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BioPAX – biological pathway data exchange format

Part 4. Bioinformatics

4.7. Structuring and Integrating Data

Introductory Review

  1. Gary D. Bader,
  2. Michael P. Cary,
  3. Chris Sander

Published Online: 15 JUL 2006

DOI: 10.1002/047001153X.g408117

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Bader, G. D., Cary, M. P. and Sander, C. 2006. BioPAX – biological pathway data exchange format. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.7.

Author Information

  1. Memorial Sloan-Kettering Cancer Center, New York, NY, US

Publication History

  1. Published Online: 15 JUL 2006

Abstract

Pathway information is vital for successful modeling of cellular systems. The over 215 on-line pathway databases vary widely in representation and coverage of biological processes, making their combined use extremely difficult. Future pathway information systems for querying, visualization, and analysis must support standard exchange formats to successfully integrate data on a large scale. BioPAX (www.biopax.org) is a data exchange format for biological pathways developed by pathway databases, such as BioCyc, WIT, Kyoto Encyclopedia of Genes and Genomes (KEGG), aMAZE, Integrating Network Objects with Hierarchies (INOH), PATIKA, Reactome, Biomolecular Interaction Database (BIND), and others. Level 1 supports metabolic pathways. Level 2 adds support for molecular interactions. Level 3 will add additional support for signal transduction and genetic regulatory networks. The ultimate goal of BioPAX is to enable seamless collection and use of pathway information so that it may be efficiently applied to answer biological questions.

Keywords:

  • pathway data integration;
  • pathway database;
  • standard exchange format;
  • ontology;
  • information system