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

 

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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