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Bioinformatics Advance Access originally published online on November 7, 2007
Bioinformatics 2008 24(8):1100-1101; doi:10.1093/bioinformatics/btm518
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© 2008 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 1,2,{dagger}, Nianhua Li 2,{dagger}, Sandra Orchard 1, Samuel Kerrien 1, Henning Hermjakob 1, Robert Gentleman 2 and Wolfgang Huber 1,*

1EBI-EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Computational Biology – FHCRC, 1100 Fairview Avenue North, M2-B876, Seattle, WA 98109, USA

*To whom correspondence should be addressed.


  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: Alfonso Valencia

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

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

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