WikiPathways: Connecting Communities

Marvin Martens, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N Slenter, Kristina Hanspers, Ryan Miller, Daniela Digles, Elisson Lopes, Friederike Ehrhart, Lauren Dupuis, Laurent Winckers, Susan L Coort, Egon L. Willighagen, Chris T. Evelo, Alexander R Pico, Martina Kutmon (Corresponding author)

    Publications: Contribution to journalArticlePeer Reviewed

    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.
    Original languageEnglish
    Pages (from-to)D613–D621
    Number of pages9
    JournalNucleic Acids Research
    Volume49
    Issue numberD1
    Early online date19 Nov 2020
    DOIs
    Publication statusPublished - 8 Jan 2021

    Austrian Fields of Science 2012

    • 301207 Pharmaceutical chemistry

    Keywords

    • FRAMEWORK
    • SET ENRICHMENT ANALYSIS

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