Sources iRefIndex 3.0

Last edited: March 9th, 2009

Applies to iRefIndex release: 3.0

Release date: March 9th, 2009

Authors: Ian Donaldson and Sabry Razick (with changes from 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.

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/BIOGRID-ORGANISM-2.0.49.psi25.zip	Version 2.0.49
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/2009-02-06/psi25/ pmidMIF25.zip	August 22, 2008
MINT	PSI-MI 2.5	ftp://ftp://mint.bio.uniroma2.it/pub/release/psi/2008-04-07/full.psi25.zip	April 07, 2008
MPact	PSI-MI 2.5	ftp://ftpmips.gsf.de/yeast/PPI/ mpact-complete.psi25.xml	April 19, 2007
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

Sequence related resources

Source	Format	Location	Version (date)
SEGUID	Tab-delimited text	ftp://bioinformatics.anl.gov/seguid/ seguidannotation	September 23rd, 2008
UniProt	Text	http://beta.uniprot.org/downloads Download : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz)	UniProt release 14.0 (September 02, 2008)
UniProt, IsoForms	FASTA	http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz	September 25th, 2008
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: 56.2 (September 23rd, 2008)
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: 56.2 (September 25th, 2008)
NCBI, RefSeq	GenPept	ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files	Release 33 (January 20, 2009)
NCBI, MMDB/PDB	Tab-delimited text	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table	(Downloaded on February 19, 2009)
NCBI, PDB sequences	FASTA	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz	(Downloaded on February 19, 2009)
NCBI Gene2Refseq	Tab-delimited text	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz	(Downloaded on February 19, 2009)