Automating Clinical Chart Review: An Open-Source Natural Language Processing Pipeline Developed on Free-Text Radiology Reports From Patients With Glioblastoma.

Journal: JCO clinical cancer informatics
Published Date: Jan 1, 2020

Abstract

PURPOSE: The aim of this study was to develop an open-source natural language processing (NLP) pipeline for text mining of medical information from clinical reports. We also aimed to provide insight into why certain variables or reports are more suitable for clinical text mining than others.

Authors

  • Joeky T Senders
    Department of Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands; Computational Neurosciences Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
  • Logan D Cho
    Computational Neuroscience Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
  • Paola Calvachi
    Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America.
  • John J McNulty
    Computational Neuroscience Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
  • Joanna L Ashby
  • Isabelle S Schulte
    Computational Neuroscience Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
  • Ahmad Kareem Almekkawi
    Computational Neuroscience Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
  • Alireza Mehrtash
  • William B Gormley
    Computational Neurosciences Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
  • Timothy R Smith
    Computational Neurosciences Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
  • Marike L D Broekman
    Department of Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands; Computational Neurosciences Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
  • Omar Arnaout
    Computational Neurosciences Outcomes Center, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA. Electronic address: oarnaout@bwh.harvard.edu.

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