Sources iRefIndex 4.0

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)