Pattern search in biopax models

Ozgun Babur, Bülent Arman Aksoy, Igor Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

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.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.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.Contact: Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)139-140
Number of pages2
JournalBioinformatics
Volume30
Issue number1
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

Fingerprint

Pattern Search
Databases
Licensure
Metabolic Networks and Pathways
Computational Biology
Pathway
Documentation
Signal transduction
Graph Searching
Signal Transduction
Language
Software
Bioinformatics
Gene expression
Model
Gene Regulation
Metabolic Network
Open Source
Availability
Java

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Babur, O., Aksoy, B. A., Rodchenkov, I., Sümer, S. O., Sander, C., & Demir, E. (2014). Pattern search in biopax models. Bioinformatics, 30(1), 139-140. https://doi.org/10.1093/bioinformatics/btt539

Pattern search in biopax models. / Babur, Ozgun; Aksoy, Bülent Arman; Rodchenkov, Igor; Sümer, Selçuk Onur; Sander, Chris; Demir, Emek.

In: Bioinformatics, Vol. 30, No. 1, 01.01.2014, p. 139-140.

Research output: Contribution to journalArticle

Babur, O, Aksoy, BA, Rodchenkov, I, Sümer, SO, Sander, C & Demir, E 2014, 'Pattern search in biopax models', Bioinformatics, vol. 30, no. 1, pp. 139-140. https://doi.org/10.1093/bioinformatics/btt539
Babur O, Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E. Pattern search in biopax models. Bioinformatics. 2014 Jan 1;30(1):139-140. https://doi.org/10.1093/bioinformatics/btt539
Babur, Ozgun ; Aksoy, Bülent Arman ; Rodchenkov, Igor ; Sümer, Selçuk Onur ; Sander, Chris ; Demir, Emek. / Pattern search in biopax models. In: Bioinformatics. 2014 ; Vol. 30, No. 1. pp. 139-140.
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