irefindex-new

	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. Read more
	Publications, citing, citations and further reading iRefIndex related publications, references for source databases and works citing and using the iRefIndex.
	Download Download iRefIndex version 8.0 in PSI-MITAB tab-delimited format via FTP.
	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 iRefIndex PSICQUIC web services are now running on release 8.0 of iRefIndex
	iRefIndex Videos
	Contact info
	Technical information on the iRefIndex database Source data sets: http://irefindex.uio.no/wiki/Sources_iRefIndex_8.0 Statistics: http://irefindex.uio.no/wiki/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
	fShare this page on Facebook .

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 here: iRefIndex_Citations

---

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.

Credits and collaborations

The iRefIndex was developed at the Biotechnology Centre of Oslo, University of Oslo in the Donaldson lab by Sabry Razick and Ian Donaldson. Paul Boddie provides ongoing maintenance and development support. George Magklaras provides systems engineer support and EMBNet Norway provided hardware support.

iRefR was developed by Antonio Mora.

Disease groups were developed by Katerina Michalickova.

iRefWeb was developed in collaboration with members of the Wodak group at the Hospital for Sick Children in Toronto, Canada.

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. Please email

ian.donaldson at biotek.uio.no.

Visiting and mail address info is here.

iRefIndex Google Group

Join the iRefIndex Google group and receive announcement emails and discuss issues related to iRefIndex. Sign up at irefindex google group.

All iRefIndex Pages

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