The BioPAX community standard for pathway data sharing
Nature Publishing Group
935 - 942
Item Usage Stats
Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, 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. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.
Gene regulation network
Protein kinase B
Biological pathway exchange
Copy number variation
Protein DNA interaction
Protein protein interaction
Single nucleotide polymorphism
Databases as topic
Metabolic networks and pathways
Published Version (Please cite this version)http://dx.doi.org/10.1038/nbt.1666
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Doğrusöz, Uğur; Çetintaş, Ahmet; Demir, Emek; Babur, Özgün (BioMed Central Ltd., 2009-11-16)Background: Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate ...
Babur, Özgün; Colak, Recep; Demir, Emek; Doğrusöz, Uğur (Wiley - V C H Verlag GmbH & Co. KGaA, 2008-06)High-throughput experiments, most significantly DNA microarrays, provide us with system-scale profiles. Connecting these data with existing biological networks poses a formidable challenge to uncover facts about a cell's ...
PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization Doğrusöz, Uğur; Erson, E. Zeynep; Giral, Erhan; Demir, Emek; Babur, Özgün; Çetintaş, Ahmet; Çolak, Recep (Oxford University Press, 2006-02-01)Summary: PATIKAweb provides a Web interface for retrieving and analyzing biological pathways in the PATIKA database, which contains data integrated from various prominent public pathway databases. It features a user-friendly ...