The BioPAX community standard for pathway data sharing Journal Article
| Authors: | Demir, E.; Cary, M. P.; 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, A. C.; 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.; 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, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Dogrusoz, U.; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, N. L.; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D. |
| Article Title: | The BioPAX community standard for pathway data sharing |
| 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. © 2010 Nature America, Inc. All rights reserved. |
| Keywords: | signal transduction; protein kinase b; protein expression; promoter region; single nucleotide polymorphism; review; metabolism; computational biology; protein protein interaction; molecular dynamics; enzyme substrate; data base; molecular evolution; messenger rna; gene interaction; information dissemination; gene regulatory network; molecular interaction; molecular biology; protein structure; structure analysis; software; visualization; biological pathways; databases as topic; fragmentation reaction; protein modification; protein dna interaction; signaling pathways; copy number variation; data sharing; biological discoveries; cellular levels; community standards; computational tools; gene regulation network; genetic interaction; rapid growth; database systems; data visualization; biological pathway exchange; semantics; metabolic networks and pathways; programming languages |
| Journal Title: | Nature Biotechnology |
| Volume: | 28 |
| Issue: | 9 |
| ISSN: | 1087-0156 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2010-09-01 |
| Start Page: | 935 |
| End Page: | 942 |
| Language: | English |
| DOI: | 10.1038/nbt.1666 |
| PUBMED: | 20829833 |
| PROVIDER: | scopus |
| PMCID: | PMC3001121 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 7" - "Export Date: 20 April 2011" - "CODEN: NABIF" - "Source: Scopus" |
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