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Date: Mon, 4 Jan 2016 12:27:36 +0100
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 <CADGOtTjtHL5ddB__iUV9rN4ynJTC1+=JUoz_1z2wgyoNU3c6Vw@mail.gmail.com>
Subject: Re: Achieving YTEX negation in CuisOnlyPlaintextUMLSProcessor
From: vijay garla <vngarla@gmail.com>
To: "user@ctakes.apache.org" <user@ctakes.apache.org>
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CTAKES_HOME\desc\ctakes-ytex-uima\desc\analysis_engine\DictionaryLookupAnnotator.xml
references
CTAKES_HOME\resources\org\apache\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED.xml,
which limits all dictionary lookups
to org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation spans,
which are created by the LookupWindowAnnotator.

You can either add the LookupWindowAnnotator (not sure about its
dependencies), or you can change LookupDesc_SNOMED.xml to use a different
annotation (e.g. Noun Phrase or Sentence).

HTH,

VJ

On Thu, Dec 31, 2015 at 3:52 PM, Jessica Glover <glover.jessica.m@gmail.com>
wrote:

> I have noticed that using the AggregatePlaintextUMLSProcessor in
> ctakes-ytex-uima results in improved negation detection over the one in
> ctakes-clinical-pipeline on my test documents.
>
> I would like to get the same improvement in
> CuisOnlyPlaintextUMLSProcessor. I have tried replacing the
> DictionaryLookupAnnotator, which seemed to be the determining factor in
> AggregatePlaintextUMLSProcessor, but when I run it, I find no
> IdentifiedAnnotations. Does the YTEX DictionaryLookupAnnotator depend on an
> analysis engine I've overlooked? Any other suggestions?
>
> Thank you,
> Jessica G.
>

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<div dir=3D"ltr"><div>CTAKES_HOME\desc\ctakes-ytex-uima\desc\analysis_engin=
e\DictionaryLookupAnnotator.xml references CTAKES_HOME\resources\org\apache=
\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED.xml, which limits all dict=
ionary lookups to=C2=A0org.apache.ctakes.typesystem.type.textspan.LookupWin=
dowAnnotation spans, which are created by the=C2=A0LookupWindowAnnotator.</=
div><div><br></div><div>You can either add the LookupWindowAnnotator (not s=
ure about its dependencies), or you can change LookupDesc_SNOMED.xml to use=
 a different annotation (e.g. Noun Phrase or Sentence).</div><div><br></div=
><div>HTH,</div><div><br></div><div>VJ</div></div><div class=3D"gmail_extra=
"><br><div class=3D"gmail_quote">On Thu, Dec 31, 2015 at 3:52 PM, Jessica G=
lover <span dir=3D"ltr">&lt;<a href=3D"mailto:glover.jessica.m@gmail.com" t=
arget=3D"_blank">glover.jessica.m@gmail.com</a>&gt;</span> wrote:<br><block=
quote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc=
 solid;padding-left:1ex"><p dir=3D"ltr">I have noticed that using the Aggre=
gatePlaintextUMLSProcessor in ctakes-ytex-uima results in improved negation=
 detection over the one in ctakes-clinical-pipeline on my test documents.</=
p>
<p dir=3D"ltr">I would like to get the same improvement in CuisOnlyPlaintex=
tUMLSProcessor. I have tried replacing the DictionaryLookupAnnotator, which=
 seemed to be the determining factor in AggregatePlaintextUMLSProcessor, bu=
t when I run it, I find no IdentifiedAnnotations. Does the YTEX DictionaryL=
ookupAnnotator depend on an analysis engine I&#39;ve overlooked? Any other =
suggestions?</p>
<p dir=3D"ltr">Thank you,<br>
Jessica G.</p>
</blockquote></div><br></div>

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