Default clinical pipeline does not appear to work as advertised by the docs' graphic showing its use, how to get there?

[Reed Villanueva <vi...@gmail.com>]

Running the exact same test ("The patient underwent a CT scan in April
which did not reveal lesions in his liver") as shown for the default
clinical pipeline (
https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline)
and examining the XMI output in the ctakesCVD, does not seem to extract the
same information as shown in the graphic in the docs demonstrating what
information is taken from that same sentence.

Eg.
* The only detect EntityMention was "liver" and I could not find where it
had received a tag value of "Anatomy".
* Looking at the AnnotationIndex.IdentifiedAnnotations, there seems to be
no "Entity Properties" data as implied in the docs (such as "lesions"
having the property of "negated").

I feel that I must have missed something here, am looking in the wrong
place, or something else? Please advise, thank you.

Re: Default clinical pipeline does not appear to work as advertised by the docs' graphic showing its use, how to get there?

[Reed Villanueva <vi...@gmail.com>]

I believe that I am in fact using the UMLS, since I run the
bin/runClinicalPipeline.sh with my UMLS credentials and I have added my
credentials to the bin/runctakesCVD.sh script as recommended by the user
installation guide (
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide#cTAKES4.0UserInstallGuide-(Recommended)AddUMLSaccessrights
).
Also thanks for pointing out my Polarity=negation confusion, just started
reading through the Component Use documentation (
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Assertion#cTAKES4.0-Assertion-Negationattributeannotator
).

On Fri, Mar 23, 2018 at 6:04 AM, Schenk, Gundolf <Gu...@ucsf.edu>
wrote:

> Hi Reed,
>
>
>
> Did you enable UMLS?
>
>
>
> I am also not quite happy with the result. When I run this test sentence
> in the DefaultClinicalPipeline I am getting 4 IdentifiedAnnotation
> (AnnotationIndex -> uima.tcas.Annotation -> org.apache.ctakes.typesystem.
> type.textsem.IdentifiedAnnotation).
>
> Namely, ProcedureMention (“scan”), RomanNumericalAnnotation (“did”),
> SignSymptomAnnotation (“lesions”) and AnatomicalSiteMention (“liver”).
> “lesions” is negated as indicated by Polarity=-1.
>
>
>
> This does not seem error-free to me, still. Could anyone confirm this is
> the expected result, please?
>
>
>
> Cheers,
>
> Gundolf.
>
>
>
>
>
> *From: *Reed Villanueva <vi...@gmail.com>
> *Reply-To: *"user@ctakes.apache.org" <us...@ctakes.apache.org>
> *Date: *Friday, March 23, 2018 at 01:54
> *To: *"user@ctakes.apache.org" <us...@ctakes.apache.org>
> *Subject: *Default clinical pipeline does not appear to work as
> advertised by the docs' graphic showing its use, how to get there?
>
>
>
> Running the exact same test ("The patient underwent a CT scan in April
> which did not reveal lesions in his liver") as shown for the default
> clinical pipeline (https://cwiki.apache.org/confluence/display/CTAKES/
> Default+Clinical+Pipeline) and examining the XMI output in the ctakesCVD,
> does not seem to extract the same information as shown in the graphic in
> the docs demonstrating what information is taken from that same sentence.
>
>
>
> Eg.
>
> * The only detect EntityMention was "liver" and I could not find where it
> had received a tag value of "Anatomy".
>
> * Looking at the AnnotationIndex.IdentifiedAnnotations, there seems to be
> no "Entity Properties" data as implied in the docs (such as "lesions"
> having the property of "negated").
>
>
>
> I feel that I must have missed something here, am looking in the wrong
> place, or something else? Please advise, thank you.
>

Re: Default clinical pipeline does not appear to work as advertised by the docs' graphic showing its use, how to get there?

["Schenk, Gundolf" <Gu...@ucsf.edu>]

Hi Reed,

Did you enable UMLS?

I am also not quite happy with the result. When I run this test sentence in the DefaultClinicalPipeline I am getting 4 IdentifiedAnnotation (AnnotationIndex -> uima.tcas.Annotation -> org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation).
Namely, ProcedureMention (“scan”), RomanNumericalAnnotation (“did”), SignSymptomAnnotation (“lesions”) and AnatomicalSiteMention (“liver”). “lesions” is negated as indicated by Polarity=-1.

This does not seem error-free to me, still. Could anyone confirm this is the expected result, please?

Cheers,
Gundolf.


From: Reed Villanueva <vi...@gmail.com>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Friday, March 23, 2018 at 01:54
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: Default clinical pipeline does not appear to work as advertised by the docs' graphic showing its use, how to get there?

Running the exact same test ("The patient underwent a CT scan in April which did not reveal lesions in his liver") as shown for the default clinical pipeline (https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline) and examining the XMI output in the ctakesCVD, does not seem to extract the same information as shown in the graphic in the docs demonstrating what information is taken from that same sentence.

Eg.
* The only detect EntityMention was "liver" and I could not find where it had received a tag value of "Anatomy".
* Looking at the AnnotationIndex.IdentifiedAnnotations, there seems to be no "Entity Properties" data as implied in the docs (such as "lesions" having the property of "negated").

I feel that I must have missed something here, am looking in the wrong place, or something else? Please advise, thank you.