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From "Lee, Richard A. [USA]" <lee_rich...@bah.com>
Subject RE: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Date Thu, 19 Jun 2014 02:06:28 GMT
Done. It is indeed “the same results” (as when trying to use the old non-ytex AE): the
same runtime exception popup. “See the log file”, it says, but as before I’m not seeing
anything obvious in ctakes.log (attached).

From: vijay garla [mailto:vngarla@gmail.com]
Sent: Wed, 18 Jun, 2014 10:12
To: user@ctakes.apache.org
Subject: Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml

The YTEX AggregatePlaintextUMLSProcessor differs from the default AggregatePlaintextUMLSProcessor
in the following a ways:
* Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator
* Use SentenceDetectorAnnotator without splitting on newlines
* Added SenseDisambiguatorAnnotator
* Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES DictionaryLookupAnnotatorDB

The YTEX dictionary lookup is different from cTAKES':
* uses the old dictionary lookup
* uses a single dictionary
* uses a single lookup consumer that creates plain-vanilla EntityMention annotations (none
of the subtypes)

I think that if you change the YTEX AggregatePlaintextUMLSProcessor to point at the cTAKES
dictionary lookup, you will get approximately same annotations (probably more if sentences
do not end on newlines, as dictionary lookup is not performed across sentences)

could you try the following please:
In desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml change
                        <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
                                    <import location="./DictionaryLookupAnnotator.xml"
/>
                        </delegateAnalysisEngine>
To
    <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
      <import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
    </delegateAnalysisEngine>

And re-run.  You should get the same results (keep in mind the newline thing).




On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] <lee_richard@bah.com<mailto:lee_richard@bah.com>>
wrote:
Yes, that exactly the problem I’ve been reporting. I think you’ll see that it you still
get the non-Medical annotations, like Date, RomanNumeral, et al, but not DiseaseDisorderMention
and the other Medical ones, right?

I’m still hoping someone can assist with this.

From: Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in<mailto:abhishekrm@iitrpr.ac.in>]
Sent: Wed, 18 Jun, 2014 04:43
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml

Found a fix. Will post it here in case it helps someone. When using ctakes-3.1.2, load the
AggregatePlainTextUmlsProcessor.xml from "CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
and not from the usual "CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml"
as given here<https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>.

However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" produced
even less annotations than "ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml".
I expected ytex-specific AE to produce better results. But clearly that's not the case.

On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <abhishekrm@iitrpr.ac.in<mailto:abhishekrm@iitrpr.ac.in>>
wrote:
Hi. Thanks for the reply.
I have a file named LookupDesc_Db.xml which has the line <jdbcImpl tableName="@db.schema@.v_snomed_fword_lookup"/>
instead of LookupDesc_SNOMED.template.xml. Also, my ytex.properties file seems fine. I have
attached the file for your reference.
And yes, when running the ant setup by following #7 on this<https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation>
link, it sends the output to "setup.out". The build was successful though. I didn't see any
errors. I am attaching the file for your reference as well. Please have a look and let me
know.


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