Proteomics Standard Initiative Common QUery InterfaCe for iRefIndex

New iRefIndex release

Background: The Computational Biology and Bioinformatics Initiative of VIB supports software projects of bioinformatics research groups at VIB. For the last project call, the lab of Shoshana Wodak has handed in a proposal to provide a new release of the iRefIndex database.
Results: In collaboration with Andrei Turinsky, Ian Donaldson, the VIB Bioinformatics Core has compiled a new release of the interaction reference index (iRefIndex 15). Furthermore, the PSICQUIC web service of this new version has been setup and is hosted on a virtual server at University of Ghent. We anticipate to release more regular updates in the future. Contact:
More information on the current version 19 at the iRefIndex wiki page

About iRefIndex

"Background: Interaction data for a given protein may be spread across multiple databases. We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping.
Results: We present a method to generate a key for a protein interaction record and a key for each participant protein. These keys may be generated by anyone using only the primary sequence of the proteins, their taxonomy identifiers and the Secure Hash Algorithm. Two interaction records will have identical keys if they refer to the same set of identical protein sequences and taxonomy identifiers. We define records with identical keys as a redundant group. Our method required that we map protein database references found in interaction records to current protein sequence records. Operations performed during this mapping are described by a mapping score that may provide valuable feedback to source interaction databases on problematic references that are malformed, deprecated, ambiguous or unfound. Keys for protein participants allow for retrieval of interaction information independent of the protein references used in the original records.
Conclusion: We have applied our method to protein interaction records from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. The resulting interaction reference index is provided in PSI-MITAB 2.5 format at This index may form the basis of alternative redundant groupings based on gene identifiers or near sequence identity groupings."

Razick, S., Magklaras, G., & Donaldson, I. M. (2008). iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics, 9(1), 405.


"The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement."

del-Toro, N., Dumousseau, M., Orchard, S., Jimenez, R. C., Galeota, E., Launay, G., … Hermjakob, H. (2013). A new reference implementation of the PSICQUIC web service. Nucleic Acids Research, 41(W1), W601–W606.

Access the WebService

The list of available service is available under