Re: getSeverity etc. for relation extractor

er)? Seems easier to get onboard I think. > >> > >> --Pei > >> > >> > >>> -Original Message- > >>> From: Chen, Pei > >>> Sent: Wednesday, March 19, 2014 5:58 PM > >>> To: dev@ctakes.apache.org > >>>

Re: getSeverity etc. for relation extractor

te-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java > > --Pei > > > -Original Message- > > From: Chase Master [mailto:chasemast...@gmail.com] > > Sent: Wednesday, March 19, 2014 1:56 PM > > To: dev@ctakes.apache.org >

getSeverity etc. for relation extractor

Hi, I am trying to output the relations associated with DiseaseDisorderMentions and other types. But I want to start by iterating over DiseaseDisorderMention, not BinaryTextRelations since I want to be sure to find them all, even if they have no associated relation. I always get null when using

what dictates full medication mention?

Hi, I have a quick question. When I run the cTAKES drugNER module on "Ibuprofen 100 MG" and "Propranolol 40 MG", I get an annotation for both Ibuprofen 100MG and Ibuprofen for the first case, but for the second case I only get Propranolol, by itself. It does show the strength as 40MG for Propran

help getting MedicationStrength

Hi, I'm trying to grab results after running the DrugNER AE using the UIMA framework. I am able to print all the results to the console using: FSIterator it = jcas.getAnnotationIndex(MedicationMention.type).iterator(); if (it.hasNext()) { MedicationMention med = (MedicationMention) it.next(); S

Re: Incorrect frequency in Drug NER?

Hi, I've been experimenting with the Drug NER module as well. I noticed that for the phrase "Ibuprofen increased from 200 mg to 300 mg p.o. once a day." the medicationFrequency has number = 1, but unit = null for the Ibuprofen with strength 300 mg. Also, for the phrase "Aspirin 200-mg once-a-day"

Re: Viewing MedicationMentions from drug-ner in Annotation Viewer

.xml in an html format. > --Pei > > > From: Chase Master [mailto:chasemast...@gmail.com] > Sent: Wednesday, August 21, 2013 9:28 AM > To: dev@ctakes.apache.org > Subject: Re: Viewing MedicationMentions from drug-ner in Annotation Viewer > > I loaded the AE descriptor file...I&#

Viewing MedicationMentions from drug-ner in Annotation Viewer

Hi, To get a feel for how a module works, I like viewing the annotations that it outputs with UIMA's AnnotationViewer. I'm wondering why for the drug-ner module, you can see MeasurementAnnotations (e.g. 80mg), but you can't see MedicationMentions, MedicationStrengths, etc. in the GUI even though

RelationExtractorPipeline failure

Hi, I've been running the RelationExtractorPipeline. It works ok on some text that includes relations, but I get a severe exception on other examples: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(407) SEVERE: Exception occurred org.apache.uima.a

Re: Assertion module

Thanks for your responses! Yes, I meant modifying ATTR_SUBJECT to something more specific like the example you gave. On Thu, Aug 15, 2013 at 10:51 AM, Chen, Pei wrote: > > ATTR_SUBJECT_ in edu.mayo.bmi.uima.core.type.constants.CONST, is it > > possible to meaningfully change them? > Could you

dictionary questions

Hi, If I am using DictionaryLookupAnnotatorUMLS.xml as the descriptor for that module, with my valid UMLS username and password, does this use the full SNOMED CT and RxNorm dictionaries? (I believe it connects to the online database.) Because it misses ““VANCOMYCIN RESISTANT ENTEROCOCCI”, C12651

Assertion module

Hi, I’m using v3.0-incubating (as a Maven dependency) with the default clinical pipeline, which calls the Assertion module. I noticed that for something like “Anna’s father has had knee pain for years”, the subject attribute gets set to family_member. Is it possible to be more specific? Also,

Re: logger for assertion module

s the console output for most of the pipeline. Also, the assertion module has many print statements in addition to the logger statements which would be nice to turn off... Thanks On Wed, Jul 31, 2013 at 10:05 AM, Chen, Pei wrote: > Hi Chase Master, > Welcome- > > Hi, > > I am r

logger for assertion module

Hi, I am relatively new to ctakes. I have created my own Maven application, and have specified the ctakes-clinical-pipeline as a dependency in the pom file (I have not checked out the project itself). The comments on CTAKES-76, "get third party dependencies into Maven Central", have helped me to