UM Researcher Joins New NIH Partnership to Promote Organization of Big Data in Biomedicine

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Ontology sounds a lot like a medical specialty – but it’s not related to oncology, otolaryngology, or ophthalmology – except that researchers organizing big data in biomedicine into different ‘ontologies’ or categories could help expedite new drug targets and discoveries in these specialties and others in the future.

The University of Miami Miller School of Medicine is joining a partnership to combine advances in ontologies, templates and other research tools to take digital biomedical research data to the next level.

The National Institutes of Health has awarded a $2,088,678 U01 grant to be shared under a cooperative agreement between Stephan Schürer, Ph.D., Program Director, Drug Discovery, University of Miami Center for Computational Science, and associate professor of molecular and cellular pharmacology at the Miller School of Medicine; Mark A. Musen, M.D., Ph.D., professor of medicine at Stanford University and Director of the Stanford Center for Biomedical Informatics Research; and Barry Bunin, Ph.D., CEO of the private research informatics firm Collaborative Drug Discovery.

The award is part of a larger effort under the NIH Big Data to Knowledge (BD2K) program to support the development, improvement and implementation of tools and approaches that increase the efficiency and effectiveness of curation of digital biomedical research data. One goal is to make digital research objects findable, accessible, interoperable and reusable (FAIR).

Titled "Unifying Templates, Ontologies and Tools to Achieve Effective Annotation of Bioassay Protocols," this four-year joint project is creating a "glue technology," aptly named “OntoloBridge,” to bridge the gap between regular users of controlled scientific vocabularies and the creators of the underlying ontologies. This OntoloBridge will be built upon, and simultaneously validated by, three existing technologies:

  • The BioAssay Ontology (BAO) from the University of Miami
  • The Center for Expanded Data Annotation and Retrieval (CEDAR) workbench from Stanford University
  • BioAssay Express (BAE) from Collaborative Drug Discovery

Like any good partnership, the three principal investigators and their teams each bring complementary areas of expertise. The Schürer group will develop, maintain and expand the underlying ontologies and build infrastructure to support submission and processing of new terms. The Musen group will use their metadata framework for defining templates, enabling structured and consistent annotations. The Barry Bunin team at Collaborative Drug Discovery will create and maintain tools for annotating assays, and will coordinate economical annotation of increasing amounts of public and private data.