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This page presents a partial list of the data sources we download and integrate in our database. These data sources are created and maintained by groups other than ourselves, and we wish to thank these other groups for so generously providing their data to us and the rest of the scientific community.
The first section shows "datasets". Each dataset generally consist of many files which are released as a unit. The table shows the name of each dataset which is linked to the dataset's homepage, and the name or date of the release used in the current version of our database. In a few cases, no release name or date was available.
The second section shows the individual files that we download. The table indicates the full URL of each file, the date the file was updated by its maintainer, and the date we downloaded it. Note that the URL of the file is not hyperlinked, since clicking on such a link would cause the file to be downloaded to your computer which is probably not desirable. We have not grouped the files by data source since this is usually apparent from the URL.
The list of sources presented here is incomplete. Additional sources will be added in future releases.

Dataset Release
BioCarta (linked to genes using data from NCI Cancer Gene Anatomy Project) information not available
BioConductor microarray annotation Version 2.2.0, 02-Apr-2008
BioGRID Version 2.0.43, 01-Aug-2008
Database of Interacting Proteins (DIP) 08-Jul-2008
DoTS (Database Of Transcribed Sequences) human Release 10, 10-Mar-2008
mouse Release 10, 10-Mar-2008
Ensembl Release 49, Mar-2008
Gene Ontology Consortium Version 4.432, 30-Apr-2008
Genetic Association Database 06-Jul-2006
HUGO Gene Nomenclature Committee information not available
Human Protein Reference Database (HPRD) Release 7, 01-Sep-2007
InParanoid: Eukaryotic Ortholog Groups Version 6.1, 22-Apr-2008
IntAct 06-Jul-2008
IPI (International Protein Index) Version 3.29, 22-May-2007
KEGG: Kyoto Encyclopedia of Genes and Genomes Release 46.0, 01-Apr-2008
MINT: a Molecular INTeraction database 19-May-2008
Mouse Genome Informatics (MGI), Jackson Laboratory 30-Apr-2008
NCBI Entrez Gene 21-Feb-2008
NCBI HomoloGene Release 61, 07-Mar-2008
NCBI UniGene human Build #211, 12-Mar-2008
mouse Build #170, 10-Mar-2008
rat Build #173, 11-Apr-2008
OMIM, Online Mendelian Inheritance in Man information not available
OrthoMCL Version 2.0, 28-Feb-2008
PeptideAtlas Apr-2007
Rat Genome Database information not available
Reactome - a curated knowledgebase of biological pathways Version 25, 30-Jun-2008
Sanger Interaction Map 13-Aug-2004
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) Version 7.1
The MIPS Mammalian Protein-Protein Interaction Database information not available
UCSC Genome Bioinformatics (Golden Path) human UCSC hg18, NCBI build 36.1, Mar-2006
mouse UCSC mm9, NCBI Build 37.1, July-2007
rat UCSC rn4, RGSC version 3.4, Nov-2004
UniProt (Universal Protein Resource) Release 13.3, 29-Apr-2008

File Update Date Download Date
ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip 26-Jul-2008 01-Aug-2008
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.dat.gz 22-Jul-2008 01-Aug-2008
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.MOUSE.dat.gz 22-Jul-2008 01-Aug-2008
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.RAT.dat.gz 22-Jul-2008 01-Aug-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/hsapiens_gene_ensembl__homologs_mmusculus__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/hsapiens_gene_ensembl__homologs_rnorvegicus__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/hsapiens_gene_ensembl__xref_entrezgene__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/mmusculus_gene_ensembl__homologs_hsapiens__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/mmusculus_gene_ensembl__homologs_rnorvegicus__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/mmusculus_gene_ensembl__xref_entrezgene__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/rnorvegicus_gene_ensembl__homologs_hsapiens__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/rnorvegicus_gene_ensembl__homologs_mmusculus__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_49/rnorvegicus_gene_ensembl__xref_entrezgene__dm.txt.gz 05-Mar-2008 09-Jul-2008
ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo 15-Aug-2008 19-Aug-2008
ftp://ftp.genome.ad.jp/pub/kegg/genes/ko 18-Aug-2008 19-Aug-2008
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ko.list 17-Aug-2008 19-Aug-2008
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ko.list 17-Aug-2008 19-Aug-2008
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ko.list 17-Aug-2008 19-Aug-2008
ftp://ftp.genome.ad.jp/pub/kegg/pathway/map_title.tab 04-Aug-2008 05-Aug-2008
ftp://ftp.genome.ad.jp/pub/kegg/pathway/organisms/hsa 14-Aug-2008 19-Aug-2008
ftp://ftp.genome.ad.jp/pub/kegg/pathway/organisms/mmu 14-Aug-2008 19-Aug-2008
ftp://ftp.genome.ad.jp/pub/kegg/pathway/organisms/rno 14-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human1.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human2.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human3.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human4.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat1.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat2.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat3.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat4.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman1.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman2.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman3.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman4.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.informatics.jax.org/pub/reports/MGI_EntrezGene.rpt 18-Aug-2008 19-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2unigene 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/gene/DATA/README 21-Feb-2008 09-Jul-2008
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data 28-Jul-2008 01-Aug-2008
ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z 12-Aug-2008 13-Aug-2008
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz 23-Jun-2008 09-Jul-2008
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.retired.lst.gz 23-Jun-2008 09-Jul-2008
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz 15-Jul-2008 01-Aug-2008
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.retired.lst.gz 15-Jul-2008 01-Aug-2008
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.data.gz 12-Jun-2008 09-Jul-2008
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.retired.lst.gz 12-Jun-2008 09-Jul-2008
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human 09-Jun-2008 09-Jul-2008
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse 28-Nov-2007 09-Jul-2008
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/complete.txt.gz 26-Apr-2004 10-Jul-2008
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/core.txt.gz 26-Apr-2004 10-Jul-2008
ftp://ftp.uniprot.org/pub/databases/uniprot_datafiles_by_format/flatfile/uniprot_sprot.dat.gz 22-Jul-2008 01-Aug-2008
ftp://ftp.uniprot.org/pub/databases/uniprot_datafiles_by_format/flatfile/uniprot_trembl.dat.gz 22-Jul-2008 01-Aug-2008
ftp://ftp1.nci.nih.gov/pub/CGAP/Hs_GeneData.dat 24-Jun-2008 09-Jul-2008
ftp://ftp1.nci.nih.gov/pub/CGAP/Mm_GeneData.dat 22-Jul-2008 01-Aug-2008
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/chromInfo.txt.gz 13-Apr-2006 09-Jul-2008
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/cytoBand.txt.gz 13-Apr-2006 09-Jul-2008
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/chromInfo.txt.gz 22-Aug-2007 09-Jul-2008
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/cytoBand.txt.gz 22-Aug-2007 09-Jul-2008
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/chromInfo.txt.gz 20-Jun-2006 09-Jul-2008
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/cytoBand.txt.gz 20-Jun-2006 09-Jul-2008
ftp://mint.bio.uniroma2.it/pub/release/MITAB/current/2008-05-16-Mammalia.mitab25.txt 16-May-2008 10-Jul-2008
ftp://rgd.mcw.edu/pub/data_release/GENES_HUMAN 04-Aug-2008 12-Aug-2008
ftp://rgd.mcw.edu/pub/data_release/GENES_MOUSE 11-Aug-2008 19-Aug-2008
ftp://rgd.mcw.edu/pub/data_release/GENES_RAT 11-Aug-2008 19-Aug-2008
ftp://rgd.mcw.edu/pub/data_release/RGD_ORTHOLOGS 15-Aug-2008 19-Aug-2008
http://banon.cshl.edu:5555/biomart/martservice 13-Aug-2008
http://geneticassociationdb.nih.gov/all.xls 06-Jul-2006 05-Aug-2008
http://inparanoid.sbc.su.se/download/6.1/tables_stats/InParanoid.ensHOMSA-ensRATNO 22-Apr-2008 09-Jul-2008
http://inparanoid.sbc.su.se/download/6.1/tables_stats/InParanoid.ensHOMSA-modMUSMU 22-Apr-2008 09-Jul-2008
http://inparanoid.sbc.su.se/download/6.1/tables_stats/InParanoid.ensRATNO-modMUSMU 22-Apr-2008 09-Jul-2008
http://mips.gsf.de/proj/ppi/data/mppi.gz 01-Jun-2004 10-Jul-2008
http://string.embl.de/newstring_download/protein.links.v7.1.txt.gz 03-Oct-2007 10-Jul-2008
http://string.embl.de/string_protected_download/protein.links.detailed.v7.1.txt.gz 03-Oct-2007 11-Jul-2008
http://wombat.gnf.org/downloads/gnf1h-anntable.zip 15-Aug-2005 09-Jul-2008
http://wombat.gnf.org/downloads/GNF1Hdata.zip 03-May-2005 09-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu133a.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu133a2.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu133b.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu133plus2.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu95a.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu95av2.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu95b.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu95c.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu95d.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu95e.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/mgu74a.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/mgu74av2.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/mouse4302.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/rae230a.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/rat2302.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.bioconductor.org/packages/2.3/data/annotation/src/contrib/rgu34a.db_2.2.0.tar.gz 28-Apr-2008 10-Jul-2008
http://www.cbil.upenn.edu/downloads/DoTS/current_human/humDoTS_DTToGeneId.dat.gz 10-Mar-2008 09-Jul-2008
http://www.cbil.upenn.edu/downloads/DoTS/current_mouse/musDoTS_DTToGeneId.dat.gz 06-Apr-2007 09-Jul-2008
http://www.genenames.org/cgi-bin/hgnc_downloads.cgi 13-Aug-2008
http://www.orthomcl.org/common/downloads/2/groups_orthomcl-2.txt 27-Feb-2008 09-Jul-2008
http://www.orthomcl.org/common/downloads/2/seqs_id_map_orthomcl-2.txt 07-May-2008 09-Jul-2008
http://www.peptideatlas.org/builds/human/HumanP0.9/200704/APD_ensembl_hits.tsv 13-Apr-2007 09-Jul-2008
http://www.peptideatlas.org/builds/human/plasma/data/2007_04/PA_HsP_2007-04_Ens43_P0.9_pep2prot.tsv 13-Apr-2007 09-Jul-2008
http://www.reactome.org/download/current/homo_sapiens.interactions.txt.gz 24-Jun-2008 10-Jul-2008
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