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From John Green <hephaestus.stu...@gmail.com>
Subject Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml
Date Wed, 16 Jul 2014 15:28:57 GMT
A manual query such as SELECT * FROM ytex.v_snomed_fword_lookup WHERE
fword="mesna"; works OK btw.


On Wed, Jul 16, 2014 at 11:24 AM, John Green <hephaestus.studio@gmail.com>
wrote:

> So, tableName="@db.schema@.v_snomed_fword_lookup" to
> tableName="ytex.v_snomed_fword_lookup" in LookupDesc_Db.xml?
>
> If so, I tried this and same error, with just the names swapped.
>
> Thanks Vijay,
> JG
>
>
> On Wed, Jul 16, 2014 at 11:20 AM, vijay garla <vngarla@gmail.com> wrote:
>
>> replace db.schema with your database schema name.  For sql server, this
>> is dbo, for mysql this is the database/schema name, for oracle this is the
>> schema name.  This should have been done automatically by the ant setup
>> script, not sure why it isn't happening in some configs.
>>
>> -vj
>>
>>
>> On Wed, Jul 16, 2014 at 4:53 PM, John Green <hephaestus.studio@gmail.com>
>> wrote:
>>
>>> 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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