Using semantic predications to uncover drug-drug interactions in clinical data

Rui Zhang, Michael J. Cairelli, Marcelo Fiszman, Graciela Rosemblat, Halil Kilicoglu, Thomas C. Rindflesch, Serguei V. Pakhomov, Genevieve B. Melton

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


In this study we report on potential drug-drug interactions between drugs occurring in patient clinical data. Results are based on relationships in SemMedDB, a database of structured knowledge extracted from all MEDLINE citations (titles and abstracts) using SemRep. The core of our methodology is to construct two potential drug-drug interaction schemas, based on relationships extracted from SemMedDB. In the first schema, Drug1 and Drug2 interact through Drug1's effect on some gene, which in turn affects Drug2. In the second, Drug1 affects Gene1, while Drug2 affects Gene2. Gene1 and Gene2, together, then have an effect on some biological function. After checking each drug pair from the medication lists of each of 22 patients, we found 19 known and 62 unknown drug-drug interactions using both schemas. For example, our results suggest that the interaction of Lisinopril, an ACE inhibitor commonly prescribed for hypertension, and the antidepressant sertraline can potentially increase the likelihood and possibly the severity of psoriasis. We also assessed the relationships extracted by SemRep from a linguistic perspective and found that the precision of SemRep was 0.58 for 300 randomly selected sentences from MEDLINE. Our study demonstrates that the use of structured knowledge in the form of relationships from the biomedical literature can support the discovery of potential drug-drug interactions occurring in patient clinical data. Moreover, SemMedDB provides a good knowledge resource for expanding the range of drugs, genes, and biological functions considered as elements in various drug-drug interaction pathways.

Original languageEnglish (US)
Pages (from-to)134-147
Number of pages14
JournalJournal of Biomedical Informatics
StatePublished - Jun 2014

Bibliographical note

Funding Information:
This research was supported in part by an appointment to the NLM Research Participation Program, which is administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and the National Library of Medicine. This project was supported in part by the Intramural Research Program of the NIH, National Library of Medicine.


  • Drug-drug interactions
  • Natural language processing
  • SemMedDB
  • SemRep
  • Semantic predication


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