title: Pattern search in BioPAX models.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  BACKGROUND
  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.
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
authors.forename: Özgün
authors.initials: Ö
authors.lastname: Babur
authors.forename: Bülent Arman
authors.initials: BA
authors.lastname: Aksoy
authors.forename: Igor
authors.initials: I
authors.lastname: Rodchenkov
authors.forename: Selçuk Onur
authors.initials: SO
authors.lastname: Sümer
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.forename: Emek
authors.initials: E
authors.lastname: Demir
mesh_terms: D002468:Cell Physiological Phenomena; D016208:Databases, Factual; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010766:Phosphorylation; D011381:Programming Languages
references.citation: Bioinformatics. 2010 Feb 1;26(3):429-31
references.pmid: 20007251
references.citation: BMC Syst Biol. 2013 Jan 18;7:7
references.pmid: 23331499
references.citation: Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14689-94
references.pmid: 15448202
references.citation: Nat Biotechnol. 2010 Sep;28(9):935-42
references.pmid: 20829833
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D504-6
references.pmid: 16381921
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D793-9
references.pmid: 21097778
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90
references.pmid: 21071392
references.citation: PLoS Comput Biol. 2013;9(9):e1003194
references.pmid: 24068901
references.citation: Bioinformatics. 2007 Apr 1;23(7):910-2
references.pmid: 17277332