The Biological Pathway Exchange format (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. It is expressed in OWL.

Normative definitions

BioPAX is defined in a set of specification documents, that describe the elements of the language, its syntax, and provides validation rules, and a set of OWL files.

The latest specification is BioPAX Level 3.

Governance

BioPAX development is coordinated by an editorial board elected by the community.

Communication

BioPAX development is discussed on the mailing list biopax-discuss@googlegroups.com.

Software support

Many databases and tools support BioPAX. This includes a recommended API.

Contact

For information about BioPAX contact biopax-discuss@googlegroups.com.

How to cite BioPAX

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, Gopinathrao 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, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Carrillo M, Cheung KH, 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. BioPAX – A Community Standard for Pathway Data Sharing. Nature Biotechnology (2010), 28: 935–942. http://identifiers.org/pubmed/20829833

History

TBW