Toward an ontology-based framework for clinical research databases

J Biomed Inform. 2011 Feb;44(1):48-58. doi: 10.1016/j.jbi.2010.05.001. Epub 2010 May 10.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biomedical Research*
  • Computational Biology
  • Database Management Systems*
  • Databases, Factual*
  • Medical Informatics*
  • Models, Theoretical*
  • Research Design