Sources iRefIndex 2.0

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Last edited: November 11th, 2008
Applies to iRefIndex release: beta 2.0
Release date: October 17th, 2008
Authors: Ian Donaldson and Sabry Razick
Database: iRefIndex (
Organization: Biotechnology Centre of Oslo, University of Oslo (


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.







These file are no longer available via ftp but are available from the authors. BIND archival content is now managed by Thomson Scientific. See and

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

via the at the internet archive at


BioGRID PSI-MI 2.5 Version 2.0.45
DIP PSI-MI 2.5 dip20080708.mif25 07/08/08
HPRD, PSI-MI 2.5 Release 7. September 01, 2007
IntAct, PSI-MI 2.5 August 22, 2008
MINT PSI-MI 2.5 ftp:// April 07, 2008
MPact PSI-MI 2.5 mpact-complete.psi25.xml April 19, 2007
MPPI PSI-MI 1.0 Not available
OPHID PSI-MI 1.0 (This service no longer available, please refer to 07/18/06

Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text seguidannotation September 23rd, 2008
UniProt Text 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 uniprot_sprot_varsplic.fasta.gz September 25th, 2008
UniProt, SGD Tab-delimited text file. Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD Release: 56.2 (September 23rd, 2008)
UniProt, FLY Tab-delimited text file. Drosophila: entries, gene names and cross-references to FlyBase. Release: 56.2 (September 25th, 2008)
NCBI, RefSeq GenPept see *.protein.gpff.gz files Release 31 (August 30, 2008)
NCBI, MMDB/PDB Tab-delimited text (Downloaded on October 08th,2008)
NCBI, PDB sequences FASTA (Downloaded on October 08th,2008)
NCBI Gene2Refseq Tab-delimited text gene2refseq.gz (Downloaded on October 08th,2008)