Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Oct 24, 2019
- Source ID
- 10.1093/nar/gkz946
Entities
People
- Augustin Luna
- Benjamin J Gross
- Bulent Arman Aksoy
- Caitlin O’callaghan
- Chris Sander
- Christian Dallago
- Dylan Fong
- Emek Demir
- Ethan Cerami
- Gary D. Bader
- Geoffrey Elder
- Harsh Mistry
- Igor Rodchenkov
- Jeffrey V Wong
- Jonah Dlin
- Logan Mosier
- Manfred Cheung
- Max Franz
- Metin Can Siper
- Michael Wrana
- Ozgun Babur
- Peter T Smith
- Qizhi Wen
- Uğur Doğrusöz
- Wanxin Li
Organizations
- Bilkent University
- Dana–Farber Cancer Institute
- Defense Advanced Research Projects Agency
- Harvard Medical School
- Memorial Sloan Kettering Cancer Center
- National Institutes of Health
- Oregon Health & Science University
- Technical University of Munich
- University of Toronto