Hi Chris,
No, you are not missing anything.
The example on the wiki was concocted to display what ctakes should do. There
are a few different negation modules (and you can write your own). Using the
Assertion module you will not get negated lesions. Using the ContextAnnotator
you will.
I did the following:
In ctakes-examples , edit
org.apache.ctakes.examples.pipeline.HelloWorldPropsPiperRunner.java
HelloWorldPropsPiperRunner uses the ContextAnnotator for negation.
Change DOC_TEXT to be the example sentence. The output is:
4,11 patient
| affirmed | certain | not conditional | not
generic | Patient | history of: 0
24,26 CT
| affirmed | certain | not conditional | not
generic | Patient | history of: 0
27,31 Scan
| affirmed | certain | not conditional | not
generic | Patient | history of: 0
35,40 April
| affirmed | certain | not conditional | not
generic | Patient | history of: 0
47,50 did
| negated | certain | not conditional | not
generic | Patient | history of: 0
47,54 did not
| affirmed | certain | not conditional | not
generic | Patient | history of: 0
51,54 not
| affirmed | certain | not conditional | not
generic | Patient | history of: 0
62,69 lesions
| negated | certain | not conditional | not
generic | Patient | history of: 0
77,82 liver
| negated | certain | not conditional | not
generic | Patient | history of: 0
Notice that the context annotator marked lesions as negated.
I hope that makes sense.
Sean
From: Chris Hinkle [mailto:hin...@all-turtles.com]
Sent: Tuesday, August 08, 2017 5:00 PM
To: dev@ctakes.apache.org
Subject: default clinical pipeline: questions about polarity [EXTERNAL]
Hi cTAKES Team,
I've recently started exploring cTAKES and I'm excited about the potential.
However, I'm having trouble seeing the results as they're exemplified in the
documentation using the example input "The patient underwent a CT Scan in April
which did not reveal lesions in his liver."
Specifically negation (polarity) values don't seem to be populated as they are
shown in the Default Clinical Pipeline documentation wiki
page<https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Default-2BClinical-2BPipeline&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=dTK9VzFknYGrOowQ4jIqy8xeqw9DIClZjRUaj_xs894&s=26Dy4rIl2LIwaRk5o3q8pmAhISj_lyCX90hVe2sAV58&e=>.
I've built a simple java class which instantiates the Default Pipeline like so
static AnalysisEngine pipeline;
…
log.info( "Initilizing Pipeline..." );
try
{
AggregateBuilder builder = new AggregateBuilder( );
builder.add( ClinicalPipelineFactory.getDefaultPipeline( ) );
pipeline = builder.createAggregate( );
}
catch( Exception e )
{
log.error( e );
}
…
I then instantiate a CAS and process it like so:
try
{
JCas jcas = pipeline.newJCas( );
jcas.setDocumentText( "The patient underwent a CT Scan in April which did
not reveal lesions in his liver." );
pipeline.process( jcas );
}
catch( Exception e )
{
log.error( e );
}
…
I've set my UMLS username and password as environment variables, and UMLS
lookups are working just fine. The CAS contains the same identified annotations
as the example, i.e. The AnatomicalSiteMentions, SignSymptomMentions, etc,
however, the fields for polarity are all 1. The documentation on the wiki page
for Assertion Component Use
Guide<https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BAssertion&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=dTK9VzFknYGrOowQ4jIqy8xeqw9DIClZjRUaj_xs894&s=AdLHU8Zne1EOqbGocT4o22Ylyl32B-xRHMtogDho9r4&e=>,
and the aforementioned wiki page for the default clinical pipeline lead me to
think that the polarity field for the 'lesions' concept would be set to 1, and
leave the rest -1.
Is there something I'm missing? Perhaps I'm not looking in the right place, or
haven't done all of the configuration required to exercise those features of
cTAKES?
I've attached the serialized CAS object to this email for reference.
Best,
Chris
--
Chris Hinkle
All Turtles
347-407-4993
