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From <Abad.Ay...@cognizant.com>
Subject Values missing for few attributes and how to populate demographic details
Date Fri, 21 Feb 2020 12:19:39 GMT
Hello Team,

We are working on extracting the clinical data from medical documents and some of the attributes
that I list below are critical for our profile.
Could you pls. advise on how can we get a valid values for the below attributes which is coming
under every Event/EntityMention

SlNO
AttributeName
Remarks
1
conditional
Always got this as FALSE
2
originalText
Always got this as NULL
3
event
Always got this as NULL
4
alleviatingFactor
Always got this as NULL
5
associatedSignSymptom
Always got this as NULL
6
course
Always got this as NULL
7
duration
Always got this as NULL
8
endTime
Always got this as NULL
9
exacerbatingFactor
Always got this as NULL
10
startTime
Always got this as NULL
11
relativeTemporalContext
Always got this as NULL

Also we need to identify how can we extract below details regarding Patient from the document


  *   Demographic details - Patient Age, weight, BMI, BP, race, gender as present in the medical
records
  *   Patient history - Patient's past medical history and social history will be displayed.
Social history includes smoking, alcohol and drug and other details
  *   Family history - Patient's family history will also be displayed in this section
Kindly advise whether we need to add any new AE's to our existing piper file so that cTAKES
will provide us the requested O/P as mentioned above. PFB the contents of AE's configured
in our piper file.



// Load a simple token processing pipeline from another pipeline file
load DefaultTokenizerPipeline.piper
add ContextDependentTokenizerAnnotator
addDescription POSTagger
// Add Chunkers
load ChunkerSubPipe.piper
// Commands and parameters to create a default chunker processing sub-pipeline.  This is not
a full pipeline.
// Default fast dictionary //lookup
add DefaultJCasTermAnnotator
load AttributeCleartkSubPipe.piper
# Parameters for AssertionAnalysisEngine and ConceptConverterAnalysisEngine
set assertionModelResource=file: org/apache/ctakes/assertion/models/i2b2.model
set scopeModelResource=file: org/apache/ctakes/assertion/models/scope.model
set cueModelResource=file: org/apache/ctakes/assertion/models/cue.model
set enabledFeaturesResource=file: org/apache/ctakes/assertion/models/featureFile11b
set posModelResource=file: org/apache/ctakes/assertion/models/pos.model
package org.apache.ctakes.assertion.medfacts
package org.apache.ctakes.assertion.attributes
add ConceptConverterAnalysisEngine
add GenericAttributeAnalysisEngine
add SubjectAttributeAnalysisEngine
//  Creates modifier annotations needed to handle the drug mentions.
add org.apache.ctakes.drugner.ae.DrugMentionAnnotator STATUS_BOUNDARY_ANN_TYPE="org.apache.ctakes.typesystem.type.textsem.MedicationMention"
add org.apache.ctakes.constituency.parser.ae.ConstituencyParser
// Modifiers. Use addLogged to log start and finish of processing.  There aren't default models,
so set specifically
addLogged ModifierExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar
// Degree of severity, etc.
addLogged DegreeOfRelationExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/degree_of/model.jar
// Location.
addLogged LocationOfRelationExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/location_of/model.jar
add org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator
//Remaining statements not reflected in the XMI (Not checked). It is for relation extraction
// 'Generic' Events.  Use addDescription and let the EventAnnotator set itself up with defaults.
//For getting the relation between the events
addDescription EventAnnotator
// Times.  Use addLogged to log start and finish of processing.  There aren't default models,
so set specifically
add BackwardsTimeAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar
// DocTimeRel: the relation bin for Events to the Document Creation Time.
// add DocTimeRelAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/doctimerel/model.jar
// Event - Time binary relations.
add EventTimeRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventtime/model.jar
// Event - Event binary relations.
add EventEventRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventevent/model.jar



Thanks & Regards
[cid:D3145E69-CD94-48C1-877F-5134EEAFB598]
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028


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