Cohort profile: St. Michael's Hospital Tuberculosis Database (SMH-TB), a retrospective cohort of electronic health record data and variables extracted using natural language processing.

Journal: PloS one
Published Date: Jan 1, 2021

Abstract

BACKGROUND: Tuberculosis (TB) is a major cause of death worldwide. TB research draws heavily on clinical cohorts which can be generated using electronic health records (EHR), but granular information extracted from unstructured EHR data is limited. The St. Michael's Hospital TB database (SMH-TB) was established to address gaps in EHR-derived TB clinical cohorts and provide researchers and clinicians with detailed, granular data related to TB management and treatment.

Authors

  • David Landsman
    MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.
  • Ahmed Abdelbasit
    Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
  • Christine Wang
    Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
  • Michael Guerzhoy
    Princeton University, Princeton, New Jersey, United States of America.
  • Ujash Joshi
    University of Toronto, Toronto, Ontario, Canada.
  • Shaun Mathew
    Department of Computer Science, Ryerson University, Toronto, Ontario, Canada.
  • Chloe Pou-Prom
    Unity Health Toronto (Verma, Murray, Straus, Pou-Prom, Mamdani); Li Ka Shing Knowledge Institute of St. Michael's Hospital (Verma, Straus, Pou-Prom, Mamdani); Department of Medicine (Verma, Shojania, Straus, Mamdani) and Institute of Health Policy, Management, and Evaluation (Verma, Mamdani) and Department of Statistics (Murray), University of Toronto, Toronto, Ont.; University of Alberta (Greiner); Alberta Machine Intelligence Institute (Greiner), Edmonton, Alta.; Montreal Institute for Learning Algorithms (Cohen), Montréal, Que.; Centre for Quality Improvement and Patient Safety (Shojania), University of Toronto; Sunnybrook Health Sciences Centre (Shojania); Vector Institute (Ghassemi, Mamdani) and Department of Computer Science (Ghassemi); Leslie Dan Faculty of Pharmacy (Mamdani), University of Toronto, Toronto, Ont.; Department of Radiology, Stanford University (Cohen), Stanford, Calif.
  • David Dai
    Unity Health Toronto, Toronto, Ontario, Canada.
  • Victoria Pequegnat
    Decision Support Services, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.
  • Joshua Murray
    Unity Health Toronto (Verma, Murray, Straus, Pou-Prom, Mamdani); Li Ka Shing Knowledge Institute of St. Michael's Hospital (Verma, Straus, Pou-Prom, Mamdani); Department of Medicine (Verma, Shojania, Straus, Mamdani) and Institute of Health Policy, Management, and Evaluation (Verma, Mamdani) and Department of Statistics (Murray), University of Toronto, Toronto, Ont.; University of Alberta (Greiner); Alberta Machine Intelligence Institute (Greiner), Edmonton, Alta.; Montreal Institute for Learning Algorithms (Cohen), Montréal, Que.; Centre for Quality Improvement and Patient Safety (Shojania), University of Toronto; Sunnybrook Health Sciences Centre (Shojania); Vector Institute (Ghassemi, Mamdani) and Department of Computer Science (Ghassemi); Leslie Dan Faculty of Pharmacy (Mamdani), University of Toronto, Toronto, Ont.; Department of Radiology, Stanford University (Cohen), Stanford, Calif.
  • Kamalprit Chokar
    Division of Respirology, Department of Medicine, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.
  • Michaelia Banning
    Unity Health Toronto, Toronto, Ontario, Canada.
  • Muhammad Mamdani
    Unity Health Toronto (Verma, Murray, Straus, Pou-Prom, Mamdani); Li Ka Shing Knowledge Institute of St. Michael's Hospital (Verma, Straus, Pou-Prom, Mamdani); Department of Medicine (Verma, Shojania, Straus, Mamdani) and Institute of Health Policy, Management, and Evaluation (Verma, Mamdani) and Department of Statistics (Murray), University of Toronto, Toronto, Ont.; University of Alberta (Greiner); Alberta Machine Intelligence Institute (Greiner), Edmonton, Alta.; Montreal Institute for Learning Algorithms (Cohen), Montréal, Que.; Centre for Quality Improvement and Patient Safety (Shojania), University of Toronto; Sunnybrook Health Sciences Centre (Shojania); Vector Institute (Ghassemi, Mamdani) and Department of Computer Science (Ghassemi); Leslie Dan Faculty of Pharmacy (Mamdani), University of Toronto, Toronto, Ont.; Department of Radiology, Stanford University (Cohen), Stanford, Calif. muhammad.mamdani@unityhealth.to amol.verma@mail.utoronto.ca.
  • Sharmistha Mishra
    MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.
  • Jane Batt
    Keenan Research Center for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada.

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