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WikiPathways: connecting communities

Nucleic Acids Research, 2021-01, Vol.49 (D1), p.D613-D621 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021 ;The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. ;2020. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkaa1024 ;PMID: 33211851

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  • Title:
    WikiPathways: connecting communities
  • Author: Martens, Marvin ; Ammar, Ammar ; Riutta, Anders ; Waagmeester, Andra ; Slenter, Denise N ; Hanspers, Kristina ; A. Miller, Ryan ; Digles, Daniela ; Lopes, Elisson N ; Ehrhart, Friederike ; Dupuis, Lauren J ; Winckers, Laurent A ; Coort, Susan L ; Willighagen, Egon L ; Evelo, Chris T ; Pico, Alexander R ; Kutmon, Martina
  • Subjects: COVID-19 - pathology ; Data Curation ; Database Issue ; Databases, Factual ; Humans ; User-Computer Interface
  • Is Part Of: Nucleic Acids Research, 2021-01, Vol.49 (D1), p.D613-D621
  • Description: 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. 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.
  • Publisher: England: Oxford University Press
  • Language: English
  • Identifier: ISSN: 0305-1048
    EISSN: 1362-4962
    DOI: 10.1093/nar/gkaa1024
    PMID: 33211851
  • Source: Coronavirus Research Database
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