The BioPAX community standard for pathway data sharing.

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TitleThe BioPAX community standard for pathway data sharing.
Publication TypeJournal Article
Year of Publication2010
AuthorsDemir, E, Cary, MP, Paley, S, Fukuda, K, Lemer, C, Vastrik, I, Wu, G, D'Eustachio, P, Schaefer, C, Luciano, J, Schacherer, F, Martinez-Flores, I, Hu, Z, Jimenez-Jacinto, V, Joshi-Tope, G, Kandasamy, K, Lopez-Fuentes, AC, Mi, H, Pichler, E, Rodchenkov, I, Splendiani, A, Tkachev, S, Zucker, J, Gopinath, G, Rajasimha, H, Ramakrishnan, R, Shah, I, Syed, M, Anwar, N, Babur, O, Blinov, M, Brauner, E, Corwin, D, Donaldson, S, Gibbons, F, Goldberg, R, Hornbeck, P, Luna, A, Murray-Rust, P, Neumann, E, Ruebenacker, O, Reubenacker, O, Samwald, M, van Iersel, M, Wimalaratne, S, Allen, K, Braun, B, Whirl-Carrillo, M, Cheung, K-H, Dahlquist, K, Finney, A, Gillespie, M, Glass, E, Gong, L, Haw, R, Honig, M, Hubaut, O, Kane, D, Krupa, S, Kutmon, M, Leonard, J, Marks, D, Merberg, D, Petri, V, Pico, A, Ravenscroft, D, Ren, L, Shah, N, Sunshine, M, Tang, R, Whaley, R, Letovksy, S, Buetow, KH, Rzhetsky, A, Schachter, V, Sobral, BS, Dogrusoz, U, McWeeney, S, Aladjem, M, Birney, E, Collado-Vides, J, Goto, S, Hucka, M, Le Novère, N, Maltsev, N, Pandey, A, Thomas, P, Wingender, E, Karp, PD, Sander, C, Bader, GD
JournalNat Biotechnol
Volume28
Issue9
Pagination935-42
Date Published2010 Sep
ISSN1546-1696
KeywordsComputational Biology, Databases as Topic, Information Dissemination, Metabolic Networks and Pathways, Programming Languages, Signal Transduction, Software
Abstract

<p>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.</p>

DOI10.1038/nbt.1666
Alternate JournalNat. Biotechnol.
PubMed ID20829833
PubMed Central IDPMC3001121
Grant List1R13GM076939 / GM / NIGMS NIH HHS / United States
BB/F010516/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
P30 CA069533 / CA / NCI NIH HHS / United States
P41 HG004118 / HG / NHGRI NIH HHS / United States
P41 HG004118-01A1 / HG / NHGRI NIH HHS / United States
P41HG004118 / HG / NHGRI NIH HHS / United States
R01 GM070923 / GM / NIGMS NIH HHS / United States
R01 GM071962 / GM / NIGMS NIH HHS / United States
R01 RR022971 / RR / NCRR NIH HHS / United States
R01GM071962-07 / GM / NIGMS NIH HHS / United States
R13 GM076939 / GM / NIGMS NIH HHS / United States
R13 GM076939-01 / GM / NIGMS NIH HHS / United States
U24 GM077678 / GM / NIGMS NIH HHS / United States
U24 GM077678-18 / GM / NIGMS NIH HHS / United States
U54 AI081680 / AI / NIAID NIH HHS / United States
U54 HG004028 / HG / NHGRI NIH HHS / United States