BioPAX

BioPAX is a standard language that facilitates the integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats. BioPAX aims to enable integration of pathway data from many different sources, thereby providing a way to analyze the entirety of biological interactions.

Overview

BioPAX is a RDF-based format that models biological pathways. It covers three main types of pathway information: metabolic, protein-protein interactions, and gene regulatory. BioPAX allows the representation of complex interactions and relationships between entities in a standard format. It is designed to be software and platform independent, and is maintained by the BioPAX community.

History

BioPAX was first proposed in 2002 at a meeting of pathway database providers and researchers. The goal was to create a format that could be used to exchange pathway information, and thus facilitate the integration of data from different databases. The first version of BioPAX (Level 1) was released in 2004, focusing on metabolic pathways. Subsequent versions expanded the scope to include molecular interaction (Level 2) and gene regulatory networks (Level 3).

Format

BioPAX is based on the Resource Description Framework (RDF), a standard model for data interchange on the Web. RDF has features that facilitate data merging even if the underlying schemas differ, and it specifically supports the evolution of schemas over time without requiring all the data consumers to be changed.

BioPAX uses OWL, a semantic markup language for publishing and sharing data using RDF. OWL provides a rich language for describing classes and relationships between them, which is used in BioPAX to define the types of objects (e.g., proteins, genes, complexes) and the relationships between them (e.g., controls, participates in).

Applications

BioPAX has been used in a variety of applications, including data exchange, pathway visualization, and systems biology research. Several software tools support BioPAX, including Cytoscape, Pathway Commons, and Reactome.

See also

• Systems biology
• Biological database
• Pathway Commons
• Reactome
• Cytoscape

References

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