SCIENCE FORUM 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 SchrimlThomas Shafee, Denise Slenter, Ralf Stephan, Katherine Thornton, Ginger Tsueng, Roger Tu, Sabah Ul-hasan, Egon Willighagen, Chunlei Wu, Andrew I Su

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
Article number52614
Number of pages15
JournalElife
Volume9
DOIs
Publication statusPublished - 17 Mar 2020

Keywords

  • DISORDER

Cite this

Waagmeester, A., Stupp, G., Burgstaller-muehlbacher, S., Good, B. M., Griffith, M., Griffith, O. L., Hanspers, K., Hermjakob, H., Hudson, T. S., Hybiske, K., Keating, S. M., Manske, M., Mayers, M., Mietchen, D., Mitraka, E., Pico, A. R., Putman, T., Riutta, A., Queralt-rosinach, N., ... Su, A. I. (2020). SCIENCE FORUM Wikidata as a knowledge graph for the life sciences. Elife, 9, [52614]. https://doi.org/10.7554/eLife.52614