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Posted to user@ctakes.apache.org by Anirban Chakraborti <ch...@googlemail.com> on 2014/05/05 16:01:46 UTC
Difference between Refsem Class and TextSem class
what is the difference between refsem class and textsem class. How do I get
an ouput like
*org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder*
*Anir*
RE: Difference between Refsem Class and TextSem class
Posted by "Masanz, James J." <Ma...@mayo.edu>.
1 The simplest is to run AgregateTemplateFiller engine, which is under ctakes-template-filler
To modifiy AggregatePlaintextprocessUMLS.xml to create the refsem elements, you’d basically be re-creating AgregateTemplateFiller.xml
2. To get details of dosage and frequency, if you didn’t care about refsem, you would run the DrugAggregatePlaintextUMLSProcessor, which is under ctakes-drug-ner. But the AgregateTemplateFiller engine includes the drug ner engine, so once you switch to AgregateTemplateFiller, you should see dosage and frequency
3. There’s some documentation about the components in
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+Component+Use+Guide
Suggestions welcome
-- James
From: Anirban Chakraborti [mailto:chakraborti.anirban@googlemail.com]
Sent: Monday, May 05, 2014 10:30 AM
To: user@ctakes.apache.org
Subject: Re: Difference between Refsem Class and TextSem class
thanks James,
Now
1. I should be able to view refsem annotations via AggregatePlaintextprocessUMLS.xml if I change the script to output refsem.element . Cant I? or do I have to call some another analysis engine.
2. For a line like " Metronidazole 500 mg p.o. q.8h." , the textsem picks up the medication and refers to its ontology concept( RXNOM code) but is not able to show dosage and frequency. What should be done. Would refem be more useful.
3. Use case for each function , if available would have been great. are there any.
Anir
On Mon, May 5, 2014 at 8:44 PM, Masanz, James J. <Ma...@mayo.edu>> wrote:
org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder annotations are created by the TemplateFillerAnnotator within ctakes-template-filler. Running AggregateTemplateFiller engine, which is under ctakes-template-filler, will generate refsem annotations.
The concept behind having separate textsem and refsem annotations is if you have two textsem annotations, they might refer to a single real-world object. The goal is to (someday) have a single refsem annotation per single real-world object, using coreference resolution to determine which textsem annotations refer to the same thing, and having something to merge and resolve conflicts between attributes of the coreferenced textsem annotations. That piece (merging and dealing with conflicts of attributes) doesn’t exist yet.
So for now, the distinction between the refsem and textsem annotation is that refsem annotations use the output of the relation extraction piece to set the bodyLocation and severity attributes.
-- James
From: Anirban Chakraborti [mailto:chakraborti.anirban@googlemail.com<ma...@googlemail.com>]
Sent: Monday, May 05, 2014 9:02 AM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Difference between Refsem Class and TextSem class
what is the difference between refsem class and textsem class. How do I get an ouput like
org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder
Anir
Re: Difference between Refsem Class and TextSem class
Posted by Anirban Chakraborti <ch...@googlemail.com>.
thanks James,
Now
1. I should be able to view refsem annotations via
AggregatePlaintextprocessUMLS.xml if I change the script to output
refsem.element . Cant I? or do I have to call some another analysis engine.
2. For a line like " Metronidazole 500 mg p.o. q.8h." , the textsem picks
up the medication and refers to its ontology concept( RXNOM code) but is
not able to show dosage and frequency. What should be done. Would refem be
more useful.
3. Use case for each function , if available would have been great. are
there any.
Anir
On Mon, May 5, 2014 at 8:44 PM, Masanz, James J. <Ma...@mayo.edu>wrote:
> *org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder * annotations
> are created by the TemplateFillerAnnotator within ctakes-template-filler.
> Running AggregateTemplateFiller engine, which is under
> ctakes-template-filler, will generate refsem annotations.
>
>
>
> The concept behind having separate textsem and refsem annotations is if
> you have two textsem annotations, they might refer to a single real-world
> object. The goal is to (someday) have a single refsem annotation per
> single real-world object, using coreference resolution to determine which
> textsem annotations refer to the same thing, and having something to merge
> and resolve conflicts between attributes of the coreferenced textsem
> annotations. That piece (merging and dealing with conflicts of attributes)
> doesn’t exist yet.
>
>
> So for now, the distinction between the refsem and textsem annotation is
> that refsem annotations use the output of the relation extraction piece to
> set the bodyLocation and severity attributes.
>
>
>
> -- James
>
>
>
>
>
> *From:* Anirban Chakraborti [mailto:chakraborti.anirban@googlemail.com]
> *Sent:* Monday, May 05, 2014 9:02 AM
> *To:* user@ctakes.apache.org
> *Subject:* Difference between Refsem Class and TextSem class
>
>
>
> what is the difference between refsem class and textsem class. How do I
> get an ouput like
>
>
>
> *org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder*
>
>
>
>
>
>
>
> *Anir*
>
>
>
RE: Difference between Refsem Class and TextSem class
Posted by "Masanz, James J." <Ma...@mayo.edu>.
org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder annotations are created by the TemplateFillerAnnotator within ctakes-template-filler. Running AggregateTemplateFiller engine, which is under ctakes-template-filler, will generate refsem annotations.
The concept behind having separate textsem and refsem annotations is if you have two textsem annotations, they might refer to a single real-world object. The goal is to (someday) have a single refsem annotation per single real-world object, using coreference resolution to determine which textsem annotations refer to the same thing, and having something to merge and resolve conflicts between attributes of the coreferenced textsem annotations. That piece (merging and dealing with conflicts of attributes) doesn’t exist yet.
So for now, the distinction between the refsem and textsem annotation is that refsem annotations use the output of the relation extraction piece to set the bodyLocation and severity attributes.
-- James
From: Anirban Chakraborti [mailto:chakraborti.anirban@googlemail.com]
Sent: Monday, May 05, 2014 9:02 AM
To: user@ctakes.apache.org
Subject: Difference between Refsem Class and TextSem class
what is the difference between refsem class and textsem class. How do I get an ouput like
org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder
Anir