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From John Green <hephaestus.stu...@gmail.com>
Subject Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Date Wed, 16 Jul 2014 14:53:17 GMT
Hi Vijay - I am at the same impasse as Mr Lee and Mr Abhishek, and I didnt
come across any other solutions in the archives.

Through intuition I figured out what you mention in this post on my own,
and tried it. It didnt work. It seems to revolve around this line:
Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM
@db.schema@.v_snomed_fword_lookup
WHERE fword = ?]

It seems the query is coming from LookupDesc_SNOMED.xml, but I cant find
the @db.schema@... is this a windows/linux issue?

Before Vijay spends his precious time on answering this, did anyone else
get resolution on this?

Best,
JG


On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <vngarla@gmail.com> wrote:

> 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> 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]
>> *Sent:* Wed, 18 Jun, 2014 04:43
>> *To:* 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>
>> 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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