Gene Wiki and Wikidata: an overview of 2015

2015 was a busy year for the Gene Wiki/Wikidata team—a naturally collaborative and evolving group of researchers from our lab, UCLA, the University of Maryland, Micelio, and more. The team imported about 132 thousand genes (59,530 human, 73,130 mouse) from NCBI into Wikidata and about 44 thousand proteins (27,662 human, 16,728 mouse) proteins from Swissprot. In addition to importing human and mouse genes and proteins into Wikidata, members of the Gene Wiki/Wikidata team have been working on importing bacterial genes and proteins, sourcing info for the Gene Wiki infoboxes from Wikidata, proposing new Wikidata properties, building tools and tutorials, and sharing their love for Wikipedia.

The HeartBD2K’s Cardiac Gene Wiki group (UCLA) added or improved over 300 heart-related Gene Wiki articles and presented on their efforts on multiple occasions throughout the year, with the last update of the year presented on Dec. 11, 2015 (and available on youtube).

Elvira Mitraka, a Gene Wiki/Wikidata team member from the University of Maryland, presented at WikiConference USA 2015 (October 9–11, Washington, D.C). Of course, her slides on “Open biomedical knowledge: Wikipedia, Wikidata, and beyond” are publicly available for anyone to view at figshare and a recording of her talk is available from WikiConferenceUSA.org.

Andra Waagmeester (Micelio), presented at the Open Data Institute Summit in London (Nov. 3, 2015). His compelling talk on “Making every human gene accessible and linkable” is available on the Open Data Institute’s youtube channel.

Sebastian Burgstaller-Muehlbacher, Ben, Andra, Tim and Elvira presented a tutorial on how to use Wikidata for biomedical information and beyond at the Semantic Web Applications and Tools for the Life Sciences International meeting (SWAT4LS) (12/7/2015 – 12/10/2015 Cambridge, UK).  Links to the tutorial presentations as well as additional Wikidata-related content are at http://tinyurl.com/swat4ls-wikidata.

Even better, Elvira’s excellent presentation on the team’s work earned their paper, “Wikidata: A platform for data integration and dissemination for the life sciences and beyond”, the best SWAT4LS paper prize. This paper is available from both the SWAT4LS site and biorxiv.

With another manuscript currently in revision and another well underway, 2015 ended with a bang for the Gene Wiki/Wikidata team, and 2016 is off to a great start.


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