Annotation and Detection of Drug Effects in Text for Pharmacovigilance

Paul Thompson, Sophia Daikou, Kenju Ueno, Riza Theresa Batista-Navarro, Junichi Tsujii, Sophia Ananiadou

Research output: Contribution to journalArticlepeer-review


Pharmacovigilance (PV) databases record the benefits and risks of different drugs, as a means to ensure their safe and effective use. Creating and maintaining such resources can be complex, since a particular medication may have divergent effects in different individuals, due to specific patient characteristics and/or interactions with other drugs being administered. Textual information from various sources can provide important evidence to curators of PV databases about the usage and effects of drug targets in different medical subjects. However, the efficient identification of relevant evidence can be challenging, due to the increasing volume of textual data. Text mining (TM) techniques can support curators by automatically detecting complex information, such as interactions between drugs, diseases and adverse effects. This semantic information supports the quick identification of documents containing information of interest (e.g., the different types of patients in which a given adverse drug reaction has been observed to occur). TM tools are typically adapted to different domains by applying machine learning methods to corpora that are manually labelled by domain experts using annotation guidelines to ensure consistency. We present a semantically annotated corpus of 600 MEDLINE abstracts, PHAEDRA, encoding rich information on drug effects and their interactions, whose quality is assured through the use of detailed annotation guidelines and the demonstration of high levels of inter-annotator agreement (e.g. 92.6% F-Score for identifying named entities and 78.4% F-Score for identifying complex events, when relaxed matching criteria are applied). To our knowledge, the corpus is unique in the domain of PV, according to the level of detail of its annotations. To illustrate the utility of the corpus, we have trained TM tools based on its rich labels to recognise drug effects in text automatically.
Original languageEnglish
Article number37
Number of pages33
JournalJournal of Cheminformatics
Issue number1
Early online date13 Aug 2018
Publication statusPublished - 2018


  • Adverse drug effects
  • Corpus annotation
  • Drug effects
  • Drug–drug interactions
  • Events
  • Pharmacovigilance
  • Resource curation
  • Text mining


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