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The BioPAX community standard for pathway data sharing

Demir, Emek and Hucka, Michael (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28 (9). pp. 935-942. ISSN 1087-0156. PMCID PMC3001121. https://resolver.caltech.edu/CaltechAUTHORS:20100929-111828470

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/nbt.1666DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001121/PubMed CentralArticle
http://rdcu.be/n3ccPublisherFree ReadCube access
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Additional Information:© 2010 Nature Publishing Group. Published online 9 September. 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.
Funders:
Funding AgencyGrant Number
Department of Energy (DOE)DE-FG02-04ER63931
caBIG programUNSPECIFIED
NIH1R13GM076939
NIHP41HG004118
Genome Canada2007-OGI-TD-05
NIHR01GM071962-07
Issue or Number:9
PubMed Central ID:PMC3001121
Record Number:CaltechAUTHORS:20100929-111828470
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20100929-111828470
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:20219
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:29 Sep 2010 22:13
Last Modified:06 Nov 2020 17:06

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