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. medRxiv. Journal of American Medical Informatics Association. 2024.