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

The Reactome Pathway Knowledgebase

Antonio Fabregat  1   2 , Steven Jupe  1 , Lisa Matthews  3 , Konstantinos Sidiropoulos  1 , Marc Gillespie  4   5 , Phani Garapati  1 , Robin Haw  4 , Bijay Jassal  4 , Florian Korninger  1 , Bruce May  4 , Marija Milacic  4 , Corina Duenas Roca  1 , Karen Rothfels  4 , Cristoffer Sevilla  1 , Veronica Shamovsky  3 , Solomon Shorser  4 , Thawfeek Varusai  1 , Guilherme Viteri  1 , Joel Weiser  4 , Guanming Wu  6 , Lincoln Stein  4   7 , Henning Hermjakob  1   8 , Peter D'Eustachio  3
Affiliations

The Reactome Pathway Knowledgebase

Antonio Fabregat et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
‘Hemostasis’ top-level pathway represented as an Entity High Level Diagram (EHLD) above, and with expression data analysis results overlaid, below, showing relative overexpression of gene products involved in platelet adhesion to exposed collagen.
Figure 2.
Figure 2.
Pathway navigation with detail matched to zoom level. A user who selects the pathway ‘nucleotide metabolism’ is presented with an EHLD that shows the entire process with its major subpathways labeled (A). Double-clicking anywhere in the region of nucleobase biosynthesis (red box in A) yields a pathway diagram for that process, with its subpathways labeled and only its major components shown (B). As the user zooms in to view the last steps of purine biosynthesis (red box in B), housekeeping entities are revealed and names of all entities are displayed (C). Finally, as the user zooms in to a specific region of the pathway (red box in C), structures of small molecules and proteins are shown (D).
Figure 3.
Figure 3.
Reorganized Reactome website. From the simplified home page (A), a single step leads to the pathway browser (B), our main tool for data visualization and analysis for human users. Users needing help in navigating and interpreting the site can navigate in a single step to on-line documentation, organized by topic and including solved examples (C). The same documentation button also leads to pages for developers who want access to our analysis service, content service, graph database and widget to include Reactome pathway displays in their web applications (D).
See this image and copyright information in PMC

References

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