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Pattern search in BioPAX models.

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.

SUBMITTER: Babur O

PROVIDER: S-EPMC3866551 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Pattern search in BioPAX models.

Babur Özgün Ö Aksoy Bülent Arman BA Rodchenkov Igor I Sümer Selçuk Onur SO Sander Chris C Demir Emek E

Bioinformatics (Oxford, England) 20130916 1

<h4>Motivation</h4>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.<h4>Results</h4>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 ...[more]

PMID: 24045775

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