A reference index for protein interaction data
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.
iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.
The iRefIndex paper has been published and is available here.
Data availability and download
A subset of iRefIndex data is provided as a tab-delimited text file in PSI-MITAB format. There is no web-interface nor web services at this time.
Data is available via anonymous ftp at:
Password: enter anonymous or your email address
Data format and help
iRefIndex data is provided as a tab-delimited text file in PSI-MITAB 2.5 format. The format is described at
iRefIndex data is provided as a single file or in a number of data sets specific to the organism in which the interaction occurs. See the above link for details.
Source data for the current build is described at
If you need help, see the contact at the bottom of this page.
Data availability and license
iRefIndex data distributed on the FTP site includes only those data that may be freely distributed under the copyright license of the source database. This includes data from BIND, BioGRID, IntAct, MINT, MPPI and OPHID.
Data released on the public ftp site is released under Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/
iRefIndex also integrates data from DIP, HPRD and MPact. These data are not distributed publicly. These data may be made available to academic users under a collaborative agreement.
Contact ian.donaldson at biotek.uio.no if you are interested in using the iRefIndex database or would like your database included in the public release of the index.
Data is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Statistics for the iRefIndex include a breakdown of interactors and interactions from each data source.
For statistics on the public dataset (distributed on the FTP site contains) please refer to:
This data set contains 77,745 distinct proteins and 310665 distinct interactions and complexes.
The iRefIndex was developed at the Biotechnology Centre of Oslo, University of Oslo in the Donaldson lab by Sabry Razick and Ian Donaldson. George Magklaras provided systems engineer support and EMBNet Norway provided hardware support.
iRefIndex has been published and is available here. If you use iRefIndex, please cite:
Razick S, Magklaras G, Donaldson IM: iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics. 2008. 9(1):405 PMID 18823568.
and the source databases described below. Please contact ian.donaldson at biotek.uio.no if you would like an advance copy of the paper.
iRefIndex consolidates protein interaction data from
MPPI  and
iRefIndex uses SEGUID based identifiers to group proteins into redundant groups. The SEGUID algorithm and database are described in .
Suggestions, requests and comments are welcome. Please email
ian.donaldson at biotek.uio.no.
Visiting and mail address info is here.
iRefIndex Google Group
Join the iRefIndex Google group and receive announcement emails and discuss issues related to iRefIndex. Sign up at irefindex google group.