The BioPAX community standard for pathway data sharing

Autor: Margot Sunshine, Frank Schacherer, Nigam H. Shah, Akhilesh Pandey, Harsha Rajasimha, Andrew Finney, Rebecca Tang, Martijn P. van Iersel, Kumaran Kandasamy, Kei-Hoi Cheung, Martina Kutmon, Geeta Joshi-Tope, Matthias Samwald, Dean Ravenscroft, Mustafa H Syed, Vincent Schächter, Michael L. Blinov, Chris Sander, Liya Ren, Guanming Wu, Christian Lemer, Zhenjun Hu, Peter Hornbeck, Andrey Rzhetsky, Nicolas Le Novère, Emek Demir, Shiva Krupa, Michelle Whirl-Carrillo, Ken Fukuda, Alejandra López-Fuentes, Michael P. Cary, Erik Brauner, David Merberg, Julie Leonard, Imran Shah, David W. Kane, Alexander R. Pico, Shannon K. McWeeney, Michael Hucka, Peter D. Karp, Nadia Anwar, Andrea Splendiani, Peter D'Eustachio, Olivier Hubaut, Ugur Dogrusoz, Julio Collado-Vides, Gary D. Bader, Jeremy Zucker, Carl F. Schaefer, Keith Allen, Kam D. Dahlquist, Oliver Reubenacker, Paul Thomas, Mirit I. Aladjem, Victoria Petri, Verónica Jiménez-Jacinto, Igor Rodchenkov, Edgar Wingender, Gopal R. Gopinath, Imre Vastrik, Stan Letovksy, Susumu Goto, Ryan Whaley, Frank Gibbons, Natalia Maltsev, Özgün Babur, Ranjani Ramakrishnan, Robin Haw, Elgar Pichler, Burk Braun, Sylva L. Donaldson, Suzanne M. Paley, Huaiyu Mi, Sarala M. Wimalaratne, Elizabeth M. Glass, Sasha Tkachev, Irma Martínez-Flores, Augustin Luna, Joanne S. Luciano, Debbie Marks, Marc Gillespie, Michael Honig, Ewan Birney, Dan Corwin, Bruno S. Sobral, Kenneth H. Buetow, Li Gong, Eric K. Neumann, Robert N. Goldberg, Peter Murray-Rust
Přispěvatelé: Demir, Emek, Babur, Özgün, Doğrusöz, Uğur, Bioinformatica, RS: NUTRIM - R4 - Gene-environment interaction
Jazyk: angličtina
Rok vydání: 2010
Předmět:
Signaling pathways
interaction network
representation
Molecular biology
WikiPathways : Pathways for the people
Computer science
Biological pathways
Review
Signal transduction
Biological pathway exchange
Bioinformatics
Applied Microbiology and Biotechnology
information
Computational biology
ConsensusPathDB
information system
0302 clinical medicine
Databases as topic
pathway database
ontology
Visualization
Priority journal
0303 health sciences
Genetic interaction
Messenger RNA
software environment
Systems Biology Graphical Notation
Promoter region
systems biology
Molecular interaction
Programming languages
Semantics
Enzyme substrate
Protein modification
Databases as Topic
030220 oncology & carcinogenesis
Cellular levels
Molecular Medicine
Metabolic Networks and Pathways
Signal Transduction
standard exchange format
Biotechnology
Biomedical Engineering
Bioengineering
pathway data integration
Molecular dynamics
Structure analysis
Article
Database
Biological pathway
03 medical and health sciences
Data visualization
Protein kinase B
Fragmentation reaction
BioPAX : Biological Pathways Exchange
biological pathways
Rapid growth
Computational tools
Gene regulation network
030304 developmental biology
Electronic data interchange
Protein DNA interaction
Copy number variation
Information Dissemination
business.industry
Information dissemination
Computational Biology
knowledgebase
Single nucleotide polymorphism
Data sharing
Metabolism
Community standards
Database systems
Metabolic networks and pathways
Protein protein interaction
Protein structure
Molecular evolution
Protein expression
cellular pathways
Biological discoveries
Programming Languages
collaborative construction
business
Software
Zdroj: Nature biotechnology
Nature Biotechnology
Nature Biotechnology, 28(9), 935-42. Nature Publishing Group
ISSN: 1087-0156
Popis: BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.
Databáze: OpenAIRE