Drug knowledge bases and their applications in biomedical informatics research

Brief Bioinform. 2019 Jul 19;20(4):1308-1321. doi: 10.1093/bib/bbx169.


Recent advances in biomedical research have generated a large volume of drug-related data. To effectively handle this flood of data, many initiatives have been taken to help researchers make good use of them. As the results of these initiatives, many drug knowledge bases have been constructed. They range from simple ones with specific focuses to comprehensive ones that contain information on almost every aspect of a drug. These curated drug knowledge bases have made significant contributions to the development of efficient and effective health information technologies for better health-care service delivery. Understanding and comparing existing drug knowledge bases and how they are applied in various biomedical studies will help us recognize the state of the art and design better knowledge bases in the future. In addition, researchers can get insights on novel applications of the drug knowledge bases through a review of successful use cases. In this study, we provide a review of existing popular drug knowledge bases and their applications in drug-related studies. We discuss challenges in constructing and using drug knowledge bases as well as future research directions toward a better ecosystem of drug knowledge bases.

Keywords: adverse drug reaction analysis; biomedical text mining; drug knowledge bases; drug repositioning; pharmacogenomic analysis.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Algorithms
  • Computational Biology / methods
  • Computational Biology / trends
  • Data Mining
  • Databases, Pharmaceutical* / statistics & numerical data
  • Databases, Pharmaceutical* / trends
  • Drug Development
  • Drug Interactions
  • Drug Repositioning
  • Drug-Related Side Effects and Adverse Reactions
  • Humans
  • Knowledge Bases*
  • Machine Learning
  • Pharmacogenomic Testing
  • Social Media
  • Systems Integration