Toward an ontology-based framework for clinical research databases

Y. Megan Kong, Carl Dahlke, Qun Xiang, Yu Qian, David Karp, Richard H. Scheuermann

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


Clinical research includes a wide range of study designs from focused observational studies to complex interventional studies with multiple study arms, treatment and assessment events, and specimen procurement procedures. Participant characteristics from case report forms need to be integrated with molecular characteristics from mechanistic experiments on procured specimens. In order to capture and manage this diverse array of data, we have developed the Ontology-Based eXtensible data model (OBX) to serve as a framework for clinical research data in the Immunology Database and Analysis Portal (ImmPort). By designing OBX around the logical structure of the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI), we have found that a relatively simple conceptual model can represent the relatively complex domain of clinical research. In addition, the common framework provided by BFO makes it straightforward to develop data dictionaries based on reference and application ontologies from the OBO Foundry.

Original languageEnglish (US)
Pages (from-to)48-58
Number of pages11
JournalJournal of Biomedical Informatics
Issue number1
StatePublished - Feb 2011


  • Assay
  • Biomaterial transformation
  • Clinical trials
  • Conceptual model
  • Data transformation
  • Ontology

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics


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