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:[email protected]] Sent: Monday, May 05, 2014 10:30 AM To: [email protected] 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. <[email protected]<mailto:[email protected]>> 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:[email protected]<mailto:[email protected]>] Sent: Monday, May 05, 2014 9:02 AM To: [email protected]<mailto:[email protected]> 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
