Unable to use umls concept graph in SenseDisambiguatorAnnotator

[Bhaskar B]

I am using apache-ctakes-3.1.2 and am unable to use the WSD feature with the UMLS concept graph.  I've listed the steps that I took below.  Please note that it is working with the default concept graph: sct-msh-csp-aod.  Has anyone encountered this before?  Has the version of ConceptGraph class changed? If I need to create a new concept graph, how long does it take (rough idea)?

(1) Downloaded the concept graph umls.zip from the link (http://www.ytex-nlp.org/umls.download/secure/0.7/umls.zip) as per the instructions given on the page https://code.google.com/p/ytex/wiki/Installation_V07.

(2) Exploded umls.zip and copied umls.gz to c:\bin\apache-ctakes-3.1.2-SNAPSHOT\resources\org\apache\ctakes\ytex\conceptGraph.

(3) Added the property ytex.conceptGraphName=umls to ytex.properties in C:\bin\apache-ctakes-3.1.2-SNAPSHOT\resources\org\apache\ctakes\ytex.

(4) Started CAS Visual Debugger (CVD).

(5) Clicked on Run -> Load AE, and selected C:\bin\apache-ctakes-3.1.2-SNAPSHOT\desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml.

(6) I am getting the following error:

[Note that I had to modify the method readConceptGraph(String name) in ConceptDaoImpl.java and put in the following statement to capture the error - log.error(ioe.getMessage() + " : " + ExceptionUtils.getFullStackTrace(ioe));.  This is the only change that I introduced.] 

15:51:57,239 INFO  [ConceptDaoImpl] loading concept graph from file:/C:/bin/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/ytex/conceptGraph/umls.gz

15:51:57,287 ERROR [ConceptDaoImpl] invalid type code: 00 : java.io.StreamCorruptedException: invalid type code: 00

at java.io.ObjectInputStream.readObject0(Unknown Source)

at java.io.ObjectInputStream.defaultReadFields(Unknown Source)

at java.io.ObjectInputStream.readSerialData(Unknown Source)

at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

at java.io.ObjectInputStream.readObject0(Unknown Source)

at java.io.ObjectInputStream.readArray(Unknown Source)

at java.io.ObjectInputStream.readObject0(Unknown Source)

at java.io.ObjectInputStream.defaultReadFields(Unknown Source)

at java.io.ObjectInputStream.readSerialData(Unknown Source)

at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

at java.io.ObjectInputStream.readObject0(Unknown Source)

at java.io.ObjectInputStream.defaultReadFields(Unknown Source)

at java.io.ObjectInputStream.readSerialData(Unknown Source)

at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

at java.io.ObjectInputStream.readObject0(Unknown Source)

at java.io.ObjectInputStream.readObject(Unknown Source)

at org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl.readConceptGraph(ConceptDaoImpl.java:496)

at org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl.getConceptGraph(ConceptDaoImpl.java:341)

        . . . . . .

        . . . . . .

Thanks in advance,

Bhaskar.

[vijay garla]

I'm not sure what the issue is.  I will regenerate the UMLS concept graph and upload it.

Best,

VJ

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[Bhaskar B]

Hi VJ, thanks for the reply.  I was able to create graphs of subsets of UMLS for my purpose using ConceptDaoImpl.  Haven't yet created one from the entire UMLS but I think I should be able to create it.  But it may be useful to others in case they run into something similar.

Cheers.