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

Igor Rodchenkov,Metin Can Siper,Logan Mosier,Caitlin O’Callaghan,Dylan Fong,Chris Sander,Augustin Luna,Qizhi Wen,Jonah Dlin,Christian Dallago,Harsh Mistry,Emek Demir,Max Franz,Wanxin Li,Michael Wrana,Ethan Cerami,Manfred Cheung,Benjamin Groß ,Bülent Arman Aksoy ,Gary D Bader ,G Domingues Elder ,Peter Smith ,Uğur Doğrusöz ,Jeffrey V Wong ,Özgün Babur

doi:10.1093/nar/gkz946

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.

Highlights

Pathway information that describes interactions between molecules in biological processes can help in solving research problems, such as the interpretation of genomics data [1], generating hypotheses surrounding disease mechanisms [2,3], design of rational therapeutics [4] and treatment decision strategies [5].The number of available pathway and interaction resources has nearly tripled over the last decade, from 190 in 2006 to 702 in 2018 [6], increasing the need for integration
Pathway information downloads are made available in Biological Pathway Exchange (BioPAX) format, Gene Matrix Transposed (GMT) format, which is used in gene set enrichment analyses [29,30], Simple Interaction Format (SIF) and extended SIF with additional fields, which are useful for network analysis and visualization
The goal of Pathway Commons is to provide a comprehensive and user-friendly access point for researchers desiring pathway and molecular interaction information to support the analysis of biological data and the discovery of interesting relationships

Summary

Introduction

Pathway information that describes interactions between molecules in biological processes can help in solving research problems, such as the interpretation of genomics data [1], generating hypotheses surrounding disease mechanisms [2,3], design of rational therapeutics [4] and treatment decision strategies [5].The number of available pathway and interaction resources has nearly tripled over the last decade, from 190 in 2006 to 702 in 2018 [6] (www.pathguide.org), increasing the need for integration. 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. Pathway Commons (PC) is a resource that aggregates data from publicly available biological pathway and molecular interaction databases and provides it from a single access point on the web [7].

Results

Conclusion