Extraction of potential adverse drug events from medical case reports

Abstract

: The sheer amount of information about potential adverse drug events published in medical case reports pose major challenges for drug safety experts to perform timely monitoring. Efficient strategies for identification and extraction of information about potential adverse drug events from free-text resources are needed to support pharmacovigilance research and pharmaceutical decision making. Therefore, this work focusses on the adaptation of a machine learning-based system for the identification and extraction of potential adverse drug event relations from MEDLINE case reports. It relies on a high quality corpus that was manually annotated using an ontology-driven methodology. Qualitative evaluation of the system showed robust results. An experiment with large scale relation extraction from MEDLINE delivered under-identified potential adverse drug events not reported in drug monographs. Overall, this approach provides a scalable auto-assistance platform for drug safety professionals to automatically collect potential adverse drug events communicated as free-text data.

Figure 1

Example of an annotated sentence in the ADE corpus. Example of a sentence annotated with drug, conditions, and relations between them in the ADE corpus. True indicates presence of adverse effect relation and False indicates absence of adverse effect relation.

Figure 2

Ontologies discussed in this work. Mappings between ADE, OAE, and CLEF ontologies have been shown. Identical entities are in boxes with same colours. Condition in the CLEF ontology is mapped to Process in the OAE.