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.
Highlights
Integrating data and knowledge is a formidable challenge in biomedical research
We describe several representative biomedical use cases on how Wikidata can enable new analyses and improve the efficiency of research
Items relating to cell biochemistry. This example integrative query incorporates data on genetic associations to disease, Gene Ontology annotations for cellular compartment, protein target information for compounds, pathway data, and protein domain information. This query retrieves genes that are (i) associated with a respiratory system disease, (ii) that encode a membrane-bound protein, and (iii) that sit within the same biochemical pathway as (iv) a second gene encoding a protein with a serine-threonine kinase domain and (v) a known inhibitor, and reports a list of those inhibitors
Summary
Integrating data and knowledge is a formidable challenge in biomedical research. 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) [1], or even worse, locked away in free-text. We seeded Wikidata with content from public and authoritative resources on structured knowledge on genes and proteins [10] and chemical compounds [11].
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