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. 2021 Jan 8;49(D1):D613-D621.
doi: 10.1093/nar/gkaa1024.

WikiPathways: connecting communities

Marvin Martens  1 , Ammar Ammar  1 , Anders Riutta  2 , Andra Waagmeester  3 , Denise N Slenter  1 , Kristina Hanspers  2 , Ryan A Miller  1 , Daniela Digles  4 , Elisson N Lopes  5 , Friederike Ehrhart  1 , Lauren J Dupuis  1 , Laurent A Winckers  1 , Susan L Coort  1 , Egon L Willighagen  1 , Chris T Evelo  1   6 , Alexander R Pico  2 , Martina Kutmon  1   6
Affiliations

WikiPathways: connecting communities

Marvin Martens et al. Nucleic Acids Res. .

Abstract

WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.

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Figures

Graphical Abstract
Graphical Abstract
WikiPathways enables research communities to collaborate on molecular pathway curation to create reusable, machine-readable pathway models. The pathway collections are freely available and integrated with many analysis tools and resources.
Figure 1.
Figure 1.
Recent growth of WikiPathways. The y-axes represent data for the human pathways accumulated in the database (approved content via http://rdf.wikipathways.org), focusing on the last three years (x-axes). (A) Total counts for all revisions, including contributor and automated revisions (black squares), the subset of revisions made by contributors (black diamonds) and individual contributors (red circles). (B) Total human pathway count. (C) Total counts for genes and proteins (black squares), interactions (black diamonds) and metabolites (red circles). Data colors match corresponding y-axes.
Figure 2.
Figure 2.
The number of revisions and contributors for all pathways in the human pathway analysis collection. The x-axis depicts how often pathways were updated (revised) on a logarithmic scale. The y-axis depicts the number of contributors who have worked on a pathway. The size of the dots expresses the number of pathways for that combination of contributors and revisions.
Figure 3.
Figure 3.
The COVID-19 Portal on WikiPathways (http://covid.wikipathways.org). The portal contains relevant information for COVID-19-related research, including all molecular pathways, contributors, and publications.
Figure 4.
Figure 4.
The WikiPathways SNORQL user interface (http://sparql.wikipathways.org). The WikiPathways SNORQL semantic web browser allows for user-friendly access to the WikiPathways RDF through providing example SPARQL queries (right panel).
See this image and copyright information in PMC

References

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