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 and OPHID.

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	Download Download version 13.0 of the iRefIndex in PSI-MITAB tab-delimited format.		iRefIndex Release Notes View release notes and news for each release of iRefIndex.
	Publications, citing, citations and further reading iRefIndex related publications, references for source databases and works citing and using the iRefIndex.
	iRefScape iRefScape is a plugin for Cytoscape that exposes iRefIndex data as a navigable graphical network.		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.
	iRefR An R package providing access to iRefIndex data.		Web services New psicquic webservices are now available at psicquic.irefindex.org. See the Web Services for iRefIndex page for more. PSISCORE web services are still discontinued for the time being.
	iRefIndex videos Video learning materials for iRefIndex, iRefScape and iRefWeb.		Contact information and mailing list How to get in touch with the developers.
	Source data information Details of all the different source databases that provide the foundation for iRefIndex.		Statistical information Statistics for the current iRefIndex release.

Technical information on the iRefIndex database

Build process: iRefIndex Manual

Feedback files: README iRefIndex Feedback

Mapping files: Protein identifier mapping

Normalization of MI cv terms: Mapping of terms to MI term ids - iRefIndex

Canonicalization: Canonicalization

Disease Groups: DiG: Disease groups

All iRefIndex pages and archived releases: see below

License and disclaimer: see below

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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.

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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-delimited text files, iRefWeb interface, iRefScape plugin for Cytoscape, PSICQUIC Web services, and an interface for the R programming language environment. See the links at the top of this page. For the license and disclaimer, see below.

Credits and collaborations

Ian Donaldson presently maintains iRefIndex

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

Paul Boddie rewrote the iRefIndex codebase in Bash, Python and PostgreSQL while at the Biotechnology Centre of Oslo, University of Oslo.

George Magklaras provided systems engineer support and EMBNet Norway provided hardware support while iRefIndex was hosted at the University of Oslo.

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.

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

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License and disclaimer

Data released on the public FTP site is released under the Creative Commons Attribution 2.5 Generic (CC BY 2.5) license.

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 and mailing list

Suggestions, requests and comments are welcome.

ian@donaldsonresearch.com

Full contact details are available at the group home page.

See the iRefIndex Google Group for announcements and discussion.

All iRefIndex Pages

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