RE: [External] RE: How to augment/modify UMLS resources?

["Lee, Richard A. [USA]" <le...@bah.com>]

Rather than edit AggregatePlainTextUMLSProcessor.xml directly, I tried to keep things clean by creating a copy of it and editing that. I made the two additions you recommend, and provided the new name and updated description under <analysisEngineMetaData>. Then told CVD to load that new AE specifier file.

Sadly, that produced a "SEVERE" exception when trying to find or load DictionaryLookupAnnotatorCSV.xml, which has not changed from the downloaded version. I looked at the stacktrace in the log file (the top of which is shown below), and used a browser to confirm that the path to that file is correct and the file appears to be valid XML. Since the stacktrace is silent as to _why_ the Initialization failed, as far as I can see, I'm not sure how to resolve this.

Any suggestions?

-- stacktrace --
1/8/14 4:41:04 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator" failed.  (Descriptor: file:/.../apache-ctakes-3.1.1/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator" failed.  (Descriptor: file:/.../apache-ctakes-3.1.1/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
...

-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu] 
Sent: Mon, 06 Jan, 2014 16:50
To: 'user@ctakes.apache.org'
Subject: [External] RE: How to augment/modify UMLS resources?

Hi Lee,

As you have discovered, the dictionary1.csv is not used by AggregatePlainTextProcessor.xml

AggregatePlainTextProcessor.xml uses a (tiny) lucene index for the few words like knee and pain that are annotated without using the larger UMLS resource.

I think to use the csv instead of the other methods, you would modified AggregatePlainTextProcessor.xml to refer to DictionaryLookupAnnotatorCSV.xml instead of DictionaryLookupAnnotator.xml where there currently is the line <import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotator.xml"/>

I can't remember offhand if there are parameters you have to update too, but I don't think so.

Hopefully that will give you an idea then of what to add to AggregatePlainTextUMLSProcessor.xml to get both the UMLS and your csv dictionary in effect.

(You would add the following to the delegateAnalysisEngine list of AggregatePlainTextUMLSProcessor.xml

<delegateAnalysisEngine key="DictionaryLookupAnnotator"> <import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml"/>
</delegateAnalysisEngine>

And then add
<node>DictionaryLookupAnnotator</node>
Just before or just after
<node>DictionaryLookupAnnotatorDB</node>

-- James