Wikidata as a knowledge graph for the life sciences-Reference-Cited by-同舟云学术

Wikidata as a knowledge graph for the life sciences

Published:2020-03-17 Issue: Volume:9 Page:
ISSN:2050-084X
Container-title:eLife
language:en
Short-container-title:

Author:

Waagmeester Andra¹^ORCID,Stupp Gregory²^ORCID,Burgstaller-Muehlbacher Sebastian³^ORCID,Good Benjamin M²^ORCID,Griffith Malachi⁴^ORCID,Griffith Obi L⁴^ORCID,Hanspers Kristina⁵^ORCID,Hermjakob Henning⁶^ORCID,Hudson Toby S⁷^ORCID,Hybiske Kevin⁸^ORCID,Keating Sarah M⁶^ORCID,Manske Magnus⁹^ORCID,Mayers Michael²^ORCID,Mietchen Daniel¹⁰^ORCID,Mitraka Elvira¹¹^ORCID,Pico Alexander R⁵^ORCID,Putman Timothy²^ORCID,Riutta Anders⁵^ORCID,Queralt-Rosinach Nuria²^ORCID,Schriml Lynn M¹¹^ORCID,Shafee Thomas¹²^ORCID,Slenter Denise¹³^ORCID,Stephan Ralf¹⁴^ORCID,Thornton Katherine¹⁵^ORCID,Tsueng Ginger²^ORCID,Tu Roger²^ORCID,Ul-Hasan Sabah²^ORCID,Willighagen Egon¹³^ORCID,Wu Chunlei²^ORCID,Su Andrew I²^ORCID

Affiliation:

1. Micelio, Antwerpen, Belgium

2. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States

3. Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria

4. McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States

5. Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States

6. European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom

7. School of Chemistry, The University of Sydney, Sydney, Australia

8. Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, United States

9. Wellcome Trust Sanger Institute, Cambridge, United Kingdom

10. School of Data Science, University of Virginia, Charlottesville, United States

11. University of Maryland School of Medicine, Baltimore, United States

12. Department of Animal Plant and Soil Sciences, La Trobe University, Melbourne, Australia

13. Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands

14. Retired researcher, Berlin, Germany

15. Yale University Library, Yale University, New Haven, United States

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.

Funder

National Institute of General Medical Sciences

National Human Genome Research Institute

National Cancer Institute

V Foundation for Cancer Research

National Institute of Allergy and Infectious Diseases

National Center for Advancing Translational Sciences

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Link

https://cdn.elifesciences.org/articles/52614/elife-52614-v1.pdf

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