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| − | <!--[[Image:IRefIndex_Small.PNG]]-->
| + | __NOTOC__ |
| − | [[Image:iRefIndex_logo.png|right|The current iRefIndex logo by Sabry Razick]]
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| − | == A reference index for protein interaction data ==
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| − | iRefIndex provides an index of protein interactions available in a number of primary interaction databases including [http://bond.unleashedinformatics.com/ BIND], [http://www.thebiogrid.org/ BioGRID], [http://dip.doe-mbi.ucla.edu/ DIP], [http://www.hprd.org/ HPRD], [http://www.ebi.ac.uk/intact/site/index.jsf IntAct], [http://mint.bio.uniroma2.it/mint/Welcome.do MINT], [http://mips.gsf.de/genre/proj/mpact MPact], [http://mips.gsf.de/proj/ppi/ MPPI] and [http://ophid.utoronto.ca/ OPHID]. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. | + | iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI, Reactome, VirHostnet, and QuickGO. |
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| − | iRefIndex uses the Sequence Global Unique Identifier ([http://bioinformatics.anl.gov/SEGUID/ 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.
| + | {|class="wikitable" style="text-align:left; clear: left" border="0" cellpadding="10" |
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| − | ---- | + | <!--Download row row--> |
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| | | | |
| − | == Data availability and download ==
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| − | 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.
| + | <!--Download image--> |
| | + | |<imagemap> |
| | + | Image:Document-save-80x80.png |
| | + | default [[README_MITAB2.6_for_iRefIndex]] |
| | + | desc none |
| | + | </imagemap> |
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| − | Data is available via anonymous ftp at:
| + | <!--Download link and text--> |
| | + | | style="vertical-align: top" | |
| | + | === [[README_MITAB2.6_for_iRefIndex|Download]] === |
| | + | Download version 20.0 of the iRefIndex in PSI-MITAB tab-delimited format. |
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| − | ftp://ftp.no.embnet.org/irefindex/data
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| − | Username: <tt>ftp</tt>
| + | <!--More about iRefIndex row--> |
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| − | Password: enter <tt>anonymous</tt> or your email address
| + | <!-- iRefIndex logo --> |
| | + | |<imagemap> |
| | + | Image:iRefIndex_logo.png|80x80px |
| | + | default [[ iRefIndex more ]] |
| | + | desc none |
| | + | </imagemap> |
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| − | ---- | + | <!-- iRefIndex more link and text --> |
| | + | | style="vertical-align: top" | |
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| − | == Data format and help == | + | === [[ iRefIndex more | More about iRefIndex ]] === |
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| − | iRefIndex data is provided as a tab-delimited text file in PSI-MITAB 2.5 format. The format is described at | + | More ways to access iRefIndex, documentation, release notes, citations and references, technical details, mailing list, contact and license. |
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| − | ftp://ftp.no.embnet.org/irefindex/data/current/README
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| − | This file can also be viewed [http://biotin.uio.no/wiki/Readme here].
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| − | 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.
| + | <!--More about Donaldson Research row--> |
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| − | Source data for the current build is described at
| + | <!-- donaldson research logo --> |
| | + | |<imagemap> |
| | + | Image:donaldson_research_logo.png|80x80px |
| | + | default [[ Donaldson Research ]] |
| | + | desc none |
| | + | </imagemap> |
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| − | ftp://ftp.no.embnet.org/irefindex/data/current/sources.htm.
| + | <!-- iRefIndex more link and text --> |
| | + | | style="vertical-align: top" | |
| | + | === [[ Donaldson Research | More about Donaldson Research ]] === |
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| − | This file can also be viewed [ftp://ftp.no.embnet.org/irefindex/data/current/sources.htm here].
| + | Support for updates to and use of iRefIndex can be provided by Donaldson Research. |
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| − | If you need help, see the contact at the bottom of this page.
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| | | | |
| − | ---- | + | <!--More about VIB row--> |
| | + | |- |
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| − | == Data availability and license ==
| + | <!-- VIB logo --> |
| | + | |<imagemap> |
| | + | Image:donaldson_research_logo.png|80x80px |
| | + | default [[ Donaldson Research ]] |
| | + | desc none |
| | + | </imagemap> |
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| − | 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.
| + | <!-- VIB more link and text --> |
| | + | | style="vertical-align: top" | |
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| − | Data released on the public ftp site is released under Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/
| + | === [http://irefindex.vib.be More about the VIB Bioinformatics Core] === |
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| − | 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. | + | The iRefIndex site is now hosted at the VIB Bioinformatics Core including [http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS PSICQUIC webservices] that can be accessed [https://irefindex.vib.be/webservices here] using either SOAP or REST. |
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| − | Contact <tt>ian.donaldson at biotek.uio.no</tt> 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 ==
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| − |
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| − | 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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| | ---- | | ---- |
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| − | == Statistics == | + | == Contact == |
| − | | |
| − | Statistics for the iRefIndex include a breakdown of interactors and interactions from each data source. These will be made available in the paper.
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| − | | |
| − | Number of non-redundant proteins: 77,827
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| − | | |
| − | Number of non-redundant interactions and complexes: 318,349
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| − | | |
| − | The public dataset distributed on the FTP site contains:
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| − | Number of non-redundant proteins: 74,423
| + | If you have comments, questions or would like to be added to a list receiving news of updates, please write to us at: |
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| − | Number of non-redundant interactions and complexes: 284,310
| + | VIB Bioinformatics core [mailto:bits@vib.be] or Ian Donaldson [mailto:ian@donaldsonresearch.com email me] |
| | | | |
| | ---- | | ---- |
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| − | == Credits ==
| + | [[Category:iRefIndex]] |
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| − | 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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| − | ----
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| − | == Citation ==
| + | <!-- |
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| − | iRefIndex has been submitted for publication. If you use iRefIndex, please cite iRefIndex: http://irefindex.uio.no and the source databases described below.
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| − | iRefIndex consolidates protein interaction data from
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| − | BIND [[#ref1|[1]]], [[#ref2|[2]]],
| + | |<html> |
| | + | <form action="https://www.paypal.com/cgi-bin/webscr" method="post" target="_top"> |
| | + | <input type="hidden" name="cmd" value="_s-xclick"> |
| | + | <input type="hidden" name="hosted_button_id" value="EE635XFGX4E8L"> |
| | + | <input type="image" src="https://www.paypalobjects.com/en_US/NO/i/btn/btn_donateCC_LG.gif" border="0" name="submit" alt="PayPal - The safer, easier way to pay online!"> |
| | + | <img alt="" border="0" src="https://www.paypalobjects.com/en_US/i/scr/pixel.gif" width="1" height="1"> |
| | + | </form> |
| | + | </html> |
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| − | BioGRID [[#ref3|[3]]],
| + | | style="vertical-align: top" | |
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| − | DIP [[#ref4|[4]]],
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| − | HPRD [[#ref5|[5]]], [[#ref6|[6]]],
| + | === [[ Donations | Donations welcome ]] === |
| − | | |
| − | IntAct [[#ref7|[7]]], [[#ref8|[8]]],
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| − | | |
| − | MINT [[#ref9|[9]]],
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| − | | |
| − | MPact [[#ref10|[10]]],
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| − | | |
| − | MPPI [[#ref11|[11]]] and
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| − | | |
| − | OPHID [[#ref12|[12]]].
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| − | | |
| − | iRefIndex uses SEGUID based identifiers to group proteins into redundant groups. The SEGUID algorithm and database are
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| − | described in [[#ref13|[13]]].
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| − | | |
| − | ----
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| − | | |
| − | == References ==
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| − | | |
| − | <div id="ref1">1. Bader GD, Betel D, Hogue CW: '''BIND: the Biomolecular Interaction Network Database'''. Nucleic Acids Res 2003, 31(1):248-250.</div>
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| − | <div id="ref2">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.</div>
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| − | <div id="ref3">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.</div>
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| − | <div id="ref4">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.</div>
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| − | <div id="ref5">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.</div>
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| − | <div id="ref6">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.</div>
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| − | <div id="ref7">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.</div>
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| − | <div id="ref8">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.</div>
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| − | <div id="ref9">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.</div>
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| − | <div id="ref10">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.</div>
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| − | | |
| − | <div id="ref11">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.</div>
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| − | <div id="ref12">12. Brown KR, Jurisica I: '''Online predicted human interaction database'''. Bioinformatics 2005, 21(9):2076-2082.</div>
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| − | | |
| − | <div id="ref13">13. Babnigg G, Giometti CS: '''A database of unique protein sequence identifiers for proteome studies'''. Proteomics 2006, 6(16):4514-4522.</div>
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| − | | |
| − | == Contact ==
| |
| | | | |
| − | Suggestions, requests and comments are welcome. Please email
| + | About iRefIndex costs and donating. |
| | | | |
| − | ian.donaldson at biotek.uio.no.
| |
| | | | |
| − | Visiting and mail address info is [http://www.biotek.uio.no/research_groups/donaldson_group.html here].
| + | --> |
