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      The BioPAX community standard for pathway data sharing

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      Author(s)
      Demir, Emek
      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, Özgün
      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.
      Iersel, Martijn van
      Wimalaratne, S.
      Allen, K.
      Braun, B.
      Whirl-Carrillo, M.
      Cheung, Kei-Hoi
      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.
      Doğrusöz, Uğur
      McWeeney, S.
      Aladjem, M.
      Birney, E.
      Collado-Vides, J.
      Goto, S.
      Hucka, M.
      Novère, Nicolas Le
      Maltsev, N.
      Pandey, A.
      Thomas, P.
      Wingender, E.
      Karp, P. D.
      Sander, C.
      Bader, G. D.
      Date
      2010-09
      Source Title
      Nature Biotechnology
      Print ISSN
      1087-0156
      Publisher
      Nature Publishing Group
      Volume
      28
      Issue
      9
      Pages
      935 - 942
      Language
      English
      Type
      Article
      Item Usage Stats
      298
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      689
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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. © 2010 Nature America, Inc. All rights reserved.
      Keywords
      Biological discoveries
      Biological pathways
      Cellular levels
      Community standards
      Computational tools
      Data sharing
      Gene regulation network
      Genetic interaction
      Rapid growth
      Signaling pathways
      Database systems
      Visualization
      Data visualization
      Messenger RNA
      Protein kinase B
      Biological pathway exchange
      Copy number variation
      Database
      Enzyme substrate
      Fragmentation reaction
      Metabolism
      Molecular biology
      Molecular dynamics
      Molecular evolution
      Molecular interaction
      Priority journal
      Promoter region
      Protein DNA interaction
      Protein expression
      Protein modification
      Protein protein interaction
      Protein structure
      Review
      Semantics
      Single nucleotide polymorphism
      Structure analysis
      Computational biology
      Databases as topic
      Information dissemination
      Metabolic networks and pathways
      Programming languages
      Signal transduction
      Software
      Permalink
      http://hdl.handle.net/11693/38163
      Published Version (Please cite this version)
      http://dx.doi.org/10.1038/nbt.1666
      Collections
      • Bilkent Center for Bioinformatics (BCBI) 19
      • Department of Computer Engineering 1510
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