• Software

    • MetaMap 2016v2
  • Python packages

    • python 3.6
    • pandas
    • bcolz>=1.2.1

MetaMap installation

MetaMap is the base implement of the subpackage metamapWrap.
You need to activate a UMLS Terminology Services (UTS) account to fetch MetaMap. Please see MetaMap for more information.

MetaMap depends on Java. To install openJDK:

$ sudo apt install default-jdk

After downloading MetaMap and Extracting it, you can install it by:

$ cd ./public_mm/
$ bash ./bin/

At this point, you have successfully installed MetaMap.

Please add the bin directory to the environment variable PATH in bashrc for convenience:

$ export PATH=$PATH:/path_to_MetaMap/bin

Then, launch MetaMap server before running pyMeSHSim:

$ skrmedpostctl start
$ wsdserverctl start

Installation of pandas and bcolz

To install python package pandas and bcolz:

$ pip3 install pandas
$ pip3 install bcolz

Installation of pyMeSHSim

To install pyMeSHSim from source code:

$ git clone
$ cd pyMeSHSim
$ python3 ./ install