Concepts

Creating Concepts Dictionary

1. Create a subset of the UMLS Metathesaurus using mmsys, or downloading one of the available subsets from the NLM. BioMedICUS has two subsets configuration files available in the tools/concepts directory.
2. Run the following command from a python environment with BioMedICUS installed

   b9 java edu.umn.biomedicus.concepts.ConceptDictionaryBuilder /PATH/TO/UMLS/20XXAX/META tools/concepts/TUIsOfInterest.txt 
   tools/concepts/BannedTTYs.txt concepts

3. Copy the concepts directory into the BioMedICUS data directory.

For more information about options available for the dictionary concept builder run

b9 java edu.umn.biomedicus.concepts.ConceptDictionaryBuilder --help