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Nucleic Acids Research Advance Access published online on October 31, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn722
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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.

Database Issue

Michigan molecular interactions r2: from interacting proteins to pathways

V. Glenn Tarcea, Terry Weymouth, Alex Ade, Aaron Bookvich, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Özgür, Yuanyuan Tian, Jim Cavalcoli, Barbara Mirel, Jignesh Patel, Dragomir Radev, Brian Athey, David States and H. V. Jagadish*

Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA

*To whom correspondence should be addressed. Tel: +1 734 763 4079; Fax: +1 734 763 8094; Email: jag{at}umich.edu

Received September 16, 2008. Accepted September 30, 2008.

Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases, and deep merged this information while keeping track of provenance. Based on the feedback received from users, MiMI has been completely redesigned. This article describes the resulting MiMI Release 2 (MiMIr2). New functionality includes extension from proteins to genes and to pathways; identification of highlighted sentences in source publications; seamless two-way linkage with Cytoscape; query facilities based on MeSH/GO terms and other concepts; approximate graph matching to find relevant pathways; support for querying in bulk; and a user focus-group driven interface design. MiMI is part of the NIH's; National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: http://mimi.ncibi.org.


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