iRefIndex
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.
Contents
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:
ftp://ftp.no.embnet.org/irefindex/data
Username: ftp
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
ftp://ftp.no.embnet.org/irefindex/data/current/README
This file can also be viewed Readme here.
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
ftp://ftp.no.embnet.org/irefindex/data/current/sources.htm.
This file can also be viewed here.
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.
Disclaimer
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
Statistics for the iRefIndex include a breakdown of interactors and interactions from each data source. These will be made avaialable in the paper.
Number of non-redundant proteins: 77,827
Number of non-redundant interactions and complexes: 318,349
The public dataset distributed on the FTP site contains:
Number of non-redundant proteins: 74,423
Number of non-redundant interactions and complexes: 284,310
Credits
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.
Citation
iRefIndex has been submitted for publication. If you use iRefIndex, please cite iRefIndex: http://irefindex.uio.no and the source databases described below.
iRefIndex consolidates protein interaction data from
BIND[1, 2],
BioGRID[3],
DIP[4],
HPRD[5, 6],
IntAct[7, 8],
MINT[9],
MPact[10],
MPPI[11] and
OPHID[12].
References
1. Bader GD, Betel D, Hogue CW: BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 2003, 31(1):248-250.
2. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E et al: The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, 33(Database issue):D418-424.
3. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, 34(Database issue):D535-539.
4. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, 32(Database issue):D449-451.
5. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M et al: Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13(10):2363-2371.
6. Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM et al: Human protein reference database--2006 update. Nucleic Acids Res 2006, 34(Database issue):D411-414.
7. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A et al: IntAct: an open source molecular interaction database. Nucleic Acids Res 2004, 32(Database issue):D452-455.
8. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R et al: IntAct--open source resource for molecular interaction data. Nucleic Acids Res 2007, 35(Database issue):D561-565.
9. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G: MINT: the Molecular INTeraction database. Nucleic Acids Res 2007, 35(Database issue):D572-574.
10. Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V: MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res 2006, 34(Database issue):D436-441.
11. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW et al: The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21(6):832-834.
12. Brown KR, Jurisica I: Online predicted human interaction database. Bioinformatics 2005, 21(9):2076-2082.
13. Babnigg G, Giometti CS: A database of unique protein sequence identifiers for proteome studies. Proteomics 2006, 6(16):4514-4522.
Contact
Suggestions, requests and comments are welcome. Please email
ian.donaldson at biotek.uio.no.
Visiting and mail address info is here.
