Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

Igor Rodchenkov, Ozgun Babur, Augustin Luna, Bulent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O'Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan CeramiBenjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

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 (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) 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 4794 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.

Original languageEnglish (US)
Pages (from-to)D489-D497
JournalNucleic acids research
Volume48
Issue numberD1
DOIs
StatePublished - Jan 8 2020

ASJC Scopus subject areas

  • Genetics

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    Rodchenkov, I., Babur, O., Luna, A., Aksoy, B. A., Wong, J. V., Fong, D., Franz, M., Siper, M. C., Cheung, M., Wrana, M., Mistry, H., Mosier, L., Dlin, J., Wen, Q., O'Callaghan, C., Li, W., Elder, G., Smith, P. T., Dallago, C., ... Sander, C. (2020). Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic acids research, 48(D1), D489-D497. https://doi.org/10.1093/nar/gkz946