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The ConceptSimilarityServiceImpl java program accepts a list of concept pairs, and outputs their similarities in a tab-delimited format. It accepts the following arguments:

Java Command Line Arguments:

• -Dytex.conceptGraphName: to override the default concept graph name (defined in ytex.properties, by default sct-msh-csp-aod). e.g. -Dytex.conceptGraphName=umls to use the umls concept graph.
• -Xmx<memory>: set the java heap size.  The amount of memory needed depends on the concept graph.  For the sct-msh-csp-aod graph, 500 mb is sufficient (-Xmx500m), the larger UMLS concept graph requires 1.2GB (-Xmx1200m)

ConceptSimilarityServiceImpl Command Line Arguments:

• -metrics: required, comma separated list of metrics (see above in for valid values)
• -out: optional file to send output to. if not specified will send output to standard out.
• -lcs: should the least common subsumer and paths be output for each concept pair?
• -concepts: a list of concept pairs, or a file with concept pairs. For a file place each concept pair on a separate line, separate concepts by whitespace or commas. For a list of concept pairs, separate each concept by a comma, each pair by a semicolon:

cd CTAKES_HOME
bin\setenv.bat
java -cp %CLASSPATH% -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx1gXmx500m org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl -concepts C0018787,C0024109;C0034069,C0242379 -metrics LCH,INTRINSIC_LCH

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Web Interface

To start the Semantic Similarity Web Application, run CTAKES_HOME\bin\ytexweb.bat (windows) or CTAKES_HOME\bin\ytexweb.sh (linux) and open http://localhost:8080/semanticSim.jsf.

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