db_xref supported databases

DNA Data Bank of Japan (DDBJ), Mishima, Japan

Sequence Retrieval

DNA Sequence Submissions

European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, Hinxton, UK

Sequence Retrieval

DNA Sequence Submissions

GenBank (National Center for Biotechnology Information) Bethesda, MD, USA

Sequence Retrieval

DNA Sequence Submissions

The /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"

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 -- Insertion	/db_xref="BDGP_INS:123456"

BEETLEBASE	Tribolium Genome Database -- Insertion	/db_xref="BEETLEBASE:TC030551"

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"

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

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"

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"

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"

MycoBank	Fungal Nomenclature and Species Bank	/db_xref="MycoBank:8284"

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	/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"

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"

SubtiList	Bacillus subtilis genome sequencing project	/db_xref="SubtiList:BG10001"

taxon	NCBI's taxonomic identifier	/db_xref="taxon:4932"

TIGRFAM	TIGR protein families	/db_xref="TIGRFAM:TIGR00094"

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"

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"

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 November 27 2009

Comments and questions to: info@ncbi.nlm.nih.gov

db_xrefs

The /db_xref qualifier