eLife (Mar 2020)
Wikidata as a knowledge graph for the life sciences
- Andra Waagmeester,
- Gregory Stupp,
- Sebastian Burgstaller-Muehlbacher,
- Benjamin M Good,
- Malachi Griffith,
- Obi L Griffith,
- Kristina Hanspers,
- Henning Hermjakob,
- Toby S Hudson,
- Kevin Hybiske,
- Sarah M Keating,
- Magnus Manske,
- Michael Mayers,
- Daniel Mietchen,
- Elvira Mitraka,
- Alexander R Pico,
- Timothy Putman,
- Anders Riutta,
- Nuria Queralt-Rosinach,
- Lynn M Schriml,
- Thomas Shafee,
- Denise Slenter,
- Ralf Stephan,
- Katherine Thornton,
- Ginger Tsueng,
- Roger Tu,
- Sabah Ul-Hasan,
- Egon Willighagen,
- Chunlei Wu,
- Andrew I Su
Affiliations
- Andra Waagmeester
- ORCiD
- Micelio, Antwerpen, Belgium
- Gregory Stupp
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Sebastian Burgstaller-Muehlbacher
- ORCiD
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
- Benjamin M Good
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Malachi Griffith
- ORCiD
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States
- Obi L Griffith
- ORCiD
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States
- Kristina Hanspers
- ORCiD
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
- Henning Hermjakob
- ORCiD
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
- Toby S Hudson
- ORCiD
- School of Chemistry, The University of Sydney, Sydney, Australia
- Kevin Hybiske
- ORCiD
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, United States
- Sarah M Keating
- ORCiD
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
- Magnus Manske
- ORCiD
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Michael Mayers
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Daniel Mietchen
- ORCiD
- School of Data Science, University of Virginia, Charlottesville, United States
- Elvira Mitraka
- ORCiD
- University of Maryland School of Medicine, Baltimore, United States
- Alexander R Pico
- ORCiD
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
- Timothy Putman
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Anders Riutta
- ORCiD
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
- Nuria Queralt-Rosinach
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Lynn M Schriml
- ORCiD
- University of Maryland School of Medicine, Baltimore, United States
- Thomas Shafee
- ORCiD
- Department of Animal Plant and Soil Sciences, La Trobe University, Melbourne, Australia
- Denise Slenter
- ORCiD
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
- Ralf Stephan
- ORCiD
- Retired researcher, Berlin, Germany
- Katherine Thornton
- ORCiD
- Yale University Library, Yale University, New Haven, United States
- Ginger Tsueng
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Roger Tu
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Sabah Ul-Hasan
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Egon Willighagen
- ORCiD
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
- Chunlei Wu
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- Andrew I Su
- ORCiD
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
- DOI
- https://doi.org/10.7554/eLife.52614
- Journal volume & issue
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Vol. 9
Abstract
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.
Keywords
