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Sources iRefIndex 4.0

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Last edited:06th, June 2009

Applies to iRefIndex release: 4.0

Release date:06th, June 2009 Authors: Ian Donaldson,Sabry Razick and Paul Boddie

Database: iRefIndex (http://irefindex.uio.no)

Organization: Biotechnology Centre of Oslo, University of Oslo (http://www.biotek.uio.no/)

Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex. Statistics for the iRefIndex are available and include a breakdown of interactors and interactions from each data source. For statistics on full public dataset please refer to: http://irefindex.uio.no/wiki/Statistics_iRefIndex_4.0 For statistics on the public dataset (distributed on the FTP site contains) please refer to: http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_4.0

Interaction related resources

Source Format Location Version (date)
BIND, Tab-delimited text file. ftp://ftp.bind.ca/pub/BIND/data/bindflatfiles/bindindex/

20050525.complex2refs.txt

20050525.ints.txt

20050525.refs.txt

20050525.complexes.txt

20050525.labels.txt

20050525.complex2subunits.txt

These file are no longer available via ftp but are available from the authors. BIND archival content is now managed by Thomson Scientific. See http://bond.unleashedinformatics.com/ and http://bond.unleashedinformatics.com/downloads/data/BIND/

For historical purposes, a snapshot of the the Blueprint web-site may be viewed at...

http://web.archive.org/web/20050204013426/www.blueprint.org/index.html

...via the at the internet archive at...

http://web.archive.org/web/*/http://www.blueprint.org

05/25/05
BioGRID PSI-MI 2.5 http://www.thebiogrid.org/downloads.php Version 2.0.52
DIP PSI-MI 2.5 http://dip.doe-mbi.ucla.edu/dip/Download.cgi dip20090126.mif25 January 26, 2009
HPRD, PSI-MI 2.5 http://www.hprd.org/download/HPRD_SINGLE_PSIMI_090107.xml.tar.gz Release 7. September 01, 2007
IntAct, PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/2009-05-05/all.zip May 05, 2009
MINT PSI-MI 2.5 ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/ April 22, 2009
MPACT PSI-MI 2.5 ftp://ftpmips.gsf.de/yeast/PPI/mpact-complete.psi25.xml January 10, 2008
MPPI PSI-MI 1.0 http://mips.gsf.de/proj/ppi/data/mppi.gz Not available
OPHID PSI-MI 1.0 http://ophid.utoronto.ca/ophid/downloads.html (This service no longer available, please refer to http://ophid.utoronto.ca/ophidv2.201/) 07/18/06
CORUM PSI-MI 2.5 http://mips.gsf.de/genre/proj/corum/index.html (http://mips.gsf.de/genre/export/sites/default/corum/allComplexes.psimi.zip) Not available (time stamp of file September 08 2008)

Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/ seguidannotation September 23rd, 2008
UniProt Text http://www.uniprot.org/downloads : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz) UniProt Release 15.2 (05-May-2009)
UniProt, IsoForms FASTA http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz Release 15.2 (May 05th 2009)
UniProt, SGD Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?yeast.txt Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD Release:57.2 (May 05th 2009)
UniProt, FLY Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?fly.txt Drosophila: entries, gene names and cross-references to FlyBase. Release: 57.2 (May 05th 2009)
NCBI, RefSeq GenPept ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files Release 35 (May 4th, 2009)
NCBI, MMDB/PDB Tab-delimited text ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table (Downloaded on May 14th, 2009)
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz (Downloaded on May 14th, 2009)
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz (Downloaded on May 14th, 2009)