MetaMap Med Term Frequency Builder

Building medical term dictionary with word frequency using metamap.

MetaMap Installation

https://metamap.nlm.nih.gov/download/public_mm_linux_main_2020.tar.bz2

https://metamap.nlm.nih.gov/download/public_mm_linux_javaapi_2020.tar.bz2

Copy all files from javaapi/public_mm/bin to public_mm_linux_main_2020/public_mm/bin

Copy javaapi/public_mm/bin/mmserver to public_mm_linux_main_2020/public_mm

To install server, run inside public_mm

bin/instal.sh

MetaMap Server Run

Set working directory export $MED_FREQUENCY_WORKDIR=/YOURS_WORKDIR

Copy files from this repo ./scripts folder to public_mm_linux_main_2020/public_mm

chmod +x start.sh stop.sh

Replace absolute path for metamap public_mm folder

To run all servers execute ./start.sh (mmserver std output will start in terminal)

To stop all servers execute ./stop.sh

For install service run

./installMetamapService.sh

Example Execution

Provide spring active profile equal to example

export SPRING_PROFILES_ACTIVE=example

Example will show MetaMap results for hardcoded piece of medical document.

MIMIC III NoteEvents Execution

Unset example spring active profile if set.

unset SPRING_PROFILES_ACTIVE

Provide path to noteevents file

export APP_NOTEEVENTS=file:"$MED_FREQUENCY_WORKDIR"/noteevents.csv

By default noteevents path set to

app:
  noteEvents: file:${MED_FREQUENCY_WORKDIR}/noteevents.csv