Installation¶

Requirements¶

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/install.sh

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 https://github.com/luozhhub/pyMeSHSim.git
$ cd pyMeSHSim
$ python3 ./setup.py install