A Cytoscape Plugin to Access the MiMI Molecular Interactions

Jing Gao, V. Glenn Tarcea, Alex Ade, Barbara Mirel, James Cavalcoli, Terry Weymouth, Brian Athey H.V. Jagadish and David States

National Center for Integrative Biomedical Informatics, University of Michigan, USA

The Cytoscape Plugin for MiMI retrieves data from the MiMI repository of molecular interactions developed by National Center for Integrative Biomedical Informatics (NCIBI) and displays the interaction networks using Cytoscape. Protein interaction data exists in many repositories, each with its own data format, molecule identifier and supplementary information. MiMI integrates data from multiple well-known protein interaction databases using an intelligent deep-merging approach. We implemented a Cytoscape plugin that facilitate access to the data assembled in MiMI. Users can launch the plugin with an interaction network from MiMI web site, and they can also link out from the plugin to MiMI web and other databases. This allows biological users to readily explore and analyze interaction data from MiMI. Our Cytoscape plugin also integrates with other biological tools and software developed by NCIBI including a full text sentence level index of PubMed and PubMed Central and SAGA, an effective and efficient method for approximate subgraph matching against biological pathways. Users can choose an interactions network to get nodes and edges match to KEGG pathways built in SAGA. For molecule and interaction annotation from MiMI database, the plugin offer an editor for users to edit and add their own annotation. Bi-direction communication between Cytoscape plugin and MiMI web is implemented allowing users to save annotations to a central repository and encouraging community annotation of molecular interactions.

Data keywords: protein-protein interaction, NCBI entrez gene Identifier, BioNLP, PubMed database, KEGG pathway

Cytoscape keywords: Network and Attribute I/O, Visual style, Layout, Attribute browser