Rather than leave each research group to tackle data integration individually, Wikidata offers a new model for organizing all this information. Built on the same principles as Wikipedia, Wikidata enables anyone to add new information to an open community database.
While other Wikidata editors have added information on millions of items as diverse as works of art to U.S. cities, the TSRI team has focused on adding information on biomedical concepts.
TSRI Research Associate Sebastian Burgstaller-Muehlbacher, first author on one study, added data on all human and mouse genes, all human diseases and all drugs approved by the U.S. Food and Drug Administration.
Putman then extended Wikidata with a focus on microbial genomes. With all this information collected in one system, researchers can more easily spot connections between diseases, pathogens and biological processes. As an example, Putman used the model to show that other microorganisms in the body can influence chlamydia infections.
As a proof of concept, Putman led the development of a genome browser based on Wikidata. Rather than having to develop one browser for every sequenced genome, this genome browser allows users to browse any genome that has been loaded into Wikidata.
“You can zoom in on a gene, click on it and the sequence will pop up,” said Good. The genome browser will then link back to the original Wikidata entry. In the end, the researchers plan to have a comprehensive, uniform database that is easy to search and open to anyone who wants to add data and link related concepts. “We think this data should all be open,” said Su. “This just makes intuitive sense.” In addition to Su, Good, Putman and Burgstaller-Muehlbacher, authors of the paper, “Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes,” were Chunlei Wu of TSRI and Andra Waagmeester of Micelio. In addition to Su, Good, Putman, Burgstaller-Muehlbacher and Waagmeester, authors of the second study, “Wikidata as a semantic framework for the Gene Wiki initiative,” were Elvira Mitraka and Lynn Schriml of The University of Maryland, Baltimore; Justin Leong and Paul Pavlidis of the University of British Columbia; and Julia Turner of TSRI. Both studies were supported by the National Institutes of Health (grants GM089820, GM083924, GM114833 and DA036134).
About the Scripps Research Institute
The Scripps Research Institute (TSRI) is one of the world's largest independent, not-for-profit organizations focusing on research in the biomedical sciences. TSRI is internationally recognized for its contributions to science and health, including its role in laying the foundation for new treatments for cancer, rheumatoid arthritis, hemophilia, and other diseases. An institution that evolved from the Scripps Metabolic Clinic founded by philanthropist Ellen Browning Scripps in 1924, the institute now employs about 3,000 people on its campuses in La Jolla, CA, and Jupiter, FL, where its renowned scientists—including three Nobel laureates—work toward their next discoveries. The institute's graduate program, which awards PhD degrees in biology and chemistry, ranks among the top ten of its kind in the nation. For more information, see www.scripps.edu/.
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Database; GM089820, GM083924, GM114833 and DA036134