Sources iRefIndex 3.0

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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 (

Organization: Biotechnology Centre of Oslo, University of Oslo (

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.







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 2.0.49
DIP PSI-MI 2.5 dip20090126.mif25 January 26, 2009
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
CORUM PSI-MI 2.5 ( 08/09/18

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 33 (January 20, 2009)
NCBI, MMDB/PDB Tab-delimited text (Downloaded on February 19, 2009)
NCBI, PDB sequences FASTA (Downloaded on February 19, 2009)
NCBI Gene2Refseq Tab-delimited text gene2refseq.gz (Downloaded on February 19, 2009)