{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T01:56:53Z","timestamp":1762999013622},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1112,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: BioPAX is a standard language for representing complex cellular processes, including metabolic networks, signal transduction and gene regulation. Owing to the inherent complexity of a BioPAX model, searching for a specific type of subnetwork can be non-trivial and difficult.<\/jats:p>\n               <jats:p>Results: We developed an open source and extensible framework for defining and searching graph patterns in BioPAX models. We demonstrate its use with a sample pattern that captures directed signaling relations between proteins. We provide search results for the pattern obtained from the Pathway Commons database and compare these results with the current data in signaling databases SPIKE and SignaLink. Results show that a pattern search in public pathway data can identify a substantial amount of signaling relations that do not exist in signaling databases.<\/jats:p>\n               <jats:p>Availability: BioPAX-pattern software was developed in Java. Source code and documentation is freely available at http:\/\/code.google.com\/p\/biopax-pattern under Lesser GNU Public License.<\/jats:p>\n               <jats:p>Contact: \u00a0patternsearch@cbio.mskcc.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt539","type":"journal-article","created":{"date-parts":[[2013,9,18]],"date-time":"2013-09-18T00:32:28Z","timestamp":1379464348000},"page":"139-140","source":"Crossref","is-referenced-by-count":25,"title":["Pattern search in BioPAX models"],"prefix":"10.1093","volume":"30","author":[{"given":"\u00d6zg\u00fcn","family":"Babur","sequence":"first","affiliation":[{"name":"1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 2Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and 3Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}]},{"given":"B\u00fclent Arman","family":"Aksoy","sequence":"additional","affiliation":[{"name":"1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 2Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and 3Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"},{"name":"1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 2Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and 3Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}]},{"given":"Igor","family":"Rodchenkov","sequence":"additional","affiliation":[{"name":"1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 2Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and 3Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}]},{"given":"Sel\u00e7uk Onur","family":"S\u00fcmer","sequence":"additional","affiliation":[{"name":"1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 2Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and 3Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}]},{"given":"Chris","family":"Sander","sequence":"additional","affiliation":[{"name":"1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 2Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and 3Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}]},{"given":"Emek","family":"Demir","sequence":"additional","affiliation":[{"name":"1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 2Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and 3Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}]}],"member":"286","published-online":{"date-parts":[[2013,9,16]]},"reference":[{"key":"2023012710375321700_btt539-B1","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1093\/bioinformatics\/btp665","article-title":"ChiBE: interactive visualization and manipulation of BioPAX pathway models","volume":"26","author":"Babur","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012710375321700_btt539-B2","doi-asserted-by":"crossref","first-page":"D504","DOI":"10.1093\/nar\/gkj126","article-title":"Pathguide: a pathway resource list","volume":"34","author":"Bader","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012710375321700_btt539-B3","doi-asserted-by":"crossref","first-page":"14689","DOI":"10.1073\/pnas.0305199101","article-title":"Local graph alignment and motif search in biological networks","volume":"101","author":"Berg","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012710375321700_btt539-B4","doi-asserted-by":"crossref","first-page":"D685","DOI":"10.1093\/nar\/gkq1039","article-title":"Pathway commons, a web resource for biological pathway data","volume":"39","author":"Cerami","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012710375321700_btt539-B5","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","article-title":"The BioPAX community standard for pathway data sharing","volume":"28","author":"Demir","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2023012710375321700_btt539-B6","doi-asserted-by":"crossref","first-page":"e1003194","DOI":"10.1371\/journal.pcbi.1003194","article-title":"Using biological pathway data with Paxtools","volume":"9","author":"Demir","year":"2013","journal-title":"PloS Comput. Biol."},{"key":"2023012710375321700_btt539-B7","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1752-0509-7-7","article-title":"SignaLink 2\u2013a signaling pathway resource with multi-layered regulatory networks","volume":"7","author":"Fazekas","year":"2013","journal-title":"BMC Syst. Biol."},{"key":"2023012710375321700_btt539-B8","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":"2023012710375321700_btt539-B9","doi-asserted-by":"crossref","DOI":"10.1109\/ICPR.2002.1048250","article-title":"Graphgrep: a fast and universal method for querying graphs","volume-title":"Proceedings of the 16th International Conference on Pattern Recognition","author":"Giugno","year":"2002"},{"key":"2023012710375321700_btt539-B10","doi-asserted-by":"crossref","first-page":"D793","DOI":"10.1093\/nar\/gkq1167","article-title":"SPIKE: a database of highly curated human signaling pathways","volume":"39","author":"Paz","year":"2011","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/1\/139\/48912667\/bioinformatics_30_1_139.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/1\/139\/48912667\/bioinformatics_30_1_139.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T10:40:31Z","timestamp":1674816031000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/1\/139\/235639"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,9,16]]},"references-count":10,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt539","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,1,1]]},"published":{"date-parts":[[2013,9,16]]}}}