Pattern search in biopax models

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

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


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 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
Issue number1
StatePublished - Jan 1 2014
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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