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Bioinformatics Advance Access published online on November 7, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm518
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository

Tony Chiang a,b,*, Nianhua Li b,*, Sandra Orchard a, Samuel Kerrien a, Henning Hermjakob a, Robert Gentleman b and Wolfgang Huber a,{dagger}

aEBI-EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, bComputational Biology - FHCRC, 1100 Fairview Avenue North, M2-B876, Seattle, WA, USA 98109

* The First two authors contributed equally to this paper.


  Abstract

Motivation: The IntAct repository is one of the largest and most widely used databases for the curation and storage of molecular interaction data. These datasets need to be analyzed by computational methods. Software packages in the statistical environment R provide powerful tools for conducting such analyses.

Results: We introduce Rintact, a Bioconductor package that allows users to transform PSI-MI XML2.5 interaction data files from IntAct into R graph objects. On these, they can use methods from R and Bioconductor for a variety of tasks: determining cohesive subgraphs, computing summary statistics, fitting mathematical models to the data, or rendering graphical layouts. Rintact provides a programmatic interface to the IntAct repository and allows the use of the analytic methods provided by R and Bioconductor.

Availability: Rintact is freely available at http://bioconductor.org.

Contact: huber{at}ebi.ac.uk

Associate Editor: Prof.

{dagger}to whom correspondence should be addressed: Wolfgang Huber, E-mail: huber{at}ebi.ac.uk

Received on August 14, 2007; revised on October 10, 2007; accepted on October 10, 2007

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