Version Information

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
BioGRID Version 3.1.81, 25-Sep-2011
Database of Interacting Proteins (DIP) 10-Oct-2010
DoTS (Database Of Transcribed Sequences) human Release 10, 21-Apr-2008
mouse Release 11, 21-Apr-2008
Ensembl Release 64, Sep-2011
Gene Ontology Consortium Version 1.0, 05-Oct-2011
Genetic Association Database 01-Aug-2011
HUGO Gene Nomenclature Committee 06-Oct-2011
Human Protein Reference Database (HPRD) Release 9, 13-Apr-2010
InParanoid: Eukaryotic Ortholog Groups Version 7.0, 28-Jun-2009
IntAct 01-10-2011
KEGG: Kyoto Encyclopedia of Genes and Genomes Release 58.1, 01-Jun-2011
MINT: a Molecular INTeraction database BINARY 2.6, 07-Jul-2011
Mouse Genome Informatics (MGI), Jackson Laboratory 05-Oct-2011
NCBI Entrez Gene 06-Oct-2011
NCBI HomoloGene Release 65, 14-Feb-2011
NCBI UniGene human Build #230, 21-Mar-2011
mouse Build #190, 25-Mar-2011
rat Build #189, 06-Dec-2010
OMIM, Online Mendelian Inheritance in Man information not available
OrthoMCL Version 5.0, 31-Mar-2010
PeptideAtlas May-2010
Rat Genome Database 06-Oct-2011
Reactome - a curated knowledgebase of biological pathways Version 36, 15-Mar-2011
Sanger Interaction Map 13-Aug-2004
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) Version 9.0
The MIPS Mammalian Protein-Protein Interaction Database information not available
UCSC Genome Bioinformatics (Golden Path) human UCSC hg19, GRC build h37, Feb-2009
mouse UCSC mm9, NCBI Build 37.1, July-2007
rat UCSC rn4, RGSC version 3.4, Nov-2004
UniProt (Universal Protein Resource) Release 2011_09, 21-Sep-2011

File Update Date Download Date
ftp/grcf.jhmi.edu/OMIM/omim.txt.Z
ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip 01-Oct-2011 06-Oct-2011
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_64/hsapiens_gene_ensembl__homolog_mmus__dm.txt.gz 12-Sep-2011 06-Oct-2011
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_64/hsapiens_gene_ensembl__homolog_rnor__dm.txt.gz 12-Sep-2011 06-Oct-2011
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_64/mmusculus_gene_ensembl__homolog_hsap__dm.txt.gz 12-Sep-2011 06-Oct-2011
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_64/mmusculus_gene_ensembl__homolog_rnor__dm.txt.gz 12-Sep-2011 06-Oct-2011
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_64/rnorvegicus_gene_ensembl__homolog_hsap__dm.txt.gz 12-Sep-2011 06-Oct-2011
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_64/rnorvegicus_gene_ensembl__homolog_mmus__dm.txt.gz 12-Sep-2011 06-Oct-2011
ftp://ftp.expasy.org/databases/enzyme/enzyme.dat 14-Sep-2011 06-Oct-2011
ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo 06-Oct-2011 06-Oct-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/ko/ko
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ko.list
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ncbi-geneid.list
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_pathway.list
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ko.list
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ncbi-geneid.list
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_pathway.list
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ko.list
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ncbi-geneid.list
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_pathway.list
ftp://ftp.genome.ad.jp/pub/kegg/pathway/map_title.tab
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human1.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human2.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human3.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human4.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat1.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat2.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat3.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat4.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman1.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman2.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman3.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman4.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.informatics.jax.org/pub/reports/MGI_EntrezGene.rpt 05-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz 06-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz 06-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz 06-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz 06-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2unigene 06-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz 06-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz 06-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene 06-Oct-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/gene/DATA/README 15-Sep-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data 15-Feb-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz 31-May-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.retired.lst.gz 31-May-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz 06-Apr-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.retired.lst.gz 06-Apr-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.data.gz 29-Apr-2011 06-Oct-2011
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.retired.lst.gz 29-Apr-2011 06-Oct-2011
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human 07-Sep-2011 06-Oct-2011
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse 24-Jan-2011 06-Oct-2011
ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/data_export/CosmicHGNC_v55_130911.tsv 13-Sep-2011 06-Oct-2011
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/complete.txt.gz 26-Apr-2004 06-Oct-2011
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/core.txt.gz 26-Apr-2004 06-Oct-2011
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz 21-Sep-2011 06-Oct-2011
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.dat.gz 21-Sep-2011 06-Oct-2011
ftp://ftp1.nci.nih.gov/pub/CGAP/Hs_GeneData.dat 02-Jun-2011 06-Oct-2011
ftp://ftp1.nci.nih.gov/pub/CGAP/Mm_GeneData.dat 02-Jun-2011 06-Oct-2011
ftp://ftp1.nci.nih.gov/pub/PID/uniprot/uniprot.tab.gz 13-Sep-2011 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/chromInfo.txt.gz 22-Aug-2007 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/cytoBand.txt.gz 22-Aug-2007 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/knownToLocusLink.txt.gz 30-May-2011 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/chromInfo.txt.gz 21-Jun-2006 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/cytoBand.txt.gz 21-Jun-2006 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/knownToLocusLink.txt.gz 21-Jun-2006 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz 27-Apr-2009 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz 14-Jun-2009 06-Oct-2011
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownToLocusLink.txt.gz 06-Dec-2009 06-Oct-2011
ftp://mint.bio.uniroma2.it/pub/release/mitab26/current/2011-07-08-mint-Mammalia-binary.mitab26.txt 08-Jul-2011 06-Oct-2011
ftp://rgd.mcw.edu/pub/data_release/GENES_HUMAN.txt 01-Oct-2011 06-Oct-2011
ftp://rgd.mcw.edu/pub/data_release/GENES_MOUSE.txt 01-Oct-2011 06-Oct-2011
ftp://rgd.mcw.edu/pub/data_release/GENES_RAT.txt 01-Oct-2011 06-Oct-2011
ftp://rgd.mcw.edu/pub/data_release/RGD_ORTHOLOGS 28-Sep-2011 06-Oct-2011
http://banon.cshl.edu:5555/biomart/martservice 06-Oct-2011
http://geneticassociationdb.nih.gov/all.xls 06-Jul-2006 06-Oct-2011
http://inparanoid.sbc.su.se/download/current/table_stats/InParanoid.H.sapiens-M.musculus 29-Apr-2009 06-Oct-2011
http://inparanoid.sbc.su.se/download/current/table_stats/InParanoid.H.sapiens-R.norvegicus 29-Apr-2009 06-Oct-2011
http://inparanoid.sbc.su.se/download/current/table_stats/InParanoid.M.musculus-R.norvegicus 29-Apr-2009 06-Oct-2011
http://mips.gsf.de/proj/ppi/data/mppi.gz 01-Jun-2004 06-Oct-2011
http://string.embl.de/newstring_download/protein.links.detailed.v9.0.txt.gz 28-May-2011 06-Oct-2011
http://string.embl.de/newstring_download/protein.links.v9.0.txt.gz 29-May-2011 06-Oct-2011
http://www.cbil.upenn.edu/downloads/DoTS/current_human/humDoTS_DTToGeneId.dat.gz 10-Mar-2008 06-Oct-2011
http://www.cbil.upenn.edu/downloads/DoTS/current_mouse/musDoTS_DTToGeneId.dat.gz 06-Apr-2007 06-Oct-2011
http://www.genenames.org/cgi-bin/hgnc_downloads.cgi 06-Oct-2011
http://www.orthomcl.org/common/downloads/release-5/groups_OrthoMCL-5.txt.gz 15-Apr-2011 06-Oct-2011
http://www.peptideatlas.org/builds/human/201005/APD_ensembl_hits.tsv 29-May-2010 06-Oct-2011
http://www.peptideatlas.org/builds/human/plasma/201005/APD_ensembl_hits.tsv 27-Oct-2010 06-Oct-2011
http://www.reactome.org/download/current/homo_sapiens.interactions.txt.gz 19-Sep-2011 06-Oct-2011