Pattern search in BioPAX models.

Bioinformatics 2014 Jan 16;30(1):139-40. Epub 2013 Sep 16.

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.

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.

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866551PMC
January 2014

Publication Analysis

Top Keywords

biopax models
8
signaling relations
8
pattern search
8
proteins provide
4
provide search
4
relations proteins
4
search pattern
4
directed signaling
4
pathway commons
4
compare current
4
current data
4
database compare
4
commons database
4
signaling
4
pattern pathway
4
pattern captures
4
framework defining
4
defining searching
4
extensible framework
4
source extensible
4

Similar Publications

BioASF: a framework for automatically generating executable pathway models specified in BioPAX.

Bioinformatics 2016 06;32(12):i60-i69

Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.

Motivation: Biological pathways play a key role in most cellular functions. To better understand these functions, diverse computational and cell biology researchers use biological pathway data for various analysis and modeling purposes. For specifying these biological pathways, a community of researchers has defined BioPAX and provided various tools for creating, validating and visualizing BioPAX models. Read More

View Article and Full-Text PDF
June 2016

Using biological pathway data with paxtools.

PLoS Comput Biol 2013 19;9(9):e1003194. Epub 2013 Sep 19.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Read More

View Article and Full-Text PDF
April 2014

BioPAX support in CellDesigner.

Bioinformatics 2011 Dec 21;27(24):3437-8. Epub 2011 Oct 21.

Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.

Motivation: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. Read More

View Article and Full-Text PDF
December 2011

Qualitative translation of relations from BioPAX to SBML qual.

Bioinformatics 2012 Oct 24;28(20):2648-53. Epub 2012 Aug 24.

Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany.

Motivation: The biological pathway exchange language (BioPAX) and the systems biology markup language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus of SBML is quantitative modeling and dynamic simulation of models, whereas the BioPAX specification concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. Read More

View Article and Full-Text PDF
October 2012