The BioPAX community standard for pathway data sharing.
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SUBMITTER: Demir E
PROVIDER: S-EPMC3001121 | biostudies-literature | 2010 Sep
REPOSITORIES: biostudies-literature
Publications
The BioPAX community standard for pathway data sharing.
Demir Emek E Cary Michael P MP Paley Suzanne S Fukuda Ken K Lemer Christian C Vastrik Imre I Wu Guanming G D'Eustachio Peter P Schaefer Carl C Luciano Joanne J Schacherer Frank F Martinez-Flores Irma I Hu Zhenjun Z Jimenez-Jacinto Veronica V Joshi-Tope Geeta G Kandasamy Kumaran K Lopez-Fuentes Alejandra C AC Mi Huaiyu H Pichler Elgar E Rodchenkov Igor I Splendiani Andrea A Tkachev Sasha S Zucker Jeremy J Gopinath Gopal G Rajasimha Harsha H Ramakrishnan Ranjani R Shah Imran I Syed Mustafa M Anwar Nadia N Babur Ozgün O Blinov Michael M Brauner Erik E Corwin Dan D Donaldson Sylva S Gibbons Frank F Goldberg Robert R Hornbeck Peter P Luna Augustin A Murray-Rust Peter P Neumann Eric E Ruebenacker Oliver O Samwald Matthias M van Iersel Martijn M Wimalaratne Sarala S Allen Keith K Braun Burk B Whirl-Carrillo Michelle M Cheung Kei-Hoi KH Dahlquist Kam K Finney Andrew A Gillespie Marc M Glass Elizabeth E Gong Li L Haw Robin R Honig Michael M Hubaut Olivier O Kane David D Krupa Shiva S Kutmon Martina M Leonard Julie J Marks Debbie D Merberg David D Petri Victoria V Pico Alex A Ravenscroft Dean D Ren Liya L Shah Nigam N Sunshine Margot M Tang Rebecca R Whaley Ryan R Letovksy Stan S Buetow Kenneth H KH Rzhetsky Andrey A Schachter Vincent V Sobral Bruno S BS Dogrusoz Ugur U McWeeney Shannon S Aladjem Mirit M Birney Ewan E Collado-Vides Julio J Goto Susumu S Hucka Michael M Le Novère Nicolas N Maltsev Natalia N Pandey Akhilesh A Thomas Paul P Wingender Edgar E Karp Peter D PD Sander Chris C Bader Gary D GD
Nature biotechnology 20100909 9
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 pr ...[more]
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Project description:Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.
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Project description:MotivationBioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.AvailabilityThe plug-in is freely available and can be downloaded at ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/ CONTACT: huaiyumi@usc.eduSupplementary informationSupplementary data are available at Bioinformatics online.
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