Difference between revisions of "iRefIndex"

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default [[iRefIndex#A_reference_index_for_protein_interaction_data]]
 
default [[iRefIndex#A_reference_index_for_protein_interaction_data]]
 
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| '''About iRefIndex'''
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=== About iRefIndex ===
  
 
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.  
 
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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[[iRefIndex#A_reference_index_for_protein_interaction_data|Read more]]
 
[[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_Citations | Publications, citing, citations and further reading]] ===
  
 
iRefIndex related publications, references for source databases and works citing and using the iRefIndex.  
 
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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=== [[README_MITAB2.6_for_iRefIndex_8.0|Download]] ===
  
 
Download iRefIndex version 8.0 in PSI-MITAB tab-delimited format via FTP.
 
Download iRefIndex version 8.0 in PSI-MITAB tab-delimited format via FTP.
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=== [[iRefScape|iRefScape]] ===
  
 
iRefScape is a plugin for [http://www.cytoscape.org/ Cytoscape] that exposes iRefIndex data as a navigable graphical network.
 
iRefScape is a plugin for [http://www.cytoscape.org/ Cytoscape] that exposes iRefIndex data as a navigable graphical network.
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default [http://wodaklab.org/iRefWeb/]
 
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| [http://wodaklab.org/iRefWeb/ '''iRefWeb''']  
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=== [http://wodaklab.org/iRefWeb/ iRefWeb] ===
  
 
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.
 
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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default [[iRefR]]
 
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| [[iRefR|'''iRefR''']]  
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=== [[iRefR]] ===
  
 
An R package providing access to iRefIndex data.
 
An R package providing access to iRefIndex data.
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=== [[PSICQUIC|Web services]] ===
  
 
iRefIndex PSICQUIC web services are now running on release 8.0 of iRefIndex  
 
iRefIndex PSICQUIC web services are now running on release 8.0 of iRefIndex  
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| '''Technical information on the iRefIndex database'''
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Source data sets: http://irefindex.uio.no/wiki/Sources_iRefIndex_8.0
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== Technical information on the iRefIndex database ==
  
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Statistics: http://irefindex.uio.no/wiki/Statistics_iRefIndex_8.0
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Source data sets: [[Sources iRefIndex 8.0]]
  
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Build process: [[iRefIndex_Manual]]
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Statistics: [[Statistics iRefIndex 8.0]]
  
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Feedback files: [[README_iRefIndex_Feedback_8.0]]
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Build process: [[iRefIndex Manual]]
  
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Normalization of MI cv terms: [[Mapping_of_terms_to_MI_term_ids_-_iRefIndex_8.0]]
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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]]
  
 
Canonicalization: [[Canonicalization]]
 
Canonicalization: [[Canonicalization]]
  
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Disease Groups: [[DiG:_Disease_groups|'''DiG: Disease Groups''']]
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Disease Groups: [[DiG: Disease Groups]]
  
 
All iRefIndex pages and Archived releases: [[iRefIndex#All_iRefIndex_Pages | see below]]
 
All iRefIndex pages and Archived releases: [[iRefIndex#All_iRefIndex_Pages | see below]]
  
 
License and disclaimer: [[iRefIndex#License_and_disclaimer | see below]]
 
License and disclaimer: [[iRefIndex#License_and_disclaimer | see below]]
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== A reference index for protein interaction data ==
 
== A reference index for protein interaction data ==
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== Publications and further reading ==
 
== Publications and further reading ==
  
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iRefIndex related publications, references for source databases and works citing and using the iRefIndex are provided here: [[iRefIndex_Citations]]
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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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iRefIndex is a PSIMex partner: http://www.psimex.org
 
iRefIndex is a PSIMex partner: http://www.psimex.org
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Found in real-life: [http://www.biotek.uio.no/research/donaldson_group/ here].
 
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]
 
[http://groups.google.com/group/irefindex?hl=en '''iRefIndex Google Group''' Announcements and discussion]
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== All iRefIndex Pages ==
 
== All iRefIndex Pages ==

Revision as of 14:32, 17 October 2011


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iRefIndex logo.png
About this image

About iRefIndex

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.

The iRefScape plugin for Cytoscape has been published recently here.

Read more

pubmed-logo.png
About this image

Publications, citing, citations and further reading

iRefIndex related publications, references for source databases and works citing and using the iRefIndex.

download-icon.png
About this image

Download

Download iRefIndex version 8.0 in PSI-MITAB tab-delimited format via FTP.

CytoscapeLogo.png
About this image

iRefScape

iRefScape is a plugin for Cytoscape that exposes iRefIndex data as a navigable graphical network.

firefox.png
About this image

iRefWeb

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.

R-logo.jpg
About this image

iRefR

An R package providing access to iRefIndex data.

ws-icon.jpg
About this image

Web services

iRefIndex PSICQUIC web services are now running on release 8.0 of iRefIndex

Youtube-256.png
About this image

iRefIndex Videos

mail.png
About this image

Contact info

info.png
About this image

Technical information on the iRefIndex database

Source data sets: Sources iRefIndex 8.0

Statistics: Statistics iRefIndex 8.0

Build process: iRefIndex Manual

Feedback files: README iRefIndex Feedback_8.0

Normalization of MI cv terms: Mapping of terms to MI term ids - iRefIndex_8.0

Canonicalization: Canonicalization

Disease Groups: DiG: Disease Groups

All iRefIndex pages and Archived releases: see below

License and disclaimer: see below

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, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and 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.

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.

Publications and further reading

iRefIndex related publications, references for source databases and works citing and using the iRefIndex are provided on the iRefIndex Citations page.

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.

To this end, the iRefIndex project has three long term objectives:

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.
2) to consolidate interaction data from multiple sources.
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.
3) to provide feedback to source interaction databases.
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.

iRefIndex availability

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: see below.

Credits and collaborations

Sabry Razick and Ian Donaldson developed iRefIndex at the Biotechnology Centre of Oslo, University of Oslo.

Paul Boddie provides ongoing maintenance and development.

George Magklaras provides systems engineer support and EMBNet Norway provided hardware support.

Antonio Mora developed iRefR.

Katerina Michalickova developed Disease groups.

Brian Turner and Andrei Turinsky from the Wodak group at the Hospital for Sick Children in Toronto, Canada developed the iRefWeb interface.

IMEx logo webmedium.jpg
About this image

iRefIndex is a PSIMex partner: http://www.psimex.org

License and disclaimer

Data released on the public FTP site is released under Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/.


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.

Contact

Suggestions, requests and comments are welcome. 

ian.donaldson@biotek.uio.no

Found in real-life: here.

google-groups-logo.gif
About this image

iRefIndex Google Group Announcements and discussion

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).

Retrieved from "http://irefindex.vib.be/wiki/index.php?title=iRefIndex&oldid=3845"