The reactome pathway knowledgebase.

Bijay Jassal,Robin Haw,Peter D’Eustachio,Joel Weiser,Fred Loney,Chuqiao Gong,Karen Rothfels,Cristoffer Sevilla,Veronica Shamovsky,Justin Cook,Thawfeek Varusai,Solomon Shorser,Marija Milacic,Lisa Matthews,Pascual Lorente,Konstantinos Sidiropoulos,Marc Gillespie,Antonio Fabregat,Guilherme Viteri,Lincoln Stein,Guanming Wu,Bruce May,Henning Hermjakob

doi:10.1093/nar/gkz1031

Abstract

The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data model, an extended version of a classic metabolic map. Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To extend our ability to annotate human disease processes, we have implemented a new drug class and have used it initially to annotate drugs relevant to cardiovascular disease. Our annotation model depends on external domain experts to identify new areas for annotation and to review new content. New web pages facilitate recruitment of community experts and allow those who have contributed to Reactome to identify their contributions and link them to their ORCID records. To improve visualization of our content, we have implemented a new tool to automatically lay out the components of individual reactions with multiple options for downloading the reaction diagrams and associated data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.

Highlights

At the cellular level, life is a network of molecular reactions that enable signal transduction, transport, DNA replication, protein synthesis and intermediary metabolism
Processes are systematically described in molecular detail to generate an ordered network of molecular transformations, resulting in an extended version of a classic metabolic map [5,6]
Notable recent changes in Reactome include expanding the scope of the project to support annotation of the molecular function of drugs, developing new tools to facilitate community participation in annotation and to explicitly acknowledge it, and developing new web features to improve the layout of individual reactions and the visualization of our event hierarchy

Summary

Introduction

Life is a network of molecular reactions that enable signal transduction, transport, DNA replication, protein synthesis and intermediary metabolism. Notable recent changes in Reactome include expanding the scope of the project to support annotation of the molecular function of drugs, developing new tools to facilitate community participation in annotation and to explicitly acknowledge it, and developing new web features to improve the layout of individual reactions and the visualization of our event hierarchy.

Results

Conclusion