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Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655. doi: 10.1093/nar/gkx1132.

The Reactome Pathway Knowledgebase.

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
2
Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
3
NYU School of Medicine, New York, NY 10016, USA.
4
Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada.
5
College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA.
6
Oregon Health Sciences University, Portland, OR 97239, USA.
7
Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.
8
National Center for Protein Sciences, Beijing, China.

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-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression profiles or somatic mutation catalogues from tumor cells. To support the continued brisk growth in the size and complexity of Reactome, we have implemented a graph database, improved performance of data analysis tools, and designed new data structures and strategies to boost diagram viewer performance. To make our website more accessible to human users, we have improved pathway display and navigation by implementing interactive Enhanced High Level Diagrams (EHLDs) with an associated icon library, and subpathway highlighting and zooming, in a simplified and reorganized web site with adaptive design. To encourage re-use of our content, we have enabled export of pathway diagrams as 'PowerPoint' files.

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