Difference between revisions of "Bioinformatics databases links"

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Revision as of 01:36, 11 June 2007

Note: The following list was inspired by databases cross-referenced in UniProtKB/Swiss-Prot.

• AGD

Name  : Ashbya genome database

Ref  : BMC Genomics 8:9-9(2007); PubMed:17212814 ; DOI:10.1186/1471-2164-8-9 ;

LinkTp: Explicit

Server: http://agd.vital-it.ch/

Db_URL: http://agd.vital-it.ch/Ashbya_gossypii/geneview?gene=%s

Cat  : Organism-specific gene databases

• ANU-2DPAGE

Name  : Australian National University 2-DE database

Ref  : Proteomics 1:1149-1161(2001); PubMed:11990509 ; DOI:<1149::AID-PROT1149>3.0.CO;2-R 10.1002/1615-9861(200109)1:9<1149::AID-PROT1149>3.0.CO;2-R ;

LinkTp: Explicit

Server: http://semele.anu.edu.au

Cat  : 2D gel databases

• AraC-XylS

Name  : AraC-XylS; a database on a family of Helix-Turn-Helix transcription factors from bacteria

Ref  : Nucleic Acids Res. 30:318-321(2002); PubMed:11752325 ;

LinkTp: Implicit; All bacterial Swiss-Prot entries with a cross-reference to PROSITE PS01124

Server: http://www.eez.csic.es/arac-xyls/

Db_URL: http://www.eez.csic.es/arac-xyls/wfichas/%s.HTM

Cat  : Protein family/group databases

• ArrayExpress

Name  : ArrayExpress repository for microarray data

Ref  : Nucleic Acids Res. 35:D747-D750(2007); PubMed:17132828 ; DOI:10.1093/nar/gkl995 ;

LinkTp: Explicit

Server: http://www.ebi.ac.uk/arrayexpress/

Db_URL: http://www.ebi.ac.uk/aedw/dwd?uniprot=%s

Cat  : Gene expression databases

• BioCyc

Name  : Collection of Pathway/Genome Databases

Ref  : Nucleic Acids Res. 33:6083-6089(2005); PubMed:16246909 ; DOI:10.1093/nar/gki892 ;

LinkTp: Explicit

Server: http://www.biocyc.org/

Db_URL: http://biocyc.org/getid?id=%s

Cat  : Enzyme and pathway databases

• BLOCKS

Name  : BLOCKS; a protein domain database

Ref  : Nucleic Acids Res. 28:228-230(2000); PubMed:10592233 ;

LinkTp: Implicit; All Swiss-Prot entries

Server: http://blocks.fhcrc.org/

Db_URL: http://blocks.fhcrc.org/blocks-bin/getblock.sh?%s

Cat  : Family and domain databases

• BuruList

Name  : Mycobacterium ulcerans genome database

LinkTp: Explicit

Server: http://genolist.pasteur.fr/BuruList/

Cat  : Organism-specific gene databases

• CleanEx

Name  : CleanEx database of gene expression profiles

Ref  : Nucleic Acids Res. 32:D542-D547(2004); PubMed:14681477 ; DOI:10.1093/nar/gkh107 ;

LinkTp: Implicit; all human and mouse entries with >= HGNC or MGI X-ref

Server: http://www.cleanex.isb-sib.ch/

Db_URL: http://www.cleanex.isb-sib.ch/cgi-bin/cleanex_query_result.pl?out_format=NICE&Entry_0=HGNC:%s

Cat  : Gene expression databases

• CMR

Name  : Comprehensive Microbial Resource

LinkTp: Implicit; all entries from completely sequenced microbial genomes which don't have an explicit link to TIGR

Server: http://http://cmr.tigr.org/

Cat  : Genome annotation databases

• COMPLUYEAST-2DPAGE

Name  : 2-DE database at Universidad Complutense de Madrid

Ref  : J. Chromatogr. B. Biomed. Sci. Appl. 787:129-148(1993); PubMed:12659738 ;

LinkTp: Explicit

Server: http://babbage.csc.ucm.es/2d/2d.html

Cat  : 2D gel databases

• Cornea-2DPAGE

Name  : Human Cornea 2-DE database

LinkTp: Explicit

Server: http://www.cornea-proteomics.com/

Db_URL: http://www.daimi.au.dk/cgi-jje/2d/2d.cgi?ac=%s&database=cornea

Cat  : 2D gel databases

• CYGD

Name  : Comprehensive Yeast Genome Database

Ref  : Nucleic Acids Res. 33:D364-D368(2005); PubMed:15608217 ; DOI:10.1093/nar/gki053 ;

LinkTp: Explicit

Server: http://mips.gsf.de/genre/proj/yeast

Db_URL: http://mips.gsf.de/genre/proj/yeast/singleGeneReport.html?entry=%s

Cat  : Organism-specific gene databases

• dbSNP

Name  : Database of single nucleotide polymorphism

Ref  : Nucleic Acids Res. 35:D5-12(2007); PubMed:17170002 ; DOI:10.1093/nar/gkl1031 ;

LinkTp: Explicit

Server: http://www.ncbi.nlm.nih.gov/SNP/

Db_URL: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s

Cat  : Polymorphism databases

• DDBJ

Name  : DNA Data Bank of Japan; a nucleotide sequence database

Ref  : Nucleic Acids Res. 35:D13-D15(2007); PubMed:17108353 ; DOI:10.1093/nar/gkl908 ;

LinkTp: Implicit; All Swiss-Prot entries with >=1 EMBL Xref.

Server: http://www.ddbj.nig.ac.jp/

Cat  : Sequence databases

• DictyBase

Name  : Dictyostelium discoideum online informatics resource

Ref  : Nucleic Acids Res. 34:D423-D427(2006); PubMed:16381903 ; DOI:10.1093/nar/gkj090 ;

LinkTp: Explicit

Server: http://dictybase.org/

Db_URL: http://dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus=%s

Cat  : Organism-specific gene databases

• DIP

Name  : Database of interacting proteins

Ref  : Nucleic Acids Res. 32:D449-D451(2004); PubMed:14681454 ; DOI:10.1093/nar/gkh086 ;

LinkTp: Explicit

Server: http://dip.doe-mbi.ucla.edu/

Db_URL: http://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=%s

Cat  : Protein-protein interaction databases

• DOSAC-COBS-2DPAGE

Name  : DOSAC-COBS 2D-PAGE database

LinkTp: Explicit

Server: http://www.dosac.unipa.it/2d/

Db_URL: http://www.dosac.unipa.it/cgi-bin/2d/2d.cgi?ac=%s

Cat  : 2D gel databases

• DrugBank

Name  : Drug and drug target database

Ref  : Nucleic Acids Res. 34:D668-D672(2006); PubMed:16381955 ; DOI:10.1093/nar/gkj067 ;

LinkTp: Explicit

Server: http://redpoll.pharmacy.ualberta.ca/drugbank/

Db_URL: http://redpoll.pharmacy.ualberta.ca/drugbank/cgi-bin/getCard.cgi?CARD=%s.txt

Cat  : Other

• EchoBASE

Name  : EchoBASE - an integrated post-genomic database for E. coli

Ref  : Nucleic Acids Res. 33:D329-D333(2005); PubMed:15608209 ; DOI:10.1093/nar/gki028 ;

LinkTp: Explicit

Server: http://www.biolws1.york.ac.uk/echobase/

Db_URL: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=%s

Cat  : Organism-specific gene databases

• EcoGene

Name  : Escherichia coli strain K12 genome database

Ref  : Nucleic Acids Res. 28:60-64(2000); PubMed:10592181 ;

LinkTp: Explicit

Server: http://www.ecogene.org/

Db_URL: http://www.ecogene.org/geneInfo.php?eg_id=%s

Cat  : Organism-specific gene databases

• EMBL

Name  : EMBL nucleotide sequence database

Ref  : Nucleic Acids Res. 35:D16-D20(2007); PubMed:17148479 ; DOI:10.1093/nar/gkl913 ;

LinkTp: Explicit

Server: http://www.ebi.ac.uk/embl/

Db_URL: http://www.ebi.ac.uk/htbin/expasyfetch?%s

Cat  : Sequence databases

• Ensembl

Name  : Ensembl eukaryotic genome annotation project

Ref  : Nucleic Acids Res. 35:D610-D617(2007); PubMed:17148474 ; DOI:10.1093/nar/gkl996 ;

LinkTp: Explicit

Server: http://www.ensembl.org/

Cat  : Genome annotation databases

• ENZYME

Name  : Enzyme nomenclature database

Ref  : Nucleic Acids Res. 28:304-305(2000); PubMed:10592255 ;

LinkTp: Implicit; All Swiss-Prot entries that contain >=1 EC numbers in their description lines

Server: http://www.expasy.org/enzyme/

Cat  : Enzyme and pathway databases

• euHCVdb

Name  : European Hepatitis C Virus database

Ref  : Nucleic Acids Res. 35:D363-D366(2007); PubMed:17142229 ; DOI:10.1093/nar/gkl970 ;

LinkTp: Explicit

Server: http://euhcvdb.ibcp.fr/euHCVdb/

Db_URL: http://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=%s

Cat  : Organism-specific gene databases

• FlyBase

Name  : Drosophila genome database

Ref  : Nucleic Acids Res. 35:D486-D491(2007); PubMed:17099233 ; DOI:10.1093/nar/gkl827 ;

LinkTp: Explicit

Server: http://flybase.bio.indiana.edu/

Db_URL: http://flybase.bio.indiana.edu/.bin/fbidq.html?%s

Note  : Obsolete abbreviation: DMAP

Cat  : Organism-specific gene databases

• GenAtlas

Name  : GenAtlas: human gene database

Ref  : C. R. Acad. Sci. III, Sci. Vie 321:805-817(1998); PubMed:9835018 ;

LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref.

Server: http://www.dsi.univ-paris5.fr/genatlas/

Db_URL: http://www.dsi.univ-paris5.fr/genatlas/fiche.php?symbol=%s

Cat  : Organism-specific gene databases

• GenBank

Name  : GenBank nucleotide sequence database

Ref  : Nucleic Acids Res. 35:D5-12(2007); PubMed:17170002 ; DOI:10.1093/nar/gkl1031 ;

LinkTp: Implicit; All Swiss-Prot entries with >=1 EMBL Xref.

Server: http://www.ncbi.nlm.nih.gov/

Cat  : Sequence databases

• Gene3D

Name  : Gene3D Structural and Functional Annotation of Protein Families

Ref  : Nucleic Acids Res. 34:D281-D284(2006); PubMed:16381865 ; DOI:10.1093/nar/gkj057 ;

LinkTp: Explicit

Server: http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/

Db_URL: http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/GotoCath.pl?cath=%s

Cat  : Family and domain databases

• GeneCards

Name  : GeneCards: human genes, protein and diseases

Ref  : Bioinformatics 18:1542-1543(2002); PubMed:12424129 ;

LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref.

Server: http://www.genecards.org/

Db_URL: http://www.genecards.org/cgi-bin/carddisp?%s

Cat  : Organism-specific gene databases

• GeneDB_Spombe

Name  : Schizosaccharomyces pombe GeneDB

Ref  : Nucleic Acids Res. 32:D339-D343(2004); PubMed:14681429 ; DOI:10.1093/nar/gkh007 ;

LinkTp: Explicit

Server: http://www.genedb.org/genedb/pombe/

Db_URL: http://www.genedb.org/genedb/Search?submit=Search+for&name=%s&organism=pombe&desc=yes

Cat  : Organism-specific gene databases

• GeneFarm

Name  : Structural and functional annotation of Arabidopsis thaliana gene and protein families.

Ref  : Nucleic Acids Res. 33:D641-D646(2005); PubMed:15608279 ; DOI:10.1093/nar/gki115 ;

LinkTp: Explicit

Server: http://urgi.versailles.inra.fr/Genefarm/index.htpl

Db_URL: http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=%s

Cat  : Organism-specific gene databases

• GeneLynx

Name  : GeneLynx; a portal to the human, mouse and rat genomes

Ref  : Genome Res. 11:2151-2157(2001); PubMed:11731507 ; DOI:10.1101/gr.199801 ;

LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref or mouse sequence with >=1 MGI X-ref or rat sequence with >=1 RGD X-ref.

Server: http://www.genelynx.org/

Cat  : Organism-specific gene databases

• GenomeReviews

Name  : Genome Reviews; an annotated view of completely sequenced genomes

Ref  : Nucleic Acids Res. 33:D297-D302(2005); PubMed:15608201 ; DOI:10.1093/nar/gki039 ;

LinkTp: Explicit

Server: http://www.ebi.ac.uk/GenomeReviews/

Cat  : Genome annotation databases

• GermOnline

Name  : GermOnline - a gateway for gametogenesis

Ref  : Nucleic Acids Res. 35:D457-D462(2007); PubMed:17145711 ; DOI:10.1093/nar/gkl957 ;

LinkTp: Explicit

Server: http://www.germonline.org/

Db_URL: http://www.germonline.org/%s/geneview?gene=%s

Cat  : Gene expression databases

• GlycoSuiteDB

Name  : GlycoSuiteDB; an annotated and curated relational database of glycan structures

Ref  : Nucleic Acids Res. 31:511-513(2003); PubMed:12520065 ;

LinkTp: Explicit

Server: https://tmat.proteomesystems.com/glycosuite/

Cat  : PTM databases

• GO

Name  : Gene Ontology

Ref  : Nucleic Acids Res. 34:D322-D326(2006); PubMed:16381878 ; DOI:10.1093/nar/gkj021 ;

LinkTp: Explicit

Server: http://www.geneontology.org/

Db_URL: http://www.ebi.ac.uk/ego/QuickGO?mode=display&entry=%s

Cat  : Ontologies

• GPCRDB

Name  : Information system for G protein-coupled receptors (GPCRs)

Ref  : Nucleic Acids Res. 29:346-349(2001); PubMed:11125133 ;

LinkTp: Implicit; All Swiss-Prot entries that contains a CC line of the type: "-!- SIMILARITY: Belongs to the G-protein coupled receptor ..."

Server: http://www.gpcr.org/7tm/

Cat  : Protein family/group databases

• Gramene

Name  : Gramene; a comparative mapping resource for grains

Ref  : Nucleic Acids Res. 34:D717-D723(2006); PubMed:16381966 ; DOI:10.1093/nar/gkj154 ;

LinkTp: Explicit

Server: http://www.gramene.org/

Db_URL: http://www.gramene.org//db/protein/protein_search?acc=%s

Cat  : Organism-specific gene databases

• H-InvDB

Name  : H-Invitational Database, human transcriptome db

Ref  : Gene 364:99-107(2005); PubMed:16185827 ; DOI:10.1016/j.gene.2005.05.036 ;

LinkTp: Explicit

Server: http://www.h-invitational.jp/

Db_URL: http://www.jbirc.aist.go.jp/hinv/soup/pub_Locus.pl?locus_id=%s

Cat  : Organism-specific gene databases

• HAMAP

Name  : HAMAP database of microbial protein families

Ref  : Comput. Biol. Chem. 27:49-58(2003); PubMed:12798039 ;

LinkTp: Explicit

Server: http://www.expasy.org/sprot/hamap/

Db_URL: http://www.expasy.org/cgi-bin/hamap/nicemf.cgi?%s

Cat  : Family and domain databases

• HGNC

Name  : Human Gene Nomenclature Database

Ref  : Nucleic Acids Res. 34:D319-D321(2006); PubMed:16381876 ; DOI:10.1093/nar/gkj147 ;

LinkTp: Explicit

Server: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl

Db_URL: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/get_data.pl?hgnc_id=%s

Note  : Obsolete abbreviation: Genew

Cat  : Organism-specific gene databases

• HIV

Name  : HIV sequence database

LinkTp: Explicit

Server: http://www.hiv.lanl.gov/content/hiv-db/mainpage.html

Cat  : Organism-specific gene databases

• HOGENOM

Name  : Homologous Sequences from Complete Genomes database

LinkTp: Implicit; entries from Bacteria and Archaea except fragments of <100 AA

Server: http://pbil.univ-lyon1.fr/databases/hogenom.html

Db_URL: http://pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?db=Hogenprot&query=%s

Cat  : Organism-specific gene databases

• HOVERGEN

Name  : Homologous vertebrate genes database

Ref  : Nucleic Acids Res. 22:2360-2365(1994); PubMed:8036164 ;

LinkTp: Implicit; entries from Vertebrata except fragments of <100 AA

Server: http://pbil.univ-lyon1.fr/databases/hovergen.html

Db_URL: http://pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?db=Hoverprot&query=%s

Cat  : Organism-specific gene databases

• HPA

Name  : Human Protein Atlas

Ref  : Mol. Cell. Proteomics 4:1920-1932(2005); PubMed:16127175 ; DOI:10.1074/mcp.M500279-MCP200 ;

LinkTp: Explicit

Server: http://www.proteinatlas.org/

Db_URL: http://www.proteinatlas.org/tissue_profile.php?antibody_id=%s

Cat  : Organism-specific gene databases

• HSC-2DPAGE

Name  : 2-DE gel protein databases at Harefield

Ref  : Electrophoresis 18:471-479(1997); PubMed:9150926 ;

LinkTp: Explicit

Server: http://www.doc.ic.ac.uk/vip/hsc-2dpage/

Cat  : 2D gel databases

• HSSP

Name  : Homology-derived secondary structure of proteins database

Ref  : Nucleic Acids Res. 27:244-247(1999); PubMed:9847191 ;

LinkTp: Explicit

Server: http://www.sander.ebi.ac.uk/hssp/

Db_URL: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e

Cat  : 3D structure databases

• HUGE

Name  : Human Unidentified Gene-Encoded large proteins database

Ref  : Nucleic Acids Res. 32:D502-D504(2004); PubMed:14681467 ; DOI:10.1093/nar/gkh035 ;

LinkTp: Implicit; Human sequence entries with KIAAnnnn in a GN line

Server: http://www.kazusa.or.jp/huge/

Cat  : Organism-specific gene databases

• IMGT

Name  : ImMunoGeneTics db

Ref  : Nucleic Acids Res. 34:D781-D784(2006); PubMed:16381979 ; DOI:10.1093/nar/gkj088 ;

LinkTp: Implicit; All entries with a KW "Immunoglobulin [CV] region" and >=1 EMBL X-ref.

Server: http://imgt.cines.fr/

Cat  : Protein family/group databases

• IntAct

Name  : Protein interaction database and analysis system

Ref  : Nucleic Acids Res. 35:D561-D565(2007); PubMed:17145710 ; DOI:10.1093/nar/gkl958 ;

LinkTp: Explicit

Server: http://www.ebi.ac.uk/intact/

Db_URL: http://www.ebi.ac.uk/intact/search/do/hvWelcome?searchClass=Interactor&searchString=%s

Cat  : Protein-protein interaction databases

• InterPro

Name  : Integrated resource of protein families, domains and functional sites

Ref  : Nucleic Acids Res. 35:D224-D228(2007); PubMed:17202162 ; DOI:10.1093/nar/gkl841 ;

LinkTp: Explicit

Server: http://www.ebi.ac.uk/interpro/

Db_URL: http://www.ebi.ac.uk/interpro/IEntry?ac=%s

Cat  : Family and domain databases

• KEGG

Name  : KEGG: Kyoto Encyclopedia of Genes and Genomes

Ref  : Nucleic Acids Res. 34:D354-D357(2006); PubMed:16381885 ; DOI:10.1093/nar/gkj102 ;

LinkTp: Explicit

Server: http://www.genome.jp/kegg/

Db_URL: http://www.genome.jp/dbget-bin/www_bget?%s

Cat  : Genome annotation databases

• LegioList

Name  : Legionella pneumophila genome database

Ref  : BMC Genomics 6:14-14(2005); PubMed:15698474 ; DOI:10.1186/1471-2164-6-14 ;

LinkTp: Explicit

Server: http://genolist.pasteur.fr/LegioList/

Cat  : Organism-specific gene databases

• Leproma

Name  : Mycobacterium leprae genome database

LinkTp: Explicit

Server: http://genolist.pasteur.fr/Leproma/

Cat  : Organism-specific gene databases

• LinkHub

Name  : LinkHub; links to different genomics and protein resources

LinkTp: Explicit

Server: http://hub.gersteinlab.org/

Db_URL: http://hub.gersteinlab.org/id/%s/link_origin/UNIPROT

Cat  : Other

• ListiList

Name  : Listeria innocua and Listeria monocytogenes genomes database

LinkTp: Explicit

Server: http://genolist.pasteur.fr/ListiList/

Cat  : Organism-specific gene databases

• MaizeGDB

Name  : Maize Genetics and Genomics Database

Ref  : Nucleic Acids Res. 35:D895-D900(2007); PubMed:17202174 ; DOI:10.1093/nar/gkl1048 ;

LinkTp: Explicit

Server: http://www.maizegdb.org/

Db_URL: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=%s

Note  : Obsolete abbreviation: MaizeDB

Cat  : Organism-specific gene databases

• MEROPS

Name  : MEROPS protease database

Ref  : Nucleic Acids Res. 34:D270-D272(2006); PubMed:16381862 ; DOI:10.1093/nar/gkj089 ;

LinkTp: Explicit

Server: http://merops.sanger.ac.uk/

Db_URL: http://merops.sanger.ac.uk/cgi-bin/make_frame_file?id=%s

Cat  : Protein family/group databases

• MGI

Name  : Mouse genome database (MGD) from Mouse Genome Informatics (MGI)

Ref  : Nucleic Acids Res. 35:D630-D637(2007); PubMed:17135206 ; DOI:10.1093/nar/gkl940 ;

LinkTp: Explicit

Server: http://www.informatics.jax.org/

Db_URL: http://www.informatics.jax.org/searches/accession_report.cgi?id=%s

Note  : Obsolete abbreviation: MGD

Cat  : Organism-specific gene databases

• Micado

Name  : Microbial advanced database

LinkTp: Implicit; All Swiss-Prot entries with >=1 SubtiList Xref where the gene name does not start with "Y"

Server: http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi

Db_URL: http://genome.jouy.inra.fr/micado/gene.cgi?species=Bacillus+subtilis&gene=%2

Cat  : Organism-specific gene databases

• MIM

Name  : Online Mendelian Inheritance in Man (OMIM)

Ref  : Nucleic Acids Res. 33:D514-D517(2005); PubMed:15608251 ; DOI:10.1093/nar/gki033 ;

LinkTp: Explicit

Server: http://www.ncbi.nlm.nih.gov/omim/

Db_URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=OMIM&dopt=Detailed&tmpl=dispomimTemplate&list_uids=%s

Cat  : Organism-specific gene databases

• ModBase

Name  : Database of comparative protein structure models

Ref  : Nucleic Acids Res. 34:D291-D295(2006); PubMed:16381869 ; DOI:10.1093/nar/gkj059 ;

LinkTp: Implicit; All Swiss-Prot and TrEMBL entries

Server: http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi

Cat  : 3D structure databases

• MypuList

Name  : Mycoplasma pulmonis genome database

LinkTp: Explicit

Server: http://genolist.pasteur.fr/MypuList/

Cat  : Organism-specific gene databases

• NIEHS-SNPs

Name  : NIEHS SNPs Program at the University of Washington

LinkTp: Implicit; all entries with >= HGNC X-ref and an RT line starting with "NIEHS-SNPs"

Server: http://egp.gs.washington.edu/

Db_URL: http://egp.gs.washington.edu/data/%s/

Cat  : Polymorphism databases

• NucleaRDB

Name  : Information system for nuclear receptors

Ref  : Nucleic Acids Res. 29:346-349(2001); PubMed:11125133 ;

LinkTp: Implicit; All Swiss-Prot entries that contain a CC line of the type: "-!- SIMILARITY: Belongs to the nuclear hormone receptor family."

Server: http://www.receptors.org/NR/

Cat  : Protein family/group databases

• OGP

Name  : Oxford GlycoProteomics 2-DE database, Oxford University, England

LinkTp: Explicit

Server: http://proteomewww.bioch.ox.ac.uk/2d/2d.html

Db_URL: http://proteomewww.bioch.ox.ac.uk/cgi-bin/get-2d-entry?%s

Cat  : 2D gel databases

• Orphanet

Name  : Orphanet; a database dedicated to information on rare diseases and orphan drugs

Server: http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB

Db_URL: http://www.orpha.net//consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=%s

Cat  : Organism-specific gene databases

• PANTHER

Name  : The PANTHER Classification System

Ref  : Nucleic Acids Res. 35:D247-D252(2007); PubMed:17130144 ; DOI:10.1093/nar/gkl869 ;

LinkTp: Explicit

Server: http://www.pantherdb.org/

Db_URL: http://www.pantherdb.org/panther/family.do?clsAccession=%s

Cat  : Family and domain databases

• PDB

Name  : The RCSB Protein Data Bank; a repository for 3D biological macromolecular structure data

Ref  : Nucleic Acids Res. 34:D302-D305(2006); PubMed:16381872 ; DOI:10.1093/nar/gkj120 ;

LinkTp: Explicit

Server: http://www.rcsb.org/pdb/

Db_URL: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e

Cat  : 3D structure databases

• PeroxiBase

Name  : PeroxiBase, a plant peroxidase database

LinkTp: Explicit

Server: http://peroxidase.isb-sib.ch/index.php

Db_URL: http://peroxidase.isb-sib.ch/listing.php?action=view&id=%s

Cat  : Protein family/group databases

• Pfam

Name  : Pfam protein domain database

Ref  : Nucleic Acids Res. 34:D247-D251(2006); PubMed:16381856 ; DOI:10.1093/nar/gkj149 ;

LinkTp: Explicit

Server: http://www.sanger.ac.uk/Software/Pfam/ ~OR~ http://pfam.wustl.edu/

Db_URL: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?%s

Cat  : Family and domain databases

• PHCI-2DPAGE

Name  : Parasite host cell interaction 2D-PAGE database

LinkTp: Explicit

Server: http://www.gram.au.dk/2d/2d.html

Cat  : 2D gel databases

• PhosSite

Name  : Phosphorylation site database for Archaea and Bacteria

LinkTp: Explicit

Server: http://vigen.biochem.vt.edu/xpd/xpd.htm

Db_URL: http://vigen.biochem.vt.edu/xpd/xpd2.cfm?extf=swissprot&extref=%s

Cat  : PTM databases

• PhotoList

Name  : Photorhabdus luminescens genome database

LinkTp: Explicit

Server: http://genolist.pasteur.fr/PhotoList/

Cat  : Organism-specific gene databases

• PIR

Name  : Protein sequence database of the Protein Information Resource

LinkTp: Explicit

Server: http://pir.georgetown.edu/

Db_URL: http://pir.georgetown.edu/cgi-bin/nbrfget?uid=%s

Cat  : Sequence databases

• PIRSF

Name  : PIR superfamilies, an integrated protein classification database

Ref  : Nucleic Acids Res. 32:D112-D114(2004); PubMed:14681371 ; DOI:10.1093/nar/gkh097 ;

LinkTp: Explicit

Server: http://pir.georgetown.edu/iproclass/

Db_URL: http://pir.georgetown.edu/cgi-bin/ipcSF?id=%s

Cat  : Family and domain databases

• PMMA-2DPAGE

Name  : Purkyne Military Medical Academy 2D-PAGE database

LinkTp: Explicit

Server: http://www.pmma.pmfhk.cz/2d/2d.html

Cat  : 2D gel databases

• PptaseDB

Name  : Prokaryotic Protein Phosphatase Database

LinkTp: Explicit

Server: http://vigen.biochem.vt.edu/p3d/p3d.htm

Db_URL: http://vigen.biochem.vt.edu/p3d/p3d2.cfm?extf=accession&extref=%s

Cat  : Protein family/group databases

• PRINTS

Name  : Protein Motif fingerprint database; a protein domain database

Ref  : Nucleic Acids Res. 31:400-402(2003); PubMed:12520033 ;

LinkTp: Explicit

Server: http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/

Db_URL: http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=%s

Note  : Obsolete abbreviation: PRINT

Cat  : Family and domain databases

• ProDom

Name  : ProDom; a protein domain database

Ref  : Nucleic Acids Res. 33:D212-D215(2005); PubMed:15608179 ; DOI:10.1093/nar/gki034 ;

LinkTp: Explicit

Server: http://prodom.prabi.fr/prodom/current/html/home.php

Db_URL: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=SPTR&query=%s

Cat  : Family and domain databases

• PROSITE

Name  : PROSITE; a protein domain and family database

Ref  : Nucleic Acids Res. 34:D227-D230(2006); PubMed:16381852 ; DOI:10.1093/nar/gkj063 ;

LinkTp: Explicit

Server: http://www.expasy.org/prosite/

Db_URL: http://www.expasy.org/cgi-bin/get-prosite-raw.pl?%s

Cat  : Family and domain databases

• ProtoNet

Name  : ProtoNet; Automatic hierarchical classification of proteins

Ref  : Protein Sci. 15:1557-1562(2006); PubMed:16672244 ; DOI:10.1110/ps.062185706 ;

LinkTp: Implicit; All Swiss-Prot entries

Server: http://www.protonet.cs.huji.ac.il/

Db_URL: http://www.protonet.cs.huji.ac.il/protonet/sp.jsp?prot=%s

Cat  : Other

• PseudoCAP

Name  : Pseudomonas genome database

Ref  : Nucleic Acids Res. 33:D338-D343(2005); PubMed:15608211 ; DOI:10.1093/nar/gki047 ;

LinkTp: Explicit

Server: http://www.pseudomonas.com/

Db_URL: http://www.pseudomonas.com/getAnnotation.do?locusID=%s

Cat  : Organism-specific gene databases

• Rat-heart-2DPAGE

Name  : 2-DE database of rat heart, at German Heart Institute Berlin, Germany

Ref  : Electrophoresis 20:891-897(1999); PubMed:10344264 ;

LinkTp: Explicit

Server: http://www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d/

Db_URL: http://www.mpiib-berlin.mpg.de/mpiib-cgi/RAT-HEART/get-2d-entry?%s

Cat  : 2D gel databases

• Reactome

Name  : Reactome - a knowledgebase of biological pathways and processes

Ref  : Nucleic Acids Res. 33:D428-D432(2005); PubMed:15608231 ; DOI:10.1093/nar/gki072 ;

LinkTp: Explicit

Server: http://www.reactome.org/

Db_URL: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%s

Note  : Obsolete abbreviation: GK

Cat  : Enzyme and pathway databases

• REBASE

Name  : Restriction enzymes and methylases database

Ref  : Nucleic Acids Res. 35:D269-D270(2007); PubMed:17202163 ; DOI:10.1093/nar/gkl891 ;

LinkTp: Explicit

Server: http://rebase.neb.com/

Db_URL: http://rebase.neb.com/rebase/enz/%s.html

Cat  : Protein family/group databases

• REPRODUCTION-2DPAGE

Name  : REPRODUCTION-2DPAGE

LinkTp: Explicit

Server: http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi

Db_URL: http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=?%s

Cat  : 2D gel databases

• RGD

Name  : Rat genome database

Ref  : Nucleic Acids Res. 35:D658-D662(2007); PubMed:17151068 ; DOI:10.1093/nar/gkl988 ;

LinkTp: Explicit

Server: http://rgd.mcw.edu/

Db_URL: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=%s

Cat  : Organism-specific gene databases

• Rouge

Name  : Rodent Unidentified Gene-Encoded large proteins database

Ref  : Nucleic Acids Res. 32:D502-D504(2004); PubMed:14681467 ; DOI:10.1093/nar/gkh035 ;

LinkTp: Implicit; Mouse sequence entries with KIAAnnnn in a GN line

Server: http://www.kazusa.or.jp/rouge/

Cat  : Organism-specific gene databases

• RZPD-ProtExp

Name  : RZPDs collection of validated ORF protein expression clones

LinkTp: Explicit

Server: http://www.rzpd.de/products/orfclones/

Db_URL: http://www.rzpd.de/gene?productId=%s

Cat  : Other

• SagaList

Name  : Streptococcus agalactiae NEM316 / Serotype III genome database

LinkTp: Explicit

Server: http://genolist.pasteur.fr/SagaList/

Cat  : Organism-specific gene databases

• SeattleSNPs

Name  : UW-FHCRC Variation Discovery Resource

LinkTp: Implicit; all entries with >= HGNC X-ref and an RT line starting with "SeattleSNPs"

Server: http://pga.gs.washington.edu/

Db_URL: http://pga.gs.washington.edu/data/%s/

Cat  : Polymorphism databases

• SGD

Name  : Saccharomyces Genome Database

Ref  : Nucleic Acids Res. 35:D468-D471(2007); PubMed:17142221 ; DOI:10.1093/nar/gkl931 ;

LinkTp: Explicit

Server: http://www.yeastgenome.org/

Db_URL: http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=%s

Cat  : Organism-specific gene databases

• Siena-2DPAGE

Name  : 2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy

LinkTp: Explicit

Server: http://www.bio-mol.unisi.it/2d/2d.html

Cat  : 2D gel databases

• SMART

Name  : Simple Modular Architecture Research Tool; a protein domain database

Ref  : Nucleic Acids Res. 34:D257-D260(2006); PubMed:16381859 ; DOI:10.1093/nar/gkj079 ;

LinkTp: Explicit

Server: http://smart.embl.de/

Db_URL: http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s

Cat  : Family and domain databases

• SMR

Name  : SWISS-MODEL Repository - a database of annotated 3D protein structure models

Ref  : Nucleic Acids Res. 34:D315-D318(2006); PubMed:16381875 ; DOI:10.1093/nar/gkj056 ;

LinkTp: Explicit

Server: http://swissmodel.expasy.org/repository/

Db_URL: http://swissmodel.expasy.org/repository/smr.php?sptr_ac=%s

Cat  : 3D structure databases

• SOURCE

Name  : The Stanford Online Universal Resource for Clones and ESTs

LinkTp: Implicit; All human and mouse entries with >=1 gene name and >= 1 MIM or MGI X-ref.

Server: http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch

Cat  : Other

• SubtiList

Name  : Bacillus subtilis strain 168 genome database

Ref  : Nucleic Acids Res. 30:62-65(2002); PubMed:11752255 ;

LinkTp: Explicit

Server: http://genolist.pasteur.fr/SubtiList/

Db_URL: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+%s

Cat  : Organism-specific gene databases

• SWISS-2DPAGE

Name  : Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital

Ref  : Proteomics 4:2352-2356(2004); PubMed:15274128 ; DOI:10.1002/pmic.200300830 ;

LinkTp: Explicit

Server: http://www.expasy.org/ch2d/

Db_URL: http://www.expasy.org/cgi-bin/ch2d-search-ac?%s

Cat  : 2D gel databases

• TAIR

Name  : The Arabidopsis Information Resource

Ref  : Nucleic Acids Res. 31:224-228(2003); PubMed:12519987 ;

LinkTp: Explicit

Server: http://www.arabidopsis.org/

Db_URL: http://www.arabidopsis.org/servlets/TairObject?type=locus&name=%s

Cat  : Organism-specific gene databases

• TIGR

Name  : The bacterial database(s) of 'The Institute of Genome Research'

LinkTp: Explicit

Server: http://www.tigr.org/tdb/

Db_URL: http://cmr.tigr.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=%s

Cat  : Genome annotation databases

• TIGRFAMs

Name  : TIGRFAMs; a protein family database

Ref  : Nucleic Acids Res. 35:D260-D264(2007); PubMed:17151080 ; DOI:10.1093/nar/gkl1043 ;

LinkTp: Explicit

Server: http://www.tigr.org/TIGRFAMs/

Db_URL: http://cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc=%s

Cat  : Family and domain databases

• TRANSFAC

Name  : Transcription factor database

Ref  : Nucleic Acids Res. 34:D108-D110(2006); PubMed:16381825 ; DOI:10.1093/nar/gkj143 ;

LinkTp: Explicit

Server: http://www.gene-regulation.com/

Cat  : Protein family/group databases

• TubercuList

Name  : Mycobacterium tuberculosis strain H37Rv genome database

LinkTp: Explicit

Server: http://genolist.pasteur.fr/TubercuList/

Cat  : Organism-specific gene databases

• UniGene

Name  : UniGene gene-oriented nucleotide sequence clusters

Ref  : Nucleic Acids Res. 35:D5-12(2007); PubMed:17170002 ; DOI:10.1093/nar/gkl1031 ;

LinkTp: Explicit

Server: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=UniGene

Db_URL: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s1&CID=%s2

Cat  : Sequence databases

• UniRef

Name  : UniProt Non-redundant Reference (UniRef) Databases

Ref  : Nucleic Acids Res. 34:D187-D191(2006); PubMed:16381842 ; DOI:10.1093/nar/gkj161 ;

LinkTp: Implicit; all Swiss-Prot and TrEMBL (UniProt knowledgebase) entries

Server: http://www.uniprot.org/database/nref.shtml

Cat  : Other

• WorfDB

Name  : The C.elegans ORFeome cloning project

Ref  : Nucleic Acids Res. 31:237-240(2003); PubMed:12519990 ;

LinkTp: Implicit; all C.elegans entries with an explicit cross-reference to WormPep

Server: http://worfdb.dfci.harvard.edu/

Db_URL: http://worfdb.dfci.harvard.edu/search.pl?form=1&search=%2

Cat  : Organism-specific gene databases

• WormBase

Name  : WormBase

Ref  : Nucleic Acids Res. 35:D506-D510(2007); PubMed:17099234 ; DOI:10.1093/nar/gkl818 ;

LinkTp: Explicit

Server: http://www.wormbase.org/

Db_URL: http://www.wormbase.org/db/gene/gene?name=%s

Cat  : Organism-specific gene databases

• WormPep

Name  : Caenorhabditis elegans genome sequencing project protein database

Ref  : Genomics 46:200-216(1997); PubMed:9417907 ;

LinkTp: Explicit

Server: http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/wormpep.shtml

Db_URL: http://www.sanger.ac.uk/cgi-bin/Projects/C_elegans/wormpep_fetch.pl?entry=%s&what=protein&type=exact

Cat  : Organism-specific gene databases

• Yeast-GFP

Name  : Yeast GFP fusion localization database

Ref  : Nature 425:737-741(2003); PubMed:14562106 ; DOI:10.1038/nature02046 ;

LinkTp: Implicit; All Swiss-Prot entries from Saccharomyces cerevisiae with Y[A-Z]{2}[0-9]{3}[A-Z] in the GN line

Server: http://yeastgfp.ucsf.edu

Db_URL: http://yeastgfp.ucsf.edu/getOrf.php?orf=%s

Cat  : Organism-specific gene databases

• ZFIN

Name  : Zebrafish Information Network genome database

Ref  : Nucleic Acids Res. 34:D581-D585(2006); PubMed:16381936 ; DOI:10.1093/nar/gkj086 ;

LinkTp: Explicit

Server: http://zfin.org/

Db_URL: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=%s

Cat  : Organism-specific gene databases

• Aarhus/Ghent-2DPAGE

Name  : Human keratinocyte 2D gel protein database from Aarhus and Ghent universities

Ref  : FEBS Lett. 430:64-72(1998); PubMed:9678596 ;

LinkTp: Explicit

Server: None

Cat  : 2D gel databases

• ECO2DBASE

Name  : Escherichia coli gene-protein database; a 2-DE gel database

Ref  : Electrophoresis 20:2149-2159(1999); PubMed:9298644 ;

LinkTp: Explicit

Server: None

Note  : Obsolete abbreviation: EC-2D-GEL

Cat  : 2D gel databases

• StyGene

Name  : Salmonella typhimurium LT2 genome database

LinkTp: Explicit

Server: None

Cat  : Organism-specific gene databases