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

Title

Open biomedical knowledge: Wikipedia, Wikidata, and beyond

Theme

Outreach

Type of submission

Presentation

Author

Elvira Mitraka, Andra Waagmeester, Sebastian Burgstaller, Benjamin Good, Lynn Schriml and Andrew Su

E-mail address

elvira.mitraka@gmail.com

Username

emitraka aka lv_ra

Affiliation

The Scripps Research Institute
University of Maryland
micelio

Abstract

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.

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.

Will you attend WikiConference USA if your submission is not accepted?

Yes.

Interested attendees

If you are interested in attending this session, please sign with your username below. This will help reviewers to decide which sessions are of high interest. Sign with four tildes. (~~~~).

1. Emw (talk) 19:23, 31 August 2015 (EDT)
2. Gaurav (talk) 22:13, 31 August 2015 (EDT)
3. Add your username here.