Difference between revisions of "iRefIndex"

From irefindex
 
(224 intermediate revisions by 4 users not shown)
Line 1: Line 1:
<!--[[Image:IRefIndex_Small.PNG]]-->
+
__NOTOC__
[[Image:iRefIndex_logo.png|right|The current iRefIndex logo by Sabry Razick]]
 
== A reference index for protein interaction data ==
 
  
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.  
  
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"
  
The iRefIndex paper has been published and is available [http://www.biomedcentral.com/1471-2105/9/405/abstract here].
+
<!--Download row row-->
 +
|-
  
----
 
 
== Long term goals of the iRefIndex project ==
 
 
We believe that protein interaction data hold incredible potential for biomedical research.  Presently, these data are collected and archived by multiple groups around the world and the number of groups taking part in this work is growing rather than diminishing. 
 
  
As such, it is important that these databases have the means to effectively exchange and compare data and that they are curating and representing data using similar standards in order to make their data accessible and allow effective use.
+
<!--Download image-->
 +
|<imagemap>
 +
Image:Document-save-80x80.png
 +
default [[README_MITAB2.6_for_iRefIndex]]
 +
desc none
 +
</imagemap>
  
To this end, the iRefIndex project has three long term objectives:
+
<!--Download link and text-->
 +
| style="vertical-align: top" |
 +
=== [[README_MITAB2.6_for_iRefIndex|Download]] ===
 +
Download version 17.0 of the iRefIndex in PSI-MITAB tab-delimited format.
  
;1) to facilitate exchange of interaction data between interaction databases. 
 
  
:The iRefIndex paper describes a method for assigning unique and global identifiers to protein interactors, interactions and complexes.  This method is independent of the iRefIndex resource and may be used by anyone to facilitate exchange and consolidation of data.
+
<!--More about iRefIndex row-->
 +
|-
  
;2) to consolidate interaction data from multiple sources.
+
<!-- iRefIndex logo -->
 +
|<imagemap>
 +
Image:iRefIndex_logo.png|80x80px
 +
default [[ iRefIndex more ]]
 +
desc none
 +
</imagemap>
  
:The method has been used by to index interaction records from multiple sources.  The resulting iRefIndex may be used search for the existence of interaction data for any protein regardless of the original resource.  Nine interaction databases have been incorporated so far, others will follow.
+
<!-- iRefIndex more link and text -->
 +
| style="vertical-align: top" |
  
;3) to provide feedback to source interaction databases. 
+
=== [[ iRefIndex more | More about iRefIndex ]] ===
  
:During the process of data consolidation, iRefIndex uses a sophisticated method to keep track of potential problems with source records such as outdated or unfound protein identifiers or incorrectly assigned taxonomy identifiers.  These data are provided as feedback files to source interaction databases for correction, clarification or improvements to our own system.  This process will help to harmonize data representation and improve the overall quality of interaction records for all source databases.  This process will also help source databases to exchange data with one another.
+
More ways to access iRefIndex, documentation, release notes, citations and references, technical details, mailing list, contact and license.
  
== Data availability and download ==
 
  
A subset of iRefIndex data is provided as a tab-delimited text file in PSI-MITAB format.
 
  
Data is available via anonymous ftp at:
+
<!--More about Donaldson Research row-->
 +
|-
  
ftp://ftp.no.embnet.org/irefindex/data
+
<!-- donaldson research logo -->
 +
|<imagemap>
 +
Image:donaldson_research_logo.png|80x80px
 +
default [[ Donaldson Research ]]
 +
desc none
 +
</imagemap>
  
Username: <tt>ftp</tt>
+
<!-- iRefIndex more link and text -->
 +
| style="vertical-align: top" |
 +
=== [[ Donaldson Research | More about Donaldson Research ]] ===
  
Password: enter <tt>anonymous</tt> or your email address
+
Support for updates to and use of iRefIndex can be provided by Donaldson Research.
  
There is no web-interface nor web services at this time.  However, a beta Cytoscape plugin is available for testing purposes.
 
See [[README_Cytoscape_plugin_3.0_Beta]] for more details.
 
  
----
+
<!--More about VIB row-->
 +
|-
  
== Data format and help ==
+
<!-- VIB logo -->
 +
|<imagemap>
 +
Image:donaldson_research_logo.png|80x80px
 +
default [[ Donaldson Research ]]
 +
desc none
 +
</imagemap>
  
iRefIndex data is provided as a tab-delimited text file in PSI-MITAB 2.5 format. The format is described at
+
<!-- VIB more link and text -->
 +
| style="vertical-align: top" |
  
http://irefindex.uio.no/wiki/README_iRefIndex_MITAB_2.0
+
=== [http://irefindex.vib.be More about the VIB Bioinformatics Core] ===
   
 
  
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.
+
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.  
  
Source data for the current build is described at
+
|}
  
http://irefindex.uio.no/wiki/Sources_iRefIndex_2.0
 
  
 
If you need help, see the contact at the bottom of this page.
 
  
 
----
 
----
  
== Data availability and license ==
+
== Contact ==
 
 
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 <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.
 
 
 
----
 
 
 
== 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.
 
 
 
For statistics on the public dataset (distributed on the FTP site contains) please refer to:
 
http://irefindex.uio.no/wiki/Statistics_iRefIndex_2.0 <br>
 
This data set contains 77,745 distinct proteins and 310665 distinct interactions and complexes.
 
 
 
----
 
 
 
== 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 published and is available [http://www.biomedcentral.com/1471-2105/9/405/abstract 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.
 
  
 +
If you have comments, questions or would like to be added to a list receiving news of updates, please write to us at:
  
and the source databases described below.  Please contact ian.donaldson at biotek.uio.no if you would like an advance copy of the paper.
+
VIB Bioinformatics core [mailto:bits@vib.be] or Ian Donaldson [mailto:ian@donaldsonresearch.com email me]  
 
 
iRefIndex consolidates protein interaction data from
 
 
 
BIND [[#ref1|[1]]], [[#ref2|[2]]],
 
 
 
BioGRID [[#ref3|[3]]],
 
 
 
DIP [[#ref4|[4]]],
 
 
 
HPRD [[#ref5|[5]]], [[#ref6|[6]]],
 
 
 
IntAct [[#ref7|[7]]], [[#ref8|[8]]],
 
 
 
MINT [[#ref9|[9]]],
 
 
 
MPact [[#ref10|[10]]],
 
 
 
MPPI [[#ref11|[11]]] and
 
 
 
OPHID [[#ref12|[12]]].
 
 
 
iRefIndex uses SEGUID based identifiers to group proteins into redundant groups.  The SEGUID algorithm and database are
 
described in [[#ref13|[13]]].
 
  
 
----
 
----
  
== References ==
+
[[Category:iRefIndex]]
 
 
<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>
 
 
 
<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>
 
 
 
<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>
 
 
 
<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>
 
 
 
<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>
 
 
 
<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>
 
 
 
<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>
 
 
 
<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>
 
 
 
<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>
 
  
<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>
 
  
<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>
 
  
<div id="ref12">12. Brown KR, Jurisica I: '''Online predicted human interaction database'''. Bioinformatics 2005, 21(9):2076-2082.</div>
+
<!--
  
<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>
 
 
== Contact  ==
 
  
Suggestions, requests and comments are welcome. Please email
 
  
ian.donaldson at biotek.uio.no.
+
|<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>
  
 +
| style="vertical-align: top" |
  
  
Visiting and mail address info is [http://www.biotek.uio.no/research_groups/donaldson_group.html here].
+
=== [[ Donations | Donations welcome ]] ===
  
 +
About iRefIndex costs and donating.
  
== iRefIndex Google Group ==
 
  
Join the iRefIndex Google group and receive announcement emails and discuss issues related to iRefIndex.
+
-->
Sign up at [http://groups.google.com/group/irefindex?hl=en irefindex google group].
 

Latest revision as of 10:43, 1 July 2020


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.

Document-save-80x80.png

Download

Download version 17.0 of the iRefIndex in PSI-MITAB tab-delimited format.


iRefIndex logo.png

More about iRefIndex

More ways to access iRefIndex, documentation, release notes, citations and references, technical details, mailing list, contact and license.


donaldson research logo.png

More about Donaldson Research

Support for updates to and use of iRefIndex can be provided by Donaldson Research.


donaldson research logo.png

More about the VIB Bioinformatics Core

The iRefIndex site is now hosted at the VIB Bioinformatics Core including PSICQUIC webservices that can be accessed here using either SOAP or REST.



Contact

If you have comments, questions or would like to be added to a list receiving news of updates, please write to us at:

VIB Bioinformatics core [1] or Ian Donaldson email me