Feature Article
Science Forum Wikidata as a knowledge graph for the life sciences
Rephetio results over time (Figure 5—figure supplement 1). This analysis demonstrates the value of a community-maintained, centralized knowledge base to which many researchers are contributing. It suggests that scientific analyses based on Wikidata may continually improve irrespective of any changes to the underlying algorithms, but simply based on progress in curating knowledge through the distributed, and largely uncoordinated efforts of the Wikidata community.
Outlook We believe that the design of Wikidata is wellaligned with the FAIR data principles. Findable: Wikidata items are assigned globally unique identifiers with direct cross-links into the massive online ecosystem of Wikipedias. Wikidata also has broad visibility within the Linked Data community and is listed in the life science registries FAIRsharing (https://fairsharing.org/; Sansone et al., 2019) and Identifiers. org (Wimalaratne et al., 2018). Wikidata has already attracted a robust, global community of contributors and consumers. Accessible: Wikidata provides access to its underlying knowledge graph via both an online graphical user interface and an API, and access includes both read- and write-privileges. Wikidata provides database dumps at least weekly (https:// www.wikidata.org/wiki/Wikidata:Database_ download), ensuring the long-term accessibility of the Wikidata knowledge graph independent of the organization and web application. Finally, Wikidata is also natively multilingual. Interoperable: Wikidata items are extensively cross-linked to other biomedical resources using Universal Resource Identifiers (URIs), which unambiguously anchor these concepts in the Linked Open Data cloud (Jacobsen et al., 2018). Wikidata is also available in many standard formats in computer programming and knowledge management, including JSON, XML, and RDF. Reusable: Data provenance is directly tracked in the reference section of the Wikidata statement model. The Wikidata knowledge graph is released under the Creative Commons Zero (CC0) Public Domain Declaration, which explicitly declares that there are no restrictions on downstream reuse and redistribution. The open data licensing of Wikidata is particularly notable. The use of data licenses in biomedical research has rapidly proliferated, presumably in an effort to protect intellectual property and/or justify long-term grant funding
Waagmeester et al. eLife 2020;9:e52614. DOI: https://doi.org/10.7554/eLife.52614
(see, for example, Reiser et al., 2016). However, even seemingly innocuous license terms (like requirements for attribution) still impose legal requirements and therefore expose consumers to legal liability. This liability is especially problematic for data integration efforts, in which the license terms of all resources (dozens or hundreds or more) must be independently tracked and satisfied (a phenomenon referred to as ’license stacking’). Because it is released under CC0, Wikidata can be freely and openly used in any other resource without any restriction. This freedom greatly simplifies and encourages downstream use, albeit at the cost of not being able to incorporate ontologies or datasets with more restrictive licensing. In addition to simplifying data licensing, Wikidata offers significant advantages in centralizing the data harmonization process. Consider the use case of trying to get a comprehensive list of disease indications for the drug bupropion. The National Drug File – Reference Terminology (NDF-RT) reported that bupropion may treat nicotine dependence and attention deficit hyperactivity disorder, the Inxight database listed major depressive disorder, and the FDA Adverse Event Reporting System (FAERS) listed anxiety and bipolar disorder. While no single database listed all these indications, Wikidata provided an integrated view that enabled seamless query and access across resources. Integrating drug indication data from these individual data resources was not a trivial process. Both Inxight and NDFRT mint their own identifiers for both drugs and diseases. FAERS uses Medical Dictionary for Regulatory Activities (MedDRA) names for diseases and free-text names for drugs (Stupp and Su, 2018). By harmonizing and integrating all resources in the context of Wikidata, we ensure that those data are immediately usable by others without having to repeat the normalization process. Moreover, by harmonizing data at the time of data loading, consumers of that data do not need to perform the repetitive and redundant work at the point of querying and analysis. As the biomedical data within Wikidata continues to grow, we believe that its unencumbered use will spur the development of many new innovative tools and analyses. These innovations will undoubtedly include the machine learning-based mining of the knowledge graph to predict new relationships (also referred to as knowledge graph reasoning; Das et al., 2017; Lin et al., 2018; Xiong et al., 2017). For those who subscribe to this vision for cultivating a FAIR and open graph of biomedical
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