Wikidata as a knowledge graph for the life sciences

eLife

Sebastian Burgstaller-Muehlbacher¹  Thomas Shafee²  Egon Willighagen³  Denise Slenter³  Michael Mayers⁴  Ginger Tsueng⁴  Roger Tu⁴  Nuria Queralt-Rosinach⁴  Timothy Putman⁴  Gregory Stupp⁴  Benjamin M Good⁴  Andrew I Su⁴  Chunlei Wu⁴  Sabah Ul-Hasan⁴  Kevin Hybiske⁵  Sarah M Keating⁶  Henning Hermjakob⁶  Anders Riutta⁷  Kristina Hanspers⁷  Alexander R Pico⁷  Obi L Griffith⁸  Malachi Griffith⁸  Andra Waagmeester⁹  Ralf Stephan^1,10  Toby S Hudson^1,11  Daniel Mietchen^1,12  Lynn M Schriml^1,13  Elvira Mitraka^1,13  Magnus Manske^1,14  Katherine Thornton^1,15 

[1] Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria;Department of Animal Plant and Soil Sciences, La Trobe University, Melbourne, Australia;Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands;Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States;Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, United States;European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom;Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States;McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States;Micelio, Antwerpen, Belgium;Retired researcher, Berlin, Germany;School of Chemistry, The University of Sydney, Sydney, Australia;School of Data Science, University of Virginia, Charlottesville, United States;University of Maryland School of Medicine, Baltimore, United States;Wellcome Trust Sanger Institute, Cambridge, United Kingdom;Yale University Library, Yale University, New Haven, United States;

关键词: science forum;    knowledge graphs;    data mining;    drug repurposing;    wikidata;   

DOI  :  10.7554/eLife.52614

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown