FEATURE ARTICLE
SCIENCE FORUM
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.
ANDRA WAAGMEESTER†, GREGORY STUPP†, SEBASTIAN BURGSTALLERMUEHLBACHER, 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 AND ANDREW I SU*
Introduction
- For correspondence: asu@
scripps.edu †
These authors contributed equally to this work
Competing interests: The authors declare that no competing interests exist. Funding: See page 12 Reviewing editor: Peter Rodgers, eLife, United Kingdom Copyright Waagmeester et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
Integrating data and knowledge is a formidable challenge in biomedical research. Although new scientific findings are being discovered at a rapid pace, a large proportion of that knowledge is either locked in data silos (where integration is hindered by differing nomenclature, data models, and licensing terms; Wilkinson et al., 2016) or locked away in freetext. The lack of an integrated and structured version of biomedical knowledge hinders efficient querying or mining of that information, thus preventing the full utilization of our accumulated scientific knowledge. Recently, there has been a growing emphasis within the scientific community to ensure all scientific data are FAIR – Findable, Accessible, Interoperable, and Reusable – and there is a growing consensus around a concrete set of principles to ensure FAIRness (Wilkinson et al., 2019; Wilkinson et al., 2016). Widespread implementation of these principles would greatly
Waagmeester et al. eLife 2020;9:e52614. DOI: https://doi.org/10.7554/eLife.52614
advance efforts by the open-data community to build a rich and heterogeneous network of scientific knowledge. That knowledge network could, in turn, be the foundation for many computational tools, applications and analyses. Most data- and knowledge-integration initiatives fall on either end of a spectrum. At one end, centralized efforts seek to bring multiple knowledge sources into a single database (see, for example, Mungall et al., 2017): this approach has the advantage of data alignment according to a common data model and of enabling high performance queries. However, centralized resources are difficult and expensive to maintain and expand (Chandras et al., 2009; Gabella et al., 2018), at least in part because of bottlenecks that are inherent in a centralized design. At the other end of the spectrum, distributed approaches to data integration result in a broad landscape of individual resources, focusing on technical infrastructure to query and integrate
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