Regular expression-based learning to extract bodyweight values from clinical notes

Journal of Biomedical Informatics
Maureen A MurtaughQing Zeng-Treitler

Abstract

Bodyweight related measures (weight, height, BMI, abdominal circumference) are extremely important for clinical care, research and quality improvement. These and other vitals signs data are frequently missing from structured tables of electronic health records. However they are often recorded as text within clinical notes. In this project we sought to develop and validate a learning algorithm that would extract bodyweight related measures from clinical notes in the Veterans Administration (VA) Electronic Health Record to complement the structured data used in clinical research. We developed the Regular Expression Discovery Extractor (REDEx), a supervised learning algorithm that generates regular expressions from a training set. The regular expressions generated by REDEx were then used to extract the numerical values of interest. To train the algorithm we created a corpus of 268 outpatient primary care notes that were annotated by two annotators. This annotation served to develop the annotation process and identify terms associated with bodyweight related measures for training the supervised learning algorithm. Snippets from an additional 300 outpatient primary care notes were subsequently annotated independently by two reviewer...Continue Reading

References

Mar 16, 2005·American Journal of Preventive Medicine·Sandeep R DasSteven J Yevich
Dec 18, 2009·BMC Health Services Research·Stephanie A RoseJames B Meigs
Mar 20, 2012·American Journal of Preventive Medicine·Beverly B GreenRobert Reid
Apr 26, 2012·Nursing·Phyllis Hart TiptonMarjory Williams
Nov 19, 2013·Tropical Medicine & International Health : TM & IH·Susan P Fisher-HochJoseph B McCormick
Feb 4, 2014·American Journal of Epidemiology·Christopher G Chute
Mar 1, 2014·Journal of the American Medical Informatics Association : JAMIA·Duy Duc An Bui, Qing Zeng-Treitler

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Citations

Jan 17, 2019·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Abhyuday JagannathaHong Yu
Sep 2, 2017·Digestive Diseases and Sciences·Joseph S RedmanFasiha Kanwal
Aug 10, 2020·Journal of Biomedical Informatics·Sunyang FuHongfang Liu
Jul 30, 2021·Current Opinion in Ophthalmology·Lily Wei Yun YangDaniel Shu Wei Ting
Jul 26, 2019··Lihong HeSlobodan Vucetic

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