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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 2.4.0, 21-Apr-2009
BioGRID Version 2.0.56, 01-Sep-2009
Database of Interacting Proteins (DIP) 26-Jan-2009
DoTS (Database Of Transcribed Sequences) human Release 9, 10-Mar-2008
mouse Release 10, 10-Mar-2008
Ensembl Release 54, May-2009
Gene Ontology Consortium Version 1.793, 17-Sept-2009
Genetic Association Database 01-Oct-2007
HUGO Gene Nomenclature Committee information not available
Human Protein Reference Database (HPRD) Release 8, 06-July-2009
InParanoid: Eukaryotic Ortholog Groups Version 7.0, 28-Jun-2009
IntAct 08-Sep-2009
IPI (International Protein Index) Version 3.60, 17-Jun-2009
KEGG: Kyoto Encyclopedia of Genes and Genomes Release 50, 01-Apr-2009
MINT: a Molecular INTeraction database BINARY 2.6, 31-Jul-2009
Mouse Genome Informatics (MGI), Jackson Laboratory 18-Sep-2009
NCBI Entrez Gene 16-Sep-2009
NCBI HomoloGene Release 63, 05-Dec-2008
NCBI UniGene human Build #219, 30-Mar-2009
mouse Build #180, 30-Jul-2009
rat Build #180, 30-Mar-2009
OMIM, Online Mendelian Inheritance in Man information not available
OrthoMCL Version 2.0, 28-Feb-2008
PeptideAtlas Mar-2009
Rat Genome Database 15-Sep-2009
Reactome - a curated knowledgebase of biological pathways Version 29, 24-Jun-2009
Sanger Interaction Map 13-Aug-2004
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) Version 8.1
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 15.7, 01-Sep-2009

File Update Date Download Date
ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip 4-Nov-2009 9-Nov-2009
ftp://ftp.ebi.ac.uk/pub/databases/IPI/old/HUMAN/ipi.HUMAN.v3.60.dat.gz 17-Jun-2009 9-Nov-2009
ftp://ftp.ebi.ac.uk/pub/databases/IPI/old/MOUSE/ipi.MOUSE.v3.60.dat.gz 17-Jun-2009 9-Nov-2009
ftp://ftp.ebi.ac.uk/pub/databases/IPI/old/RAT/ipi.RAT.v3.60.dat.gz 17-Jun-2009 9-Nov-2009
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/hsapiens_gene_ensembl__homolog_Mmus__dm.txt.gz 1-May-2009 9-Nov-2009
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/hsapiens_gene_ensembl__homolog_Rnor__dm.txt.gz 1-May-2009 9-Nov-2009
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/mmusculus_gene_ensembl__homolog_Hsap__dm.txt.gz 1-May-2009 9-Nov-2009
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/mmusculus_gene_ensembl__homolog_Rnor__dm.txt.gz 1-May-2009 9-Nov-2009
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/rnorvegicus_gene_ensembl__homolog_Hsap__dm.txt.gz 1-May-2009 9-Nov-2009
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/rnorvegicus_gene_ensembl__homolog_Mmus__dm.txt.gz 1-May-2009 9-Nov-2009
ftp://ftp.expasy.org/databases/enzyme/enzyme.dat 4-Nov-2009 9-Nov-2009
ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo 7-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/ko 7-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ko.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ncbi-geneid.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_pathway.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ko.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ncbi-geneid.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_pathway.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ko.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ncbi-geneid.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_pathway.list 8-Nov-2009 9-Nov-2009
ftp://ftp.genome.ad.jp/pub/kegg/pathway_gif/map_title.tab 17-Jun-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human1.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human2.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human3.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human4.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat1.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat2.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat3.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat4.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman1.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman2.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman3.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman4.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.informatics.jax.org/pub/reports/MGI_EntrezGene.rpt 7-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz 9-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz 9-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz 9-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz 9-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2unigene 4-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz 9-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz 9-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene 9-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/gene/DATA/README 16-Sep-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build63/homologene.data 9-Jan-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z 9-Nov-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz 29-Oct-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.retired.lst.gz 29-Oct-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz 29-Oct-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.retired.lst.gz 29-Oct-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.data.gz 19-Oct-2009 9-Nov-2009
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.retired.lst.gz 19-Oct-2009 9-Nov-2009
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/archive/Hs36.3 27-Mar-2009 9-Nov-2009
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/archive/Mm37.1 9-Nov-2009
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/complete.txt.gz 26-Apr-2004 9-Nov-2009
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/core.txt.gz 26-Apr-2004 9-Nov-2009
ftp://ftp.uniprot.org/pub/databases/uniprot_datafiles_by_format/flatfile/uniprot_sprot.dat.gz 3-Nov-2009 9-Nov-2009
ftp://ftp.uniprot.org/pub/databases/uniprot_datafiles_by_format/flatfile/uniprot_trembl.dat.gz 3-Nov-2009 9-Nov-2009
ftp://ftp1.nci.nih.gov/pub/CGAP/Hs_GeneData.dat 3-Nov-2009 9-Nov-2009
ftp://ftp1.nci.nih.gov/pub/CGAP/Mm_GeneData.dat 3-Nov-2009 9-Nov-2009
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz 5-Sep-2008 9-Nov-2009
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz 13-Apr-2006 9-Nov-2009
ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz 22-Aug-2007 9-Nov-2009
ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/cytoBand.txt.gz 22-Aug-2007 9-Nov-2009
ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/chromInfo.txt.gz 21-Jun-2006 9-Nov-2009
ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/cytoBand.txt.gz 21-Jun-2006 9-Nov-2009
ftp://mint.bio.uniroma2.it/pub/release/MITAB/current/2009-04-14-mint-Mammalia.mitab25.txt 14-Apr-2009 9-Nov-2009
ftp://rgd.mcw.edu/pub/data_release/GENES_HUMAN 3-Nov-2009 9-Nov-2009
ftp://rgd.mcw.edu/pub/data_release/GENES_MOUSE 3-Nov-2009 9-Nov-2009
ftp://rgd.mcw.edu/pub/data_release/GENES_RAT 3-Nov-2009 9-Nov-2009
ftp://rgd.mcw.edu/pub/data_release/RGD_ORTHOLOGS 6-Nov-2009 9-Nov-2009
http://banon.cshl.edu:5555/biomart/martservice 9-Nov-2009
http://geneticassociationdb.nih.gov/all.xls 9-Nov-2009
http://inparanoid.sbc.su.se/download/7.0_current/table_stats/InParanoid.H.sapiens-M.musculus 23-Apr-2009 9-Nov-2009
http://inparanoid.sbc.su.se/download/7.0_current/table_stats/InParanoid.H.sapiens-R.norvegicus 23-Apr-2009 9-Nov-2009
http://inparanoid.sbc.su.se/download/7.0_current/table_stats/InParanoid.M.musculus-R.norvegicus 23-Apr-2009 9-Nov-2009
http://mips.gsf.de/proj/ppi/data/mppi.gz 9-Nov-2009
http://string.embl.de/newstring_download/protein.links.v8.2.txt.gz 9-Nov-2009
http://string.embl.de/string_protected_download/protein.links.detailed.v8.2.txt.gz 9-Nov-2009
http://wombat.gnf.org/downloads/gnf1h-anntable.zip 20-Mar-2009 9-Nov-2009
http://wombat.gnf.org/downloads/GNF1Hdata.zip 03-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu133a.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu133a2.db_2.2.11.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu133b.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu133plus2.db_2.2.11.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu95a.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu95av2.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu95b.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu95c.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu95d.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/hgu95e.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/lumiHumanIDMapping_1.2.1.tar.gz 16-Jun-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/lumiMouseIDMapping_1.2.1.tar.gz 16-Jun-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/lumiRatIDMapping_1.2.1.tar.gz 16-Jun-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/mgu74a.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/mgu74av2.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/mouse4302.db_2.2.11.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/rae230a.db_2.2.12.tar.gz 07-May-2009 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/rat2302.db_2.2.11.tar.gz 9-Nov-2009
http://www.bioconductor.org/packages/2.4/data/annotation/src/contrib/rgu34a.db_2.2.12.tar.gz 9-Nov-2009
http://www.cbil.upenn.edu/downloads/DoTS/release_10/hum/humDoTS_DTToGeneId.dat.gz 10-Mar-2008 9-Nov-2009
http://www.cbil.upenn.edu/downloads/DoTS/release_11/mus/musDoTS_DTToGeneId.dat.gz 06-Apr-2007 9-Nov-2009
http://www.genenames.org/cgi-bin/hgnc_downloads.cgi 9-Nov-2009
http://www.orthomcl.org/common/downloads/2/groups_orthomcl-2.txt.gz 9-Nov-2009
http://www.peptideatlas.org/builds/human/HumanP0.9/200704/APD_ensembl_hits.tsv 9-Nov-2009
http://www.peptideatlas.org/builds/human/plasma/data/2007_04/PA_HsP_2007-04_Ens43_P0.9_pep2prot.tsv 9-Nov-2009
http://www.reactome.org/download/current/homo_sapiens.interactions.txt.gz 23-Sep-2009 9-Nov-2009
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