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Bioinformatics Advance Access originally published online on September 23, 2008
Bioinformatics 2009 25(1):137-138; doi:10.1093/bioinformatics/btn501
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Integrating and annotating the interactome using the MiMI plugin for cytoscape

Jing Gao , Alex S. Ade , V. Glenn Tarcea , Terry E. Weymouth , Barbara R. Mirel , H.V. Jagadish and David J. States *

National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA

*To whom correspondence should be addressed.


  Abstract

Summary: The MiMI molecular interaction repository integrates data from multiple sources, resolves interactions to standard gene names and symbols, links to annotation data from GO, MeSH and PubMed and normalizes the descriptions of interaction type. Here, we describe a Cytoscape plugin that retrieves interaction and annotation data from MiMI and links out to multiple data sources and tools. Community annotation of the interactome is supported.

Availability: MiMI plugin v3.0.1 can be installed from within Cytoscape 2.6 using the Cytoscape plugin manager in ‘Network and Attribute I/0’ category. The plugin is also preloaded when Cytoscape is launched using Java WebStart at http://mimi.ncibi.org by querying a gene and clicking ‘View in MiMI Plugin for Cytoscape’ link.

Contact: dstates{at}umich.edu

Associate Editor: Trey Ideker

Received on August 12, 2008; revised on August 12, 2008; accepted on September 17, 2008

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