Natural language processing for disease phenotyping in UK primary care records for research: a pilot study in myocardial infarction and death.

Journal: Journal of biomedical semantics
Published Date: Nov 12, 2019

Abstract

BACKGROUND: Free text in electronic health records (EHR) may contain additional phenotypic information beyond structured (coded) information. For major health events - heart attack and death - there is a lack of studies evaluating the extent to which free text in the primary care record might add information. Our objectives were to describe the contribution of free text in primary care to the recording of information about myocardial infarction (MI), including subtype, left ventricular function, laboratory results and symptoms; and recording of cause of death. We used the CALIBER EHR research platform which contains primary care data from the Clinical Practice Research Datalink (CPRD) linked to hospital admission data, the MINAP registry of acute coronary syndromes and the death registry. In CALIBER we randomly selected 2000 patients with MI and 1800 deaths. We implemented a rule-based natural language engine, the Freetext Matching Algorithm, on site at CPRD to analyse free text in the primary care record without raw data being released to researchers. We analysed text recorded within 90 days before or 90 days after the MI, and on or after the date of death.

Authors

  • Anoop D Shah
    Farr Institute of Health Informatics Research, Institute of Health Informatics, University College London, London, United Kingdom.
  • Emily Bailey
    University College London Hospitals NHS Foundation Trust, 235 Euston Road, London, NW1 2BU, UK.
  • Tim Williams
    Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, 10 South Colonnade, London, E14 4PU, UK.
  • Spiros Denaxas
    UCL Institute of Health Informatics and Farr Institute of Health Informatics Research, London, United Kingdom.
  • Richard Dobson
    King's College London, Institute of Psychiatry, NIHR Biomedical Research Centre for Mental Health at the South London and Maudsley NHS Foundation Trust, London, UK King's College London, Institute of Psychiatry, NIHR Biomedical Research Unit for Dementia at the South London and Maudsley NHS Foundation Trust, London, UK.
  • Harry Hemingway
    Institute of Health Informatics, University College London, London, UK.

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