Abstract
Open biological data are distributed over many resources making them 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. In 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, 59 721 human genes and 73 355 mouse genes have been imported from NCBI and 27 306 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 these 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 are modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for usage of the data we imported in all 280 different language Wikipedias. Apart from the Gene Wiki infobox use case, a SPARQL endpoint and exporting functionality to several standard formats (e.g. JSON, XML) enable use of the data by scientists.In 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.Database URL: https://www.wikidata.org/
Highlights
Wikipedia is a well-established encyclopedia and collection of free form text, operated by the Wikimedia Foundation and edited by thousands of volunteer editors
As a first use case of the data, we focused on using the gene and protein data imported into Wikidata to populate Wikipedia Gene Wiki infoboxes
As a first use case of this data corpus, we demonstrated a remodelled Wikipedia Gene Wiki infobox which retrieves its data entirely from Wikidata, greatly simplifying the maintenance of these infoboxes
Summary
Wikipedia (www.wikipedia.org) is a well-established encyclopedia and collection of free form text, operated by the Wikimedia Foundation and edited by thousands of volunteer editors. As the seventh most-visited site on the Internet (http://www.alexa.com/topsites), Wikipedia has articles on a broad range of topics. With respect to molecular biology articles, at least two systematic efforts have been described, both initiated in 2007. The RNA Wikiproject created 600 new Wikipedia articles on non-coding RNA families [1]. Our Gene Wiki team created a collection of 8000 Wikipedia articles on human genes [2]. The Gene Wiki has grown into an integral and strongly interlinked part of the English Wikipedia, counting >11 000 articles [3, 4]. The Gene Wiki articles have been expanded by the Wikipedia community and are highly accessed by users of Wikipedia, collectively viewed >4 million times per month The Gene Wiki articles have been expanded by the Wikipedia community and are highly accessed by users of Wikipedia, collectively viewed >4 million times per month (according to http://stats.grok. se/en/)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
