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The BioPAX community standard for pathway data sharing

A Corrigendum to this article was published on 10 April 2012

A Corrigendum to this article was published on 07 December 2010

This article has been updated

Abstract

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

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Figure 1: BioPAX is a shared language for biological pathways.
Figure 2: BioPAX enables computational data gathering, publication and use of information about biological processes.
Figure 3: The AKT pathway as represented by a traditional method (top left; from http://www.biocarta.com/), a formalized SBGN diagram (left; from http://www.sbgn.org/62) and using the BioPAX language (right).
Figure 4: High-level view of the BioPAX ontology.
Figure 5: Example uses of pathway information in BioPAX format.
Figure 6: The relationship among popular standard formats for pathway information.

Change history

  • 07 December 2010

    In the version of this article initially published, the affiliation for Ken Fukuda should be Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. The error has been corrected in the HTML and PDF versions of the article.

  • 10 April 2012

    In the version of this article initially published, Oliver Reubenacker should have been spelled Oliver Ruebenacker. In addition, the location of the author's affiliation is Farmington, not Storrs. The errors have been corrected in the HTML and PDF versions of the article.

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Acknowledgements

Funded by the US Department of Energy workshop grant DE-FG02-04ER63931, the caBIG program, the US National Institute of General Medical Sciences workshop grant 1R13GM076939, grant P41HG004118 from the US National Human Genome Research Institute and Genome Canada through the Ontario Genomics Institute (2007-OGI-TD-05) and US National Institutes of Health grant R01GM071962-07. Thanks to many people who contributed to discussions on BioPAX mailing lists, at conferences and at BioPAX workshops, especially A. Ruttenberg and J. Rees.

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Contributions

All authors helped develop the BioPAX language, ontology, documentation and examples by participating in workshops or on mailing lists and/or provided data in BioPAX format and/or wrote software that supports BioPAX. See Supplementary Table 5 for a full list of author contributions.

Corresponding author

Correspondence to Gary D Bader.

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Supplementary Tables 1–5 and Supplementary Fig. 1 (PDF 767 kb)

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Demir, E., Cary, M., Paley, S. et al. The BioPAX community standard for pathway data sharing. Nat Biotechnol 28, 935–942 (2010). https://doi.org/10.1038/nbt.1666

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