Difference between revisions of "iRefIndex"

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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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=== About iRefIndex ===
 
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iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID.
 
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The iRefScape plugin for Cytoscape has been published recently [http://www.biomedcentral.com/1471-2105/12/388 here].
 
  
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[[iRefIndex#A_reference_index_for_protein_interaction_data|Read more]]
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=== [[iRefIndex_Citations | Publications, citing, citations and further reading]] ===
 
  
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iRefIndex related publications, references for source databases and works citing and using the iRefIndex.
 
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=== [[README_MITAB2.6_for_iRefIndex_8.0|Download]] ===
 
  
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Download iRefIndex version 8.0 in PSI-MITAB tab-delimited format via FTP.
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=== [[iRefScape|iRefScape]] ===
 
  
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iRefScape is a plugin for [http://www.cytoscape.org/ Cytoscape] that exposes iRefIndex data as a navigable graphical network.
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=== [[README_MITAB2.6_for_iRefIndex|Download]] ===
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Download version 16.0 of the iRefIndex in PSI-MITAB tab-delimited format.
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default [http://wodaklab.org/iRefWeb/]
 
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=== [http://wodaklab.org/iRefWeb/ iRefWeb] ===
 
  
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iRefWeb provides a searchable web interface to the iRefIndex.  This interface was developed as part of a collaboration with the Wodak group at the hospital for Sick Children in Toronto, Canada.
 
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=== [[iRefR]] ===
 
  
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An R package providing access to iRefIndex data.
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=== [[PSICQUIC|Web services]] ===
 
  
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iRefIndex PSICQUIC web services are now running on release 8.0 of iRefIndex
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=== [[iRefIndex#Contact|Contact information]] ===
 
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=== [[Sources_iRefIndex_8.0|Source data information]] ===
 
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== Technical information on the iRefIndex database ==
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Source data sets: [[Sources iRefIndex 8.0]]
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=== [[ iRefIndex more | More about iRefIndex ]] ===
  
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Statistics: [[Statistics iRefIndex 8.0]]
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More ways to access iRefIndex, documentation, release notes, citations and references, technical details, mailing list, contact and license.
  
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Build process: [[iRefIndex Manual]]
 
  
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Feedback files: [[README iRefIndex Feedback_8.0]]
 
  
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Normalization of MI cv terms: [[Mapping of terms to MI term ids - iRefIndex_8.0]]
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Canonicalization: [[Canonicalization]]
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Disease Groups: [[DiG: Disease Groups]]
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=== [[ Donaldson Research | More about Donaldson Research ]] ===
  
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All iRefIndex pages and Archived releases: [[iRefIndex#All_iRefIndex_Pages | see below]]
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Support for updates to and use of iRefIndex can be provided by Donaldson Research.
  
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License and disclaimer: [[iRefIndex#License_and_disclaimer | see below]]
 
  
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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://mips.gsf.de/genre/proj/corum/index.html CORUM], [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 includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods.  This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.
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iRefIndex assigns a global unique identifier (rigid) which looks like 'tjWXXjgPyHyT2J6EwED8zK2x18U' to identify interactions that are identical (according to the sequence and taxon ids of the interactors). iRefIndex also assigns similar looking keys to protein interactors.  These keys are global  meaning they can be generated by anyone using the method described in the paper. 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.
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== Publications and further reading ==
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=== [http://irefindex.vib.be  More about the VIB Bioinformatics Core] ===
  
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iRefIndex related publications, references for source databases and works citing and using the iRefIndex are provided on the [[iRefIndex Citations]] page.
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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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== Long term goals of the iRefIndex project ==
 
  
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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. 
 
  
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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.
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To this end, the iRefIndex project has three long term objectives:
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== Contact  ==
  
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;1) to facilitate exchange of interaction data between interaction databases. 
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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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: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.
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VIB Bioinformatics core [mailto:bits@vib.be] or Ian Donaldson [mailto:ian@donaldsonresearch.com email me]
  
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;2) to consolidate interaction data from multiple sources. 
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: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.
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[[Category:iRefIndex]]
  
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;3) to provide feedback to source interaction databases. 
 
  
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: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.
 
  
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== iRefIndex availability ==
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iRefIndex is made available in a number of formats: MITAB tab-delimted text files, web-interface, Cytoscape plugin, web-services. and R-interface  See the links at the top of this page.  License and disclaimer: [[iRefIndex#License_and_disclaimer | see below]].
 
  
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== Credits and collaborations ==
 
  
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'''Sabry Razick and Ian Donaldson''' developed iRefIndex at the Biotechnology Centre of Oslo, University of Oslo.  
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'''Paul Boddie''' provides ongoing maintenance and development.
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'''George Magklaras''' provides systems engineer support and [http://www.no.embnet.org/ EMBNet Norway] provided hardware support.
 
  
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'''Antonio Mora''' developed [[iRefR|iRefR]].
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=== [[ Donations | Donations welcome ]] ===
  
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'''Katerina Michalickova''' developed [[DiG:_Disease_groups|Disease groups]].
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About iRefIndex costs and donating.
  
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'''Brian Turner and Andrei Turinsky''' from the [http://wodaklab.org/ws/ Wodak group] at the Hospital for Sick Children in Toronto, Canada developed the [http://wodaklab.org/iRefWeb/ iRefWeb interface].
 
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iRefIndex is a PSIMex partner: http://www.psimex.org
 
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=== iRefWeb in the NCBI LinkOut programme ===
 
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Many [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] records provided by NCBI contain links to iRefWeb in the [http://www.ncbi.nlm.nih.gov/projects/linkout/index.html LinkOut] section, allowing users to consult iRefWeb for related protein interactions when browsing gene information. The software which exposes iRefIndex information to the LinkOut programme can be found on the [[iRefWeb LinkOut Generator]] page.
 
  
 
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== License and disclaimer==
 
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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/.
 
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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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== Contact  ==
 
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Suggestions, requests and comments are welcome.
 
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<pre>ian.donaldson@biotek.uio.no</pre>
 
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Found in real-life: [http://www.biotek.uio.no/research/donaldson_group/ here].
 
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[http://groups.google.com/group/irefindex?hl=en '''iRefIndex Google Group''' Announcements and discussion]
 
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== All iRefIndex Pages ==
 
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Follow this link for a listing of all iRefIndex related pages (archived and current).
 
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[[Category:iRefIndex]]
 

Revision as of 18:09, 28 December 2019


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 16.0 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



Retrieved from "http://irefindex.vib.be/wiki/index.php?title=iRefIndex&oldid=4401"