{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T06:37:27Z","timestamp":1779345447449,"version":"3.51.4"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: MiMI plugin v3.0.1 can be installed from within Cytoscape 2.6 using the Cytoscape plugin manager in \u2018Network and Attribute I\/0\u2019 category. The plugin is also preloaded when Cytoscape is launched using Java WebStart at http:\/\/mimi.ncibi.org by querying a gene and clicking \u2018View in MiMI Plugin for Cytoscape\u2019 link.<\/jats:p>\n               <jats:p>Contact: \u00a0dstates@umich.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn501","type":"journal-article","created":{"date-parts":[[2008,9,24]],"date-time":"2008-09-24T00:26:02Z","timestamp":1222215962000},"page":"137-138","source":"Crossref","is-referenced-by-count":99,"title":["Integrating and annotating the interactome using the MiMI plugin for cytoscape"],"prefix":"10.1093","volume":"25","author":[{"given":"Jing","family":"Gao","sequence":"first","affiliation":[{"name":"National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex S.","family":"Ade","sequence":"additional","affiliation":[{"name":"National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"V. Glenn","family":"Tarcea","sequence":"additional","affiliation":[{"name":"National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terry E.","family":"Weymouth","sequence":"additional","affiliation":[{"name":"National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barbara R.","family":"Mirel","sequence":"additional","affiliation":[{"name":"National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H.V.","family":"Jagadish","sequence":"additional","affiliation":[{"name":"National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David J.","family":"States","sequence":"additional","affiliation":[{"name":"National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,9,23]]},"reference":[{"key":"2023013110023115500_B1","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1093\/bioinformatics\/btl604","article-title":"BioNetBuilder: automatic integration of biological networks","volume":"23","author":"Avila-Campillo","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110023115500_B2","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1186\/1471-2105-7-497","article-title":"cPath: open source software for collecting, storing, and querying biological pathways","volume":"7","author":"Cerami","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013110023115500_B3","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1093\/bioinformatics\/btm032","article-title":"NetMatch: a Cytoscape plugin for searching biological networks","volume":"23","author":"Ferro","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110023115500_B4","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkl859","article-title":"Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together","volume":"35","author":"Jayapandian","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013110023115500_B5","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1093\/bioinformatics\/btm107","article-title":"Cyclone: java-based querying and computing with pathway\/genome databases","volume":"23","author":"Le Fevre","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110023115500_B6","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1038\/nbt1324","article-title":"The minimum information required for reporting a molecular interaction experiment (MIMIx)","volume":"25","author":"Orchard","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"2023013110023115500_B7","article-title":"Experiments in single and multi-document summarization using MEAD","volume-title":"First Document Understanding Conference.","author":"Radev","year":"2001"},{"key":"2023013110023115500_B8","doi-asserted-by":"crossref","first-page":"2193","DOI":"10.1093\/bioinformatics\/btm304","article-title":"The MiSink Plugin: Cytoscape as a graphical interface to the database of interacting proteins","volume":"23","author":"Salwinski","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110023115500_B9","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023013110023115500_B10","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1186\/1471-2105-7-176","article-title":"The Gaggle: an open-source software system for integrating bioinformatics software and data sources","volume":"7","author":"Shannon","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013110023115500_B11","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1093\/bioinformatics\/btl571","article-title":"SAGA: a subgraph matching tool for biological graphs","volume":"23","author":"Tian","year":"2007","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/1\/137\/48982205\/bioinformatics_25_1_137.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/1\/137\/48982205\/bioinformatics_25_1_137.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:51:41Z","timestamp":1675191101000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/1\/137\/301024"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,9,23]]},"references-count":11,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn501","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,1,1]]},"published":{"date-parts":[[2008,9,23]]}}}