MetaMap

  • MetaMap installation and Running

  • All the below 3 things are required to be installed,in the same order, in case you want to use Metamap server from Java Program with UIMA. * Metamap main * Metamap Java API * Metamap UIMA

  • Allowing external hosts to access Metamap server

    • Go the folder (in server) where MetaMap is installed and edit the file ./public_mm/bin/mmserver, search for the following text in this file and edit it accordingly:

      if [ -z $ACCEPTED_HOSTS] ; then
ACCEPTED_HOSTS="['127.0.0.1','10.2.4.235','10.4.17.149']"
fi

  • Change the -Xmx options in public_mm/bin/skrmedpostctl and public_mm/bin/wsdserverctl [For Increasing the memory of MetaMap server]

  • Parsing Blogs or Clinical Texts

    • If you are parsing blogs or clinical texts which contain “newline” characters then replace them with a space (” “) before sending the input to MetaMap.
    • Although, there is another (a clean and preferred method given in 1, 2 and 3 (use –blanklines N option), somehow, I did not find success with this approach)

  • ps ax | grep java [To determine if MetaMap is running]

  • There is a cool python wrapper for MetaMap available in this repo. * This wrapper, in its current form works only for python 2.x * For making it work in python 3.x, I had to modify

    • /Users/nikhilpattisapu/miniconda2/envs/snakes/lib/python3.4/ site-packages/pymetamap-0.1-py3.4.egg/ pymetamap/__init__.py file.

    • I added the following statements in that file and everything worked fine:

      import sys
sys.path.append('/Users/nikhilpattisapu/git/pymetamap/pymetamap/')
import Concept

  • Metamap has some useful options which are of interest some of them are illustrated below. * -R SNOMEDCT_US,MEDLINE (Restrict Sources) * -A (Use strict model) * -J dsyn,sosy (Restrict to semantic types) * -K (ignore stop phrases).

  • These options can be passed to MetaMap through command line * Worked for public_mm/bin/metamap16 but did not work for public_mm/bin/mmserver16.

    • For using MetaMap as a server, I had run the public_mm/bin/mmserver16 on a different server and set the above useful options using MetaMap JavaAPI. An example snippet is shown below:

      // Include prologbeans.jar and MetaMapApi.jar
MetaMapApi api = new MetaMapApiImpl();

api.setHost("10.2.133.200");
api.setPort(8066);
List<String> theOptions = new ArrayList<String>();
api.setOptions("-y"); // Use WSD
theOptions.add("-A"); // Use strict model
theOptions.add("-K"); // Ignore stop phrases

theOptions.add("-J"); // Restrict to semantic types
theOptions.add("dsyn,sosy"); // No space between arguments

theOptions.add("-R"); // Restrict to Sources
theOptions.add("SNOMEDCT_US,MEDLINEPLUS"); // No space between arguments

if (theOptions.size() > 0)
{
    api.setOptions(theOptions);
}
String input = "I do not want a heart attack." // Example text
List<Result> resultList = api.processCitationsFromString(input);