Title | The BioPAX community standard for pathway data sharing. |
Publication Type | Journal Article |
Year of Publication | 2010 |
Authors | Demir, 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 |
Journal | Nat Biotechnol |
Volume | 28 |
Issue | 9 |
Pagination | 935-42 |
Date Published | 2010 Sep |
ISSN | 1546-1696 |
Keywords | Computational 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> |
DOI | 10.1038/nbt.1666 |
Alternate Journal | Nat. Biotechnol. |
PubMed ID | 20829833 |
PubMed Central ID | PMC3001121 |
Grant List | 1R13GM076939 / 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 |