Ontological Organization and Bioinformatic Analysis of Adverse Drug Reactions From Package Inserts: Development and...

Licensed drugs may cause unexpected adverse reactions in patients, resulting in morbidity, risk of mortality, therapy disruptions, and prolonged hospital stays. Officially approved drug package inserts list the adverse reactions identified from randomized controlled clinical trials with high evidence levels and worldwide postmarketing surveillance. Formal representation of the adverse drug reaction (ADR) enclosed in semistructured package inserts will enable deep recognition of side effects and rational drug use, substantially reduce morbidity, and decrease societal costs.

This paper aims to present an ontological organization of traceable ADR information extracted from licensed package inserts. In addition, it will provide machine-understandable knowledge for bioinformatics analysis, semantic retrieval, and intelligent clinical applications.

Based on the essential content of package inserts, a generic ADR ontology model is proposed from two dimensions (and nine subdimensions), covering the ADR information and medication instructions. This is followed by a customized natural language processing method programmed with Python to retrieve the relevant information enclosed in package inserts. After the biocuration and identification of retrieved data from the package insert, an ADR ontology is automatically built for further bioinformatic analysis.

We collected 165 package inserts of quinolone drugs from the National Medical Products Administration and other drug databases in China, and built a specialized ADR ontology containing 2879 classes and 15,711 semantic relations. For each quinolone drug, the reported ADR information and medication instructions have been logically represented and formally organized in an ADR ontology. To demonstrate its usage, the source data were further bioinformatically analyzed. For example, the number of drug-ADR triples and major ADRs associated with each active ingredient were recorded. The 10 ADRs most frequently observed among quinolones were identified and categorized based on the 18 categories defined in the proposal. The occurrence frequency, severity, and ADR mitigation method explicitly stated in package inserts were also analyzed, as well as the top 5 specific populations with contraindications for quinolone drugs.

Ontological representation and organization using officially approved information from drug package inserts enables the identification and bioinformatic analysis of adverse reactions caused by a specific drug with regard to predefined ADR ontology classes and semantic relations. The resulting ontology-based ADR knowledge source classifies drug-specific adverse reactions, and supports a better understanding of ADRs and safer prescription of medications.