standards > model/format > DOI:10.25504/FAIRsharing.sfkmej


ready Biological Pathway eXchange

Abbreviation: BioPAX


General Information
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.

Homepage http://biopax.org/

Countries that developed this resource Canada , France , Germany , Japan , United Kingdom , United States , Worldwide

Created in 2002

Taxonomic range

Knowledge Domains 

User-defined Tags





How to cite this record FAIRsharing.org: BioPAX; Biological Pathway eXchange; DOI: https://doi.org/10.25504/FAIRsharing.sfkmej; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Sep 17 2019 5:49 p.m.


This record is maintained by garybader  ORCID  and IgorRodchenkov  (rodche)

Record updated: Jan. 12, 2018, 1:24 p.m. by The FAIRsharing Team.

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In Collections
Computational Modeling (COMBINE)
Computational Modeling
FAIRDOM Community Standards


Support

General

forum https://groups.google.com/forum/#!forum/ ...

Additional Information

Contact BioPAX group

External Links

Bioportal http://bioportal.bioontology.org/ontologies/BP

Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Curation

The BioPAX Validator http://biopax.baderlab.org

Other Web Services

BioPax Tools https://biopax.github.io/Paxtools/


Publications

The BioPAX community standard for pathway data sharing.

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,Samwald M,van Iersel M,Wimalaratne S,Allen K,Braun B,Whirl-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 Novere N,Maltsev N,Pandey A,Thomas P,Wingender E,Karp PD,Sander C,Bader GD
Nat Biotechnol 2010

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined


Implementing Databases (2)
Reactome - a curated knowledgebase of biological pathways
The cornerstone of Reactome is a freely available, open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. Inferred orthologous reactions are available for 17 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, and Arabidopsis.
Pathway Commons
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.

Implementing Policies

This record is not implemented by any policy.