ClinicalTrials.gov Modules

A set of classes to be used in projects related to ClinicalTrials.gov.

cTAKES

To use the ctakes classes we need to install cTAKES:

1. Install Maven (This is for OS X, requires [Homebrew][], adapt accordingly)

    brew install maven
   

2. Run the script ctakes-extras/ctakes-install.sh, which will:

   • checkout a copy of cTAKES into ./ctakes-svn (if you haven't already) or update from the SVN repo
   • package cTAKES using Maven
   • move the compiled version to ./ctakes
   • copy over the extras in ./ctakes-extras

3. Create a file named ./umls.sh containing your UMLS username and password:

    UMLS_USERNAME='username'
    UMLS_PASSWORD='password'
   

This currently does not work correctly.

MetaMap

To use MetaMap, download and install MetaMap:

1. Download from NLM

2. Extract the archive into our root directory and rename it to metamap

3. Copy the script metamap-extras/run.sh to metamap/

4. Run the install script:

    ./metamap/bin/install.sh
   

NLTK

requirements:

• nltk