{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,27]],"date-time":"2023-08-27T09:38:37Z","timestamp":1693129117962},"reference-count":31,"publisher":"Cambridge University Press (CUP)","issue":"4-5","license":[{"start":{"date-parts":[[2011,7,6]],"date-time":"2011-07-06T00:00:00Z","timestamp":1309910400000},"content-version":"unspecified","delay-in-days":5,"URL":"https:\/\/www.cambridge.org\/core\/terms"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Theory and Practice of Logic Programming"],"published-print":{"date-parts":[[2011,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and\/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems.<\/jats:p>","DOI":"10.1017\/s1471068411000287","type":"journal-article","created":{"date-parts":[[2011,7,6]],"date-time":"2011-07-06T05:15:37Z","timestamp":1309929337000},"page":"749-766","source":"Crossref","is-referenced-by-count":9,"title":["Automatic network reconstruction using ASP"],"prefix":"10.1017","volume":"11","author":[{"given":"MARKUS","family":"DURZINSKY","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"WOLFGANG","family":"MARWAN","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"MAX","family":"OSTROWSKI","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"TORSTEN","family":"SCHAUB","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"ANNEGRET","family":"WAGLER","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"56","published-online":{"date-parts":[[2011,7,6]]},"reference":[{"key":"S1471068411000287_ref23","doi-asserted-by":"publisher","DOI":"10.1007\/s00186-007-0178-5"},{"key":"S1471068411000287_ref19","unstructured":"goforsys. Accessed 7 June 2011. URL: http:\/\/www.goforsys.de."},{"key":"S1471068411000287_ref5","unstructured":"Durzinsky M. , Marwan W. and Wagler A. 2010. Reconstructing extended petri nets. Journal of Mathematical Biology. Preprint series: 10\u201319. URL: http:\/\/www.fma.ovgu.de."},{"key":"S1471068411000287_ref27","first-page":"312","volume-title":"Proceedings of the Twenty-fifth International Conference on Logic Programming (ICLP'09)","author":"Schaub","year":"2009"},{"key":"S1471068411000287_ref31","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.092576199"},{"key":"S1471068411000287_ref20","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2004.04.037"},{"key":"S1471068411000287_ref10","unstructured":"Erdem E. 2009. PHYLO-ASP: Phylogenetic systematics with answer set programming. See Erdem et al., 567\u2013572."},{"key":"S1471068411000287_ref30","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-84996-474-6_14"},{"key":"S1471068411000287_ref13","first-page":"497","volume-title":"Proceedings of the Twelfth International Conference on Principles of Knowledge Representation and Reasoning (KR'10)","author":"Gebser","year":"2010"},{"key":"S1471068411000287_ref22","doi-asserted-by":"publisher","DOI":"10.1016\/j.artint.2004.04.004"},{"key":"S1471068411000287_ref21","first-page":"18","article-title":"Reveal, a general reverse engineering algorithm for inference of genetic network architectures.","volume":"3","author":"Liang","year":"1998","journal-title":"Pacific Symposium on Biocomputing"},{"key":"S1471068411000287_ref8","doi-asserted-by":"publisher","DOI":"10.1016\/j.biosystems.2008.04.001"},{"key":"S1471068411000287_ref3","doi-asserted-by":"crossref","unstructured":"Baral C. , Chancellor K. , Tran N. , Tran N. , Joy A. and Berens M. 2004. A knowledge based approach for representing and reasoning about signaling networks. In Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology\/Third European Conference on Computational Biology (ISMB'04\/ECCB'04). 15\u201322.","DOI":"10.1093\/bioinformatics\/bth918"},{"key":"S1471068411000287_ref11","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-04238-6"},{"key":"S1471068411000287_ref6","first-page":"328","article-title":"A combinatorial approach to reconstruct petri nets from experimental data.","volume":"5307","author":"Durzinsky","year":"2008","journal-title":"Lecture Notes in Bioinformatics"},{"key":"S1471068411000287_ref29","unstructured":"Syrj\u00e4nen T. Lparse 1.0 User's Manual. Accessed 7 June 2011. URL: http:\/\/www.tcs.hut.fi\/Software\/smodels\/lparse.ps.gz."},{"key":"S1471068411000287_ref26","doi-asserted-by":"publisher","DOI":"10.1016\/S0303-2647(02)00019-9"},{"key":"S1471068411000287_ref1","first-page":"17","volume-title":"Proceedings of the Pacific Symposium on Biocomputing","author":"Akutsu","year":"1999"},{"key":"S1471068411000287_ref2","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511543357"},{"key":"S1471068411000287_ref24","unstructured":"Ostrowski M. 2011. Asp encoding for automatic network reconstruction. Accessed 7 June 2011. URL: http:\/\/www.cs.uni-potsdam.de\/wv\/NetworkReconstruction\/."},{"key":"S1471068411000287_ref7","doi-asserted-by":"crossref","unstructured":"Durzinsky M. , Wagler A. and Weismantel R. 2010. An algorithmic framework for network reconstruction. Theoretical Computer Science. In Press, Corrected Proof. URL: http:\/\/www.sciencedirect.com.","DOI":"10.1016\/j.tcs.2010.08.016"},{"key":"S1471068411000287_ref15","first-page":"130","volume-title":"Proceedings of the Twenty-fourth International Conference on Logic Programming (ICLP'08)","author":"Gebser","year":"2008"},{"key":"S1471068411000287_ref18","unstructured":"Gifford D. and Jaakkola T. 2001. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. In Proceedings of the Pacific Symposium on Biocomputing vol. 6. 422\u2013433."},{"key":"S1471068411000287_ref14","unstructured":"Gebser M. , Kaminski R. , Kaufmann B. , Ostrowski M. , Schaub T. , and Thiele S. A user's guide to gringo, clasp, clingo, and iclingo. Accessed 7 June 2011. URl: http:\/\/potassco.sourceforge.net."},{"key":"S1471068411000287_ref4","unstructured":"Dal Pal\u00f9 A. , Dovier A. and Pontelli E. 2009. Logic programming techniques in protein structure determination: Methodologies and results. See Erdem et al., 560\u2013566."},{"key":"S1471068411000287_ref17","doi-asserted-by":"publisher","DOI":"10.1016\/S1574-6526(07)03007-6"},{"key":"S1471068411000287_ref16","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-01929-6_7"},{"key":"S1471068411000287_ref12","first-page":"436","volume-title":"Proceedings of the Twenty-third National Conference on Artificial Intelligence (AAAI'08)","author":"Erdem","year":"2008"},{"key":"S1471068411000287_ref28","doi-asserted-by":"publisher","DOI":"10.1016\/S0004-3702(02)00187-X"},{"key":"S1471068411000287_ref25","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/17.suppl_1.S215"},{"key":"S1471068411000287_ref9","doi-asserted-by":"publisher","DOI":"10.1007\/s10601-007-9031-y"}],"container-title":["Theory and Practice of Logic Programming"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S1471068411000287","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,4,27]],"date-time":"2019-04-27T04:02:03Z","timestamp":1556337723000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S1471068411000287\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,7]]},"references-count":31,"journal-issue":{"issue":"4-5","published-print":{"date-parts":[[2011,7]]}},"alternative-id":["S1471068411000287"],"URL":"https:\/\/doi.org\/10.1017\/s1471068411000287","relation":{},"ISSN":["1471-0684","1475-3081"],"issn-type":[{"value":"1471-0684","type":"print"},{"value":"1475-3081","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,7]]}}}