Submissions:2015/Open biomedical knowledge: Wikipedia, Wikidata, and beyond

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Open Biomedical Knowledge
Open biomedical knowledge: Wikipedia, Wikidata, and beyond
Type of submission
Elvira Mitraka, Andra Waagmeester, Sebastian Burgstaller, Benjamin Good, Lynn Schriml and Andrew Su
E-mail address
emitraka aka lv_ra
The Scripps Research Institute
University of Maryland
Since the Human Genome Project was completed in the year 2003, the life sciences have experienced an explosion in the quantity and diversity of data and knowledge produced. This information is spread across thousands of scientific journal articles (more than 1 million per year) and a variety databases (more than a 1000). The Gene Wiki project emerged in 2008 to provide a way to centralize information about human genes in a human-readable fashion in the form of Wikipedia articles. Now, in the second phase of this initiative, this project is expanding its scope to improve the Wikipedia representation of information about genes, diseases, drugs and their inter-relations to both foster education and stimulate scientific progress.

An important technical aspect of this work is the emergence of Wikidata, the open, centralized database now underlying all of the Wikipedias. Our basic approach is to: (1) develop programs (‘bots’) that draw structured biomedical information from trusted authorities and assemble this information in Wikidata, (2) enhance Wikipedia article infoboxes using this information (through wiki templates that query Wikidata), and (3) facilitate the community contribution of data that can be brought back into Wikidata. This approach not only increases the reliability and stability of the structured data in the relevant infoboxes, it also produces a unique, open warehouse of biomedical data in Wikidata that can be re-used in many other applications.

So far we have written bots that have generated Wikidata items for: all human genes, all mouse genes, all diseases represented in the Human Disease Ontology, and all FDA-approved drugs. We are currently working to expand our Wikidata representations of information about these items and are in the early phases of including this new content in the corresponding Wikipedia article infoboxes. We are actively seeking collaborators from the Wikipedia and Wikidata communities to help with all aspects of this initiative.

Anybody interested in our work can find informations about our ProteinBoxBot in Wikipedia and in Wikidata.

Video recording on Commons: File:Open Biomedical Knowledge - Wikipedia, Wikidata, and Beyond.webm

Length of presentation
30 min
Special schedule requests
If at all possible this would go well with Emw's workshop. So it might be nice to have them on the same day.
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  1. Emw (talk) 19:23, 31 August 2015 (EDT)
  2. Gaurav (talk) 22:13, 31 August 2015 (EDT)
  3. Hildabast (talk) 14:04, 6 October 2015 (EDT)
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