{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:43:31Z","timestamp":1761237811821},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,3]],"date-time":"2016-10-03T00:00:00Z","timestamp":1475452800000},"content-version":"vor","delay-in-days":1945,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions.<\/jats:p>\n               <jats:p>Results: The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and\/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and \u2018wet lab\u2019 scientists.<\/jats:p>\n               <jats:p>Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at http:\/\/bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.<\/jats:p>\n               <jats:p>Contact: \u00a0duccio.cavalieri@unifi.it; sorin@wayne.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr339","type":"journal-article","created":{"date-parts":[[2011,6,9]],"date-time":"2011-06-09T00:23:48Z","timestamp":1307579028000},"page":"2127-2133","source":"Crossref","is-referenced-by-count":19,"title":["The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways"],"prefix":"10.1093","volume":"27","author":[{"given":"Luca","family":"Beltrame","sequence":"first","affiliation":[{"name":"1 Department of Pharmacology \u2018M.Aiazzi Mancini\u2019, University of Firenze, 50139 Firenze, 2Department of Biology, University of Padua, 35121 Padova, Italy, 3Miravtech Corporation, Troy 48083, 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