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.

The iRefIndex paper has been published and is available here.

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iRefIndex Google Group

A new iRefIndex Google group has been set up. Join and receive announcement emails and discuss issues related to iRefIndex. Sign up at irefindex google group.

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

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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

http://irefindex.uio.no/wiki/README_iRefIndex_MITAB_1.1

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.

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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.

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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.

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Statistics

Statistics for the iRefIndex include a breakdown of interactors and interactions from each data source. These will be made available 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

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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.

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Citation

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. 9:405

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

BIND [1], [2],

BioGRID [3],

DIP [4],

HPRD [5], [6],

IntAct [7], [8],

MINT [9],

MPact [10],

MPPI [11] and

OPHID [12].

iRefIndex uses SEGUID based identifiers to group proteins into redundant groups. The SEGUID algorithm and database are described in [13].

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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.

Join the iRefIndex Google group and receive announcement emails and discuss issues related to iRefIndex. Sign up at irefindex google group.

Visiting and mail address info is here.