Pathway Commons: 2019 Update
Autor: | Caitlin O'Callaghan, Igor Rodchenkov, Qizhi Wen, Bulent Arman Aksoy, Emek Demir, Peter T. Smith, Metin Can Siper, Logan Mosier, Ugur Dogrusoz, Chris Sander, Michael Wrana, Jonah Dlin, Harsh Mistry, Manfred Cheung, Ethan Cerami, Benjamin Gross, Dylan Fong, Özgün Babur, Christian Dallago, Augustin Luna, Max Franz, Gary D. Bader, Wanxin Li, Geoffrey Elder, Jeffrey V. Wong |
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Jazyk: | angličtina |
Rok vydání: | 2019 |
Předmět: |
0303 health sciences
Proteomics Standards Initiative Computer science RNA Small molecule Biological pathway World Wide Web 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine ComputingMethodologies_PATTERNRECOGNITION chemistry Biochemical reactions BioPAX : Biological Pathways Exchange 030217 neurology & neurosurgery DNA 030304 developmental biology |
DOI: | 10.1101/788521 |
Popis: | Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g., metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (1) tools to search this comprehensive resource, (2) a download site offering integrated bulk sets of pathway data (e.g., tables of interactions and gene sets), (3) reusable software libraries for working with pathway information in several programming languages (Java, R, Python, and Javascript), and (4) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4,794 detailed human biochemical processes (i.e., pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis. |
Databáze: | OpenAIRE |
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