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

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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: Aug 11 2020 1:38 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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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

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Related Databases (5)
Rhea
Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt.

Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.

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 15 non-human species including mouse, rat, chicken, zebrafish, worm, fly, and yeast.

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.

PathBank
PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other pathway database. PathBank is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics, and systems biology. All PathBank pathways include information on the relevant organelles, subcellular compartments, protein complex cofactors, protein complex locations, metabolite locations, chemical structures, and protein complex quaternary structures. The database is easily browsed and supports full text, sequence, and chemical structure searching.

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