Biological Pathway eXchange
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: Nov 15 2019 10:28 a.m.
Record updated: Jan. 12, 2018, 1:24 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.sfkmej' by 'garybader' at 14:35, 28 Mar 2017 (approved): 'contactName' has been modified: Before: Chris Sanders After: BioPAX group Added: Removed:
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Conditions of UseApplies to: Data use
|The BioPAX Validator||http://biopax.baderlab.org|
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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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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 17 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, and Arabidopsis.
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 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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