Sources iRefIndex 6.0

Last edited:28th, December 2009

Applies to iRefIndex release: 6.0

Release date: 27th Oct 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_6.0
• For statistics on the public dataset (distributed on the FTP site contains) please refer to:http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_6.0

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 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/datasets/BIOGRID-ALL-SINGLEFILE-2.0.53.psi25.xml.gz	Version 2.0.53
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_070609.xml.tar.gz)	Release 8. July 06, 2009
IntAct,	PSI-MI 2.5	ftp://ftp.ebi.ac.uk/pub/databases/intact/2009-06-19/psi25/ (pmidMIF25.zip)	July 19, 2009
MINT	PSI-MI 2.5	ftp://mint.bio.uniroma2.it/pub/release/psi/2009-07-28/psi25/pmid/	July 28, 2009
MPACT	PSI-MI 2.5	ftp://ftpmips.gsf.de/yeast/PPI/ (mpact-complete.psi25.xml.gz)	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)
I2D	PSI-MI 2.5	http://ophid.utoronto.ca/ophidv2.201/downloads.jsp	(Not included in this release)

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 Download : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz)	UniProt Release 15.3 (May 26th 2009)
UniProt, IsoForms	FASTA	http://www.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz	Release 15.5 (July 07th 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:57.3 (May 26th 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: 57.3 (May 26th 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)