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

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"

 

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"

 

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"

 

BEETLEBASE

Tribolium Genome Database -- Insertion

/db_xref="BEETLEBASE:TC030551"

 

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"
/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"

 

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"
/db_xref="H-InvDB:HIX0000001"

 

HMP

Human Microbiome Project

/db_xref="HMP:0536"

 

HOMD

Human Oral Microbiome Database

/db_xref="HOMD:tax_078"

/db_xref="HOMD:seq_1603”

 

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"

 

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"

/db_xref="Phytozme:POPTR_1446s00200"

 

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"

 

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"

 

Osa1

Rice Genome Annotation Project

/db_xref="Osa1:LOC_Os01g12345"

 

Pathema

Pathema Genome Resource

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

 

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"

 

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"

 

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"

 

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 31, 2013