Leveraging Transformers-based models and linked data for deep phenotyping in radiology.

Journal: Computer methods and programs in biomedicine
PMID: 39787917

Abstract

BACKGROUND AND OBJECTIVE: Despite significant investments in the normalization and the standardization of Electronic Health Records (EHRs), free text is still the rule rather than the exception in clinical notes. The use of free text has implications in data reuse methods used for supporting clinical research since the query mechanisms used in cohort definition and patient matching are mainly based on structured data and clinical terminologies. This study aims to develop a method for the secondary use of clinical text by: (a) using Natural Language Processing (NLP) for tagging clinical notes with biomedical terminology; and (b) designing an ontology that maps and classifies all the identified tags to various terminologies and allows for running phenotyping queries.

Authors

  • Lluís-F Hurtado
    VRAIN: Valencian Research Institute for Artificial Intelligence, Universitat Politècnica de València, Camí de Vera s/n, València, 46020, Spain; ValgrAI: Valencian Graduate School and Research Network of Artificial Intelligence, Camí de Vera s/n, València, 46020, Spain.
  • Luis Marco-Ruiz
    Norwegian Centre for e-Health Research, University Hospital of North Norway, P.O. Box 35, N-9038 Tromsø, Norway; Department of Clinical Medicine, Faculty of Health Sciences, UIT The Arctic University of Norway, 9037 Tromsø, Norway. Electronic address: Luis.Marco.Ruiz@telemed.no.
  • Encarna Segarra
    VRAIN: Valencian Research Institute for Artificial Intelligence, Universitat Politècnica de València, Camí de Vera s/n, València, 46020, Spain; ValgrAI: Valencian Graduate School and Research Network of Artificial Intelligence, Camí de Vera s/n, València, 46020, Spain.
  • Maria Jose Castro-Bleda
    Universitat Politècnica de València, Valencia, Spain.
  • Aurelia Bustos-Moreno
    AI Research Unit, MedBravo, Alicante, 03560, Spain.
  • Maria de la Iglesia-Vayá
    Foundation for the Promotion of the Research in Healthcare and Biomedicine (FISABIO), Avda. de Catalunya, 21, València, 46020, Spain.
  • Juan Francisco Vallalta-Rueda
    Laberit, Avda. de Catalunya, 9, València, 46020, Spain.

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