BioPAX A Community Standard for Pathway Data Sharing

Published

September 9, 2010

Author(s)

Robert N. Goldberg, Michael Cary, Erek Demir

Abstract

BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways and processes at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents significant barriers to its effective use. BioPAX solves this problem by making pathway data significantly easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. The BioPAX standard was created through a community process starting in 2002 involving database groups, software developers and pathway data users. The standard is defined in the OWL XML format. Millions of interactions organized into thousands of pathways across many organisms are available in BioPAX format from a growing number of sources. Thus, large amounts of pathway data are now available in a computable form for visualization, analysis and biological discovery.

Citation

Nature Biotechnology

Volume

28

Issue

9

Pub Type

Journals

Keywords

Biological pathways, databases, data exchange, metabolism, ontologies, signaling

Citation

Goldberg, R. , Cary, M. and Demir, E. (2010), BioPAX A Community Standard for Pathway Data Sharing, Nature Biotechnology (Accessed December 15, 2024)