{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:47:01Z","timestamp":1778226421719,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.<\/jats:p>\n               <jats:p>Availability: The plug-in is freely available and can be downloaded at ftp:\/\/ftp.pantherdb.org\/CellDesigner\/plugins\/BioPAX\/<\/jats:p>\n               <jats:p>Contact: \u00a0huaiyumi@usc.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr586","type":"journal-article","created":{"date-parts":[[2011,10,22]],"date-time":"2011-10-22T02:14:00Z","timestamp":1319249640000},"page":"3437-3438","source":"Crossref","is-referenced-by-count":16,"title":["BioPAX support in CellDesigner"],"prefix":"10.1093","volume":"27","author":[{"given":"Huaiyu","family":"Mi","sequence":"first","affiliation":[{"name":"1 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 3Systems Biology Institute, Tokyo and 4Department of Biosciences and Informatics, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anushya","family":"Muruganujan","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 3Systems Biology Institute, Tokyo and 4Department of Biosciences and Informatics, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emek","family":"Demir","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 3Systems Biology Institute, Tokyo and 4Department of Biosciences and Informatics, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yukiko","family":"Matsuoka","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 3Systems Biology Institute, Tokyo and 4Department of Biosciences and Informatics, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akira","family":"Funahashi","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 3Systems Biology Institute, Tokyo and 4Department of Biosciences and Informatics, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroaki","family":"Kitano","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 3Systems Biology Institute, Tokyo and 4Department of Biosciences and Informatics, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, 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