Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development

AMIA Annu Symp Proc. 2015 Nov 5;2015:441-7. eCollection 2015.


We examined a large body of research study documents (protocols) to identify mentions of drug concepts and established base concepts and roles needed to characterize the semantics of these instances. We found these concepts in three general situations: background knowledge about the drug, study procedures involving the drug, and other roles of the drug in the study. We identified 18 more specific contexts (e.g., adverse event information, administration and dosing of the drug, and interactions between the study drug and other drugs). The ontology was validated against a test set of protocol documents from NIH and The goal is to support the automated extraction of drug information from protocol documents to support functions such as study retrieval, determination of subject eligibility, generation of order sets, and creation of logic for decision support alerts and reminders. Further work is needed to formally extend existing ontologies of clinical research.

MeSH terms

  • Biological Ontologies*
  • Clinical Protocols / standards*
  • Decision Support Systems, Clinical / standards*
  • Drug Therapy, Computer-Assisted / standards*
  • Humans
  • Information Storage and Retrieval
  • Pharmaceutical Preparations / administration & dosage*
  • Semantics


  • Pharmaceutical Preparations