GEOMMTx,  Semantic Annotator for Biomedical Text

Requires:
UMLS isntallation
MMTx installation
Internet access

Installation: 
Copy mmtxProjectJS.jar from your MMTx installation folder to the project root folder (IS THIS NEEDED?)

Create a file "geommtx.properties" in  your home directory. Edit it to define "geommtx.home" and "mmtx.home"
 
Run mvn install to download libraries



Execution:
ubic.GEOMMTx.ExampleAnnotator.java provides a simple class for executing the pipeline.  It's input is the first command line argument, and it's output is example.rdf
Note: the first run may take some time as it makes the mappings for BIRNLex and Disease Ontology (after the first run its stored locally)

Contact: [email protected]