Page History

...

YTEX allows the declarative definition of concept graphs in which nodes represent concepts and edges taxonomical relationships, and can compute the similarity between nodes in these graphs. YTEX comes with two concept graphs derived from the UMLS (version 2011AB)2013AA)

• sct-rxnorm: concepts from SNOMED-CT and RXNORM.  This is the default.
• sct-msh-csp-aod: concepts from the SNOMED-CT, MeSH, CRISP, and Alcohol and Drug thesaurus
• umls: concepts from all restriction free (level 0) UMLS source vocabularies and SNOMED-CT

...

• -Dytex.conceptGraphName: to override the default concept graph name (defined in ytex.properties, by default sct-msh-csp-aodrxnorm). 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 rxnorm graph, 500 256 mb is sufficient (-Xmx500mXmx256m), the larger UMLS concept graph requires 1.2GB 1200 mb (-Xmx1200m)

ConceptSimilarityServiceImpl Command Line Arguments:

...

cd CTAKES_HOME
bin\setenv.bat
java -cp %CLASSPATH% -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx500mXmx256m org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl -concepts C0018787,C0024109;C0034069,C0242379 -metrics LCH,INTRINSIC_LCH

...