Research article

iRefIndex: A consolidated protein interaction database with provenance

Sabry Razick^1,2 , George Magklaras¹ and Ian M Donaldson^1,3

¹The Biotechnology Centre of Oslo, University of Oslo, P.O. Box 1125 Blindern, 0317 Oslo, Norway

²Biomedical Research Group, Department of Informatics, University of Oslo, P.O. Box 1080 Blindern, 0316 Oslo, Norway

³Department for Molecular Biosciences, University of Oslo, P.O. Box 1041 Blindern, 0316 Oslo, Norway

author email corresponding author email

BMC Bioinformatics 2008, 9:405doi:10.1186/1471-2105-9-405

Published:	30 September 2008

Abstract

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 http://irefindex.uio.no webcite. This index may form the basis of alternative redundant groupings based on gene identifiers or near sequence identity groupings.