A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses.

Journal: BMC biology
PMID:

Abstract

BACKGROUND: Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a "commons." Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions.

Authors

  • Andra Waagmeester
    Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.
  • Egon L Willighagen
    Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
  • Andrew I Su
    Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA, USA.
  • Martina Kutmon
    Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.
  • Jose Emilio Labra Gayo
    WESO Research Group, University of Oviedo, Oviedo, Spain.
  • Daniel Fernández-Álvarez
    WESO Research Group, University of Oviedo, Oviedo, Spain.
  • Quentin Groom
    Botanic Garden Meise, Nieuwelaan 38, Meise, 1860, Belgium.
  • Peter J Schaap
    Laboratory of Systems and Synthetic Biology, Wageningen University and Research, The Netherlands.
  • Lisa M Verhagen
    Intravacc, PO Box 450, 3720 AL, Bilthoven, The Netherlands.
  • Jasper J Koehorst
    Department of Agrotechnology and Food Sciences, Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands. jasper.koehorst@wur.nl.