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

doi:10.7554/eLife.52614

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 journal › Article › peer-review

77 Scopus citations

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 language	English
Article number	e52614
Journal	eLife
Volume	9
DOIs	https://doi.org/10.7554/eLife.52614
State	Published - Mar 2020

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10.7554/eLife.52614

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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). Wikidata as a knowledge graph for the life sciences. eLife, 9, Article e52614. https://doi.org/10.7554/eLife.52614

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title = "Wikidata as a knowledge graph for the life sciences",

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.",

author = "Andra Waagmeester and Gregory Stupp and Sebastian Burgstaller-Muehlbacher and Good, {Benjamin M.} and Malachi Griffith and Griffith, {Obi L.} and Kristina Hanspers and Henning Hermjakob and Hudson, {Toby S.} and Kevin Hybiske and Keating, {Sarah M.} and Magnus Manske and Michael Mayers and Daniel Mietchen and Elvira Mitraka and Pico, {Alexander R.} and Timothy Putman and Anders Riutta and Nuria Queralt-Rosinach and Schriml, {Lynn M.} and Thomas Shafee and Denise Slenter and Ralf Stephan and Katherine Thornton and Ginger Tsueng and Roger Tu and Sabah Ul-Hasan and Egon Willighagen and Chunlei Wu and Su, {Andrew I.}",

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Waagmeester, A, Stupp, G, Burgstaller-Muehlbacher, S, Good, BM, Griffith, M , Griffith, OL, Hanspers, K, Hermjakob, H, Hudson, TS, Hybiske, K, Keating, SM, Manske, M, Mayers, M, Mietchen, D, Mitraka, E, Pico, AR, Putman, T, Riutta, A, Queralt-Rosinach, N, Schriml, LM, Shafee, T, Slenter, D, Stephan, R, Thornton, K, Tsueng, G, Tu, R, Ul-Hasan, S, Willighagen, E, Wu, C & Su, AI 2020, 'Wikidata as a knowledge graph for the life sciences', eLife, vol. 9, e52614. https://doi.org/10.7554/eLife.52614

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T1 - Wikidata as a knowledge graph for the life sciences

AU - Waagmeester, Andra

AU - Stupp, Gregory

AU - Burgstaller-Muehlbacher, Sebastian

AU - Good, Benjamin M.

AU - Griffith, Malachi

AU - Griffith, Obi L.

AU - Hanspers, Kristina

AU - Hermjakob, Henning

AU - Hudson, Toby S.

AU - Hybiske, Kevin

AU - Keating, Sarah M.

AU - Manske, Magnus

AU - Mayers, Michael

AU - Mietchen, Daniel

AU - Mitraka, Elvira

AU - Pico, Alexander R.

AU - Putman, Timothy

AU - Riutta, Anders

AU - Queralt-Rosinach, Nuria

AU - Schriml, Lynn M.

AU - Shafee, Thomas

AU - Slenter, Denise

AU - Stephan, Ralf

AU - Thornton, Katherine

AU - Tsueng, Ginger

AU - Tu, Roger

AU - Ul-Hasan, Sabah

AU - Willighagen, Egon

AU - Wu, Chunlei

AU - Su, Andrew I.

PY - 2020/3

Y1 - 2020/3

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AB - 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.

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JO - eLife

JF - eLife

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ER -

Wikidata as a knowledge graph for the life sciences

Abstract

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