{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,14]],"date-time":"2023-05-14T09:33:32Z","timestamp":1684056812336},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2341,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes.<\/jats:p>\n               <jats:p>Results: We present a formalism that uses the Bio\u03a8 concepts to model biological processes from molecular details to networks. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure\u2013function relationships, etc.). We illustrate its application with two examples: the functional comparison of proteases and the functional description of the glycolysis network. This computational approach is compatible with detailed biological knowledge and can be applied to different kinds of systems of simulation.<\/jats:p>\n               <jats:p>Availability: \u00a0www.sysdiag.cnrs.fr\/publications\/supplementary-materials\/BioPsi_Manager\/<\/jats:p>\n               <jats:p>Contact: \u00a0sabine.peres@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq169","type":"journal-article","created":{"date-parts":[[2010,5,7]],"date-time":"2010-05-07T02:02:03Z","timestamp":1273197723000},"page":"1542-1547","source":"Crossref","is-referenced-by-count":3,"title":["Computing biological functions using Bio\u03a8, a formal description of biological processes based on elementary bricks of actions"],"prefix":"10.1093","volume":"26","author":[{"given":"Sabine","family":"P\u00e9r\u00e8s","sequence":"first","affiliation":[{"name":"Sysdiag CNRS Bio-Rad UMR 3145, Cap delta\/Parc eurom\u00e9decine, 1682 rue de la Valsi\u00e8re CS 61003, 34184 Montpellier Cedex 4, France"}]},{"given":"Liza","family":"Felicori","sequence":"additional","affiliation":[{"name":"Sysdiag CNRS Bio-Rad UMR 3145, Cap delta\/Parc eurom\u00e9decine, 1682 rue de la Valsi\u00e8re CS 61003, 34184 Montpellier Cedex 4, France"}]},{"given":"St\u00e9phanie","family":"Rialle","sequence":"additional","affiliation":[{"name":"Sysdiag CNRS Bio-Rad UMR 3145, Cap delta\/Parc eurom\u00e9decine, 1682 rue de la Valsi\u00e8re CS 61003, 34184 Montpellier Cedex 4, France"}]},{"given":"Elodie","family":"Jobard","sequence":"additional","affiliation":[{"name":"Sysdiag CNRS Bio-Rad UMR 3145, Cap delta\/Parc eurom\u00e9decine, 1682 rue de la Valsi\u00e8re CS 61003, 34184 Montpellier Cedex 4, France"}]},{"given":"Franck","family":"Molina","sequence":"additional","affiliation":[{"name":"Sysdiag CNRS Bio-Rad UMR 3145, Cap delta\/Parc eurom\u00e9decine, 1682 rue de la Valsi\u00e8re CS 61003, 34184 Montpellier Cedex 4, France"}]}],"member":"286","published-online":{"date-parts":[[2010,5,6]]},"reference":[{"key":"2023012508045056900_B1","doi-asserted-by":"crossref","first-page":"3155","DOI":"10.1093\/nar\/21.13.3155","article-title":"The ENZYME data bank","volume":"21","author":"Bairoch","year":"1993","journal-title":"Nucleic Acids Res."},{"key":"2023012508045056900_B2","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.jtbi.2004.04.003","article-title":"Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic","volume":"229","author":"Bernot","year":"2004","journal-title":"J. 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