Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text

Robert Eriksson, Peter Bjødstrup Jensen, Sune Frankild, Lars Juhl Jensen, Søren Brunak

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

OBJECTIVE: Drugs have tremendous potential to cure and relieve disease, but the risk of unintended effects is always present. Healthcare providers increasingly record data in electronic patient records (EPRs), in which we aim to identify possible adverse events (AEs) and, specifically, possible adverse drug events (ADEs).

MATERIALS AND METHODS: Based on the undesirable effects section from the summary of product characteristics (SPC) of 7446 drugs, we have built a Danish ADE dictionary. Starting from this dictionary we have developed a pipeline for identifying possible ADEs in unstructured clinical narrative text. We use a named entity recognition (NER) tagger to identify dictionary matches in the text and post-coordination rules to construct ADE compound terms. Finally, we apply post-processing rules and filters to handle, for example, negations and sentences about subjects other than the patient. Moreover, this method allows synonyms to be identified and anatomical location descriptions can be merged to allow appropriate grouping of effects in the same location.

RESULTS: The method identified 1 970 731 (35 477 unique) possible ADEs in a large corpus of 6011 psychiatric hospital patient records. Validation was performed through manual inspection of possible ADEs, resulting in precision of 89% and recall of 75%.

DISCUSSION: The presented dictionary-building method could be used to construct other ADE dictionaries. The complication of compound words in Germanic languages was addressed. Additionally, the synonym and anatomical location collapse improve the method.

CONCLUSIONS: The developed dictionary and method can be used to identify possible ADEs in Danish clinical narratives.

Original languageEnglish
JournalJAMIA
Volume20
Issue number5
Pages (from-to)947-953
Number of pages7
ISSN1067-5027
DOIs
Publication statusPublished - 25. May 2013
Externally publishedYes

Keywords

  • Data Mining
  • Denmark
  • Dictionaries, Medical
  • Drug-Related Side Effects and Adverse Reactions
  • Electronic Health Records
  • Humans
  • Narration

Fingerprint

Dive into the research topics of 'Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text'. Together they form a unique fingerprint.

Cite this