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From Ratan Sharma <ratanc...@gmail.com>
Subject Re: SubjectClearTkAnalysisEngine not working [EXTERNAL]
Date Wed, 17 Jan 2018 17:52:53 GMT
No, I guess I am not running it anywhere explicitly. Is that the
reason segment.getPreferredText() is always null for me.

On Wed, Jan 17, 2018 at 11:14 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Are you running the BsvRegexSectionizer?
>
> -----Original Message-----
> From: Ratan Sharma [mailto:ratancomp@gmail.com]
> Sent: Wednesday, January 17, 2018 12:17 PM
> To: dev@ctakes.apache.org
> Subject: Re: SubjectClearTkAnalysisEngine not working [EXTERNAL]
>
> Thanks Timothy for the details. I guess I was looking for sections/segment
> only. I tried to work out that piece, but unable to pull information, can
> you please guide me a bit.
>
> Below is the code snippet to pull segment information.
>
> for(IdentifiedAnnotation entity : JCasUtil.select(jcas,
> IdentifiedAnnotation.class)) {
>             if(entity.getTypeID() != 0)
>                 System.out.println("Entity: " + entity.getTypeID() +
>                                         " === Text: " +
> entity.getCoveredText() +
>                                         " === Polarity: " +
> entity.getPolarity() +
>                                         " === Subject: " +
> entity.getSubject() +
>                                         " === EntityName: " +
> entity.getType());
>   }
>
> for (Segment segment : JCasUtil.select(jcas, Segment.class)) {
>      List<LabMention> mentions = JCasUtil.selectCovered(jcas,
> LabMention.class, segment);
>     System.out.println("LATEST DATA : " + segment.getPreferredText() +  "
> (" + segment.getId() + "): " + mentions.size() + " mention(s)");
>
>
> First for loop is giving me correct result, but second for loop is giving
> null error.
>
>
> On Wed, Jan 17, 2018 at 1:14 AM, Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
> > OK, it sounds like a slight misunderstanding of what "subject" refers
> > to. The subject field refers to _who_ is the subject of an event.
> >
> > This is important to differentiate diseases that are mentioned because
> > the patient is experiencing them ("pt has colon cancer") from those
> > that might be mentioned because a family member had them ("mother had
> > breast cancer").
> >
> > What you're talking about sounds more like "Sections", which I think
> > in ctakes are called "segments". There is a regex-based section finder
> > in cTAKES but it is not enabled by default because it would usually
> > need to be customized for a given institutions notes.
> >
> > Tim
> >
> >
> > On Wed, 2018-01-17 at 01:10 +0530, Ratan Sharma wrote:
> > > I am trying to find out something like If an entity falls in one of
> > > these category, and my understanding was subject can get me these
> > > information.
> > >
> > > SUBJECT it belongs to like -
> > > *"Vital Signs", "BP", "Physical Examination", "Family Medical
> > > History", "Lab Results"*
> > >
> > > Any idea how to achieve this.
> > >
> > >
> > > On Wed, Jan 17, 2018 at 1:05 AM, Miller, Timothy <
> > > Timothy.Miller@childrens.harvard.edu> wrote:
> > >
> > > >
> > > > What output would you like? What are you expecting?
> > > >
> > > > This field in theory could have a few different values: patient,
> > > > family_member, other, donor(iirc?)
> > > >
> > > > But in reality our training data was very skewed towards the
> > > > patient label, and the representation we used for training is not
> > > > great at picking up section-wide cues that would be helpful (like
> > > > a family history section header). So in practice it almost always
> > > > will say "patient." It may occasionally get something very
> > > > obvious: "Mother had breast cancer"
> > > > I don't know if it will get this exact example, it probably needs
> > > > to look exactly like a training instance because we had very few
> > > > to generalize from.
> > > > Thanks
> > > > Tim
> > > >
> > > >
> > > > On Wed, 2018-01-17 at 00:57 +0530, Ratan Sharma wrote:
> > > > >
> > > > > I am able to pull entity information for different section
> > > > > correctly.
> > > > > But
> > > > > facing issues when it comes to pull subject information. The
> > > > > subject is always pulled as "PATIENT".
> > > > >
> > > > > I do have this added in the AssertionPipeline builder.add(
> > > > > SubjectCleartkAnalysisEngine.createAnnotatorDescription() );
> > > > >
> > > > >
> > > > > Here are some sample output :
> > > > >
> > > > > Entity: 3 === Text: Blood Transfusion === Polarity: 1 ===
> > > > > Subject:
> > > > > patient
> > > > > === EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
> > > > > Entity: 6 === Text: Blood === Polarity: 1 === Subject: patient
> > > > > ===
> > > > > EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
> > > > > Entity: 3 === Text: Transfusion Reaction === Polarity: 1 ===
> > > > > Subject:
> > > > > patient === EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
> > > > > Entity: 5 === Text: Transfusion === Polarity: 1 === Subject:
> > > > > patient
> > > > > ===
> > > > > EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.ProcedureMention
> > > > > Entity: 2 === Text: HIV === Polarity: 1 === Subject: patient ===
> > > > > EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
> > > > > Entity: 6 === Text: Sickle Cell === Polarity: 1 === Subject:
> > > > > patient
> > > > > ===
> > > > > EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
> > > > > Entity: 2 === Text: Neurologic Disorders === Polarity: 1 ===
> > > > > Subject:
> > > > > patient === EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
> > > > > Entity: 2 === Text: Autoimmune Disorders === Polarity: 1 ===
> > > > > Subject:
> > > > > patient === EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
> > > > > Entity: 3 === Text: Autoimmune === Polarity: 1 === Subject:
> > > > > patient
> > > > > ===
> > > > > EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
> > > > > Entity: 2 === Text: Autoimmune Disorders === Polarity: -1 ===
> > > > > Subject:
> > > > > patient === EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
> > > > > Entity: 3 === Text: Autoimmune === Polarity: 1 === Subject:
> > > > > patient
> > > > > ===
> > > > > EntityName:
> > > > > org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
> >
>

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