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nlp4sleep

A rule-based NLP algorithm to identify sleep-related concepts from clinical notes using the OHNLP MedTagger framework.

Definition of Sleep Concepts

Concept Category Definition Example
Snoring Snoring or snoring synonyms “snoring” “sleep apnea”
Napping Napping during daytime “napping” “doze”
Sleep problem Sleep problem, Specific sleep disorder/ condition/disease mentioned in the note “sleep disorder”, “insomnia”, “hypersomnia”
Bad sleep quality Any mention related to bad sleep quality in the note “sleeplessness” “couldn’t sleep during night” “staying up all night”
Daytime sleepiness Sleepiness during daytime “sleep a lot through out the day” “excessive daytime sleepiness”
Night wakings Night time wakings “frequent night waking” “waking up in the middle” “waking up 3-5 times”
Sleep duration (Short <=6h, Medium 6-8h, or Long >=8h) Duration of night time sleep “sleeps 4-5 hours” --> Short “sleep more than 12 hours” --> Long

Getting Started

Installation and Use of MedTagger

Video demo: https://vimeo.com/392331446

  1. Download the latest release from https://github.com/OHNLP/MedTagger/releases

  2. Extract the zip file

  3. Modify the INPUTDIR, OUTPUTDIR, and RULEDIR variables in run_medtagger_win.bat or run_medtagger_unix_mac.sh, as appropriate

    • INPUT_DIR: full directory path of input folder
    • OUTPUT_DIR: full directory path of output folder
    • RULES_DIR: full directory path of 'Rule' folder

    Example for Mac:

    INPUTDIR="$YOUR_INPUT_DIRECTORY"
OUTPUTDIR="$YOUR_OUTPUT_DIRECTORY"
RULEDIR="$YOUR_MEDTAGGER_HOME/medtaggerieresources/covid19"

    Example for Windows:

    INPUTDIR="C:\$YOUR_INPUT_DIRECTORY\input"
OUTPUTDIR="C:\$YOUR_OUTPUT_DIRECTORY\output"
RULEDIR="C:\YOUR_MEDTAGGER_HOME\medtaggerieresources\covid19"

  4. Run the batch file

    Mac/linux:

    run_medtagger_unix_mac.sh

    Windows:

    run_medtagger_win.bat

Citation

Sivarajkumar S, Tam TY, Ahamed Mohammad H, Viggiano S, Oniani D, Visweswaran S, Wang Y. Extraction of Sleep Information from Clinical Notes of Patients with Alzheimer’s Disease Using Natural Language Processing. Journal of American Medical Informatics Association. 2024.