene Nomenclature Database

/db_xref="HGNC:2041"

 

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"

 

Yes

HOMD

Human Oral Microbiome Database

/db_xref="HOMD:tax_078"

/db_xref="HOMD:seq_1603”

 

Yes

HSSP

Database of homology-derived secondary structure of proteins

/db_xref="HSSP:12GS"

 

Yes

IKMC

International Knockout Mouse Consortium

/db_xref="IKMC:66303"

new

Yes

IMGT/GENE-DB

Immunogenetics database, immunoglobulin and T-cell receptor genes

/db_xref="IMGT/GENE-DB:IGKC"

 

Yes

IMGT/LIGM

Immunogenetics database, immunoglobulins and T-cell receptors

/db_xref="IMGT/LIGM:U03895"

 

Yes

IMGT/HLA

Immunogenetics database, human MHC

/db_xref="IMGT/HLA:HLA00031"

 

Yes

Interpro

InterPro protein sequence database

/db_xref="InterPro:IPR002928"

 

Yes

IntrepidBio

Intrepid BioInformatics

/db_xref="ItrepidBio:5259707746"

new

No

IRD

Influenza Research Database

/db_xref="IRD:CEIRS-CIP045-123456.2"

 

No

ISFinder

Insertion sequence elements database

/db_xref="ISFinder:ISA1083-2"

 

No

JCM

Japan Collection of Microorganisms

/db_xref="JCM:1339"

 

Yes

JGIDB

 JGI Genome Portal /db_xref="JGIDB:Chluvu1_81011"

 

Yes

JGI's Phytozome

 Comparative genomics of plants

/db_xref="Phytozome:Glyma0021s00410"

/db_xref="Phytozme:POPTR_1446s00200"

 

No

LocusID

NCBI LocusLink ID **Discontinued March 2005

/db_xref="LocusID:51199"

 

No

MaizeGDB

Maize Genome Database unique identifiers

/db_xref="MaizeGDB:635633 "

 

Yes

MGI

Mouse Genome Informatics

/db_xref="MGI:1894891"

 

Yes

MIM

Mendelian Inheritance in Man numbers

/db_xref="MIM:123456"

 

Yes

miRBase

The microRNA database

/db_xref="miRBase: MI0001857"

 

No

MycoBank

 

Fungal Databases, Nomenclature and Species Banks

/db_xref="MycoBank:MB519473"

 

Yes

NBRC

NITE Biological Resource Center

/db_xref="NBRC:3189"

 

Yes

NextDB

Nematode Expression Pattern DataBase

/db_xref="NextDB:CELK01662"

 

Yes

niaEST

NIA Mouse cDNA Project

/db_xref="niaEST:L0304H12-3"

 

Yes

NMPDR

National Microbial Pathogen Data Resource

/db_xref="NMPDR:fig|306254.1.peg.183"

 

Yes

NRESTdb

Natural Rubber EST database

/db_xref="NRESTdb:Y01A01"

 

Yes

Osa1

Rice Genome Annotation Project

/db_xref="Osa1:LOC_Os01g12345"

 

No

Pathema

Pathema Genome Resource

/db_xref="Pathema:BA_4405"
/db_xref="Pathema:191218"

 

Yes

PBmice

PiggyBac Mutagenesis Information Center

/db_xref="PBmice:38"

 

Yes

PDB

Biological macromolecule three dimensional structure database

/db_xref="PDB:12GS"

 

Yes

PFAM

Collection of protein families

/db_xref="PFAM:PF00003"

 

Yes

PGN

Plant Genome Network

/db_xref="PGN:aam01-1ms3-a05"

 

Yes

PIR

Protein Information Resource accession numbers

/db_xref="PIR:S12345"

 

Yes

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"

 

Yes

PseudoCap

Pseudomonas Genome Database

/db_xref="PseudoCap:PA0001"

 

Yes

RAP-DB

Rice Annotation Project Database

/db_xref="RAP-DB:Os01g1234567"

 

Auto

RATMAP

Rat Genome Database

/db_xref="RATMAP:5"

 

Yes

RFAM

RNA families database of alignments and CMs

/db_xref="RFAM:RF00230"

 

Yes

RGD

Rat Genome Database

/db_xref="RGD:620528"

 

Yes

RiceGenes

Rice database accession numbers

/db_xref="RiceGenes:AA231856"

 

Yes

RZPD

Resource Centre Primary Database Clone Identifiers

/db_xref="RZPD:IMAGp998I142450Q6"

 

Yes

SEED

The SEED Database

/db_xref="SEED:fig|83331.1.peg.1"

 

Yes

SGD

Saccharomyces Genome Database

/db_xref="SGD:L0000470"

new

Yes

SGN

SOL Genomics Network

/db_xref="SGN:E553090"

 

Yes

SK-FST

Saskatoon Arabidopsis T-DNA mutant population - SK Collection

/db_xref="SK-FST: FST:SK32219"

 

Yes

SoyBase

Glycine max Genome Database

/db_xref="SoyBase:Satt005"

 

Yes

SRPDB

Signal Recognition Particle Database

/db_xref="SRPDB:1234"

new

Yes

SubtiList

Bacillus subtilis genome sequencing project

/db_xref="SubtiList:BG10001"

 

Yes

taxon

NCBI's taxonomic identifier

/db_xref="taxon:4932"

 

Auto

TAIR

 The Arabidopsis Information Resource  /db_xref="TAIR:AT1F51370"

new

No

TIGRFAM

TIGR protein families

/db_xref="TIGRFAM:TIGR00094"

 

Yes

TubercuList

TubercuList

/db_xref="TubercuList:Rv3322c"

new

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"

 

Yes

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"

 

Yes

UniSTS

a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiment

/db_xref="UniSTS:486599"

new

No

UNITE

Molecular database for the identification of fungi

/db_xref="UNITE:UDB000157"

 

Yes

VBASE2

Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse

/db_xref="VBASE2:humIGKV165"

 

Yes

VectorBase

Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens

/db_xref="VectorBase:ENSANGG00000007825"

 

Yes

ViPR

 Virus Pathogen Resource /db_xref="ViPR:HRV-A34_p1058_sR263_2008"

 

Yes

WorfDB

C. elegans ORFeome cloning project

/db_xref="WorfDB:pos-1"

 

Yes

WormBase

Caenorhabditis elegans Genome Database

/db_xref="WormBase:R13H7"

new

Yes

Xenbase

Xenopus laevis and tropicalis biology and genomics resource

/db_xref=Xenbase:XB-GENE-1019547

 

Yes

ZFIN

Zebrafish Information Network

/db_xref="ZFIN:ZDB-GENE-011205-17"

 

Yes

Revised August 9, 2012

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