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bioRxiv · 10.1101/032144

Wikidata as a semantic framework for the Gene Wiki initiative

Sebastian Burgstaller-Muehlbacher·Andra Waagmeester·Elvira Mitraka·Julia Turner·Tim E. Putman·Justin Leong·Paul Pavlidis·Lynn Schriml·Benjamin M. Good·Andrew I. Su
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Abstract

Open biological data is distributed over many resources making it challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia.\n\nIn order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata. In total, 59,530 human genes and 73,130 mouse genes have been imported from NCBI and 27,662 human proteins and 16,728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike. The first use case for this data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata is modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for a usage of the data we imported in all 280 different language Wikipedias. Apart from the Gene Wiki infobox use case, a powerful SPARQL endpoint and up to date exporting functionality (e.g. JSON, XML) enable very convenient further use of the data by scientists.\n\nIn summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web.

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Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim E. Putman, Justin Leong, Paul Pavlidis, Lynn Schriml, Benjamin M. Good, Andrew I. Su. 2015-11-18. Wikidata as a semantic framework for the Gene Wiki initiative. https://doi.org/10.1101/032144

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