Hey, I am using ctakes-drug-ner/desc/analysis_engine/AggregatePlainTextUMLSProcessor.xml as the Analysis Engine in the CVD where in I am getting the other annotations such as Medication Annotations Fraction Annotation which are of ctakes.typesystem.type.textsem.IdentifiedAnnotation but do not get any of the ctakes.drugner.type annotations for eg Frequency Annotation Drug Strength Annotations etc. I dont get any errors though but I feel DrugMentionAnnotator descriptor which extracts the strength, frequency, route etc is not working for me.
Thanks, Ravi On Tue, Mar 11, 2014 at 8:18 PM, Murphy, Sean P. <[email protected]>wrote: > Ravi, > > I assume you're just using plain text as the input for the > pipeline. Did you use the provided sample DrugNER_PlainText_CPE.xml > available in the ctakes-drug-ner/desc/collection_processing_engine/ folder > to see if it can run the provided sample? > > If my assumption is correct than make sure you're using > the Analysis Engines provided for the plain text path (i.e. no aggregates > with 'CDA' in the name should be utilized). This also pertains to the > consumer which output ( make sure to use this one > 'AggregatePlaintextProcessor.xml'). > > If you are using the CVD (cas visual debugger) then > everything but the consumer would still apply. Just be sure that you are > loading the DrugAggregatePlaintextUMLSProcessor AE specifier. > > BTW. Are you seeing other annotations other than the > drugner type? > > > > Thanks, > > ~Sean > > > > *From:* ravi garg [mailto:[email protected]] > *Sent:* Tuesday, March 11, 2014 2:38 AM > > *To:* [email protected] > *Subject:* Re: How to use Drug NER > > > > Ohh Okay, I am sorry Sean, I didn't actually knew Rxnorm is an umls > dictionary and you need to have a license to use it. I have got that > working but still I dont get any annotations in drugner.type for example > RouteAnnotation, DurationAnnotation etc. Any ideas on how to get that > working > > Thanks, > > Ravi > > > > On Mon, Mar 10, 2014 at 11:56 PM, ravi garg <[email protected]> wrote: > > Hey Xiayuan, > > I ensured that the directory of the resource that is the rxnorm_index is > correct and cTAKES is also actually using it. I can see the logs wherein > cTAKES actually parses 16k docs. I get no errors though on using the > pipeline but nothing is extracted or annotated. Even the dosage, frequency > and route which I believe are not dependent on drug dictionary are also not > getting identified. I have worked on the main clinical pipeline before but > am working on the Drug pipeline for the first time so no idea whats wrong. > > Regards, > > Ravi > > > > On Mon, Mar 10, 2014 at 11:38 PM, Xiayuan Huang <[email protected]> > wrote: > > Hi Ravi, > > Currently I am doing one project using cTAKES. I am trying to use a > pipeline for identifying smoking status, SimulatedProdSmokingTAE.xml. And I > also encountered some problem on executing those pipelines. Some possible > errors will be the directory of UIMA resource, you have to set that > correctly. And I got some exceptions when I try to run pipelines. We can > discuss how to implement cTAKES later on, I guess I really need someone to > discuss and help out on this cTAKES system. > > Best, > Xiayuan Huang > > > > > On 2014-03-10 11:05, ravi garg wrote: > > Hey, > > I am using DrugAggregatePlainTextProcessor.xml as my analysis engine > annotator. I have downloaded all the required resources by cTAKES 3.1 > . I guess it uses the rxnorm_index as the drug database. But I am not > getting any annotations as the output. Please let me know the correct > way using Drug NER > > Thanks, > Ravi > > -- > > Ravi Garg > 4th Year > MSc (hons) Biological Sciences > B.E (hons) Computer Science and Engineering > BITS Pilani KK Birla Goa Campus > > > > > -- > > Ravi Garg > 4th Year > MSc (hons) Biological Sciences > B.E (hons) Computer Science and Engineering > BITS Pilani KK Birla Goa Campus > > > > > -- > > Ravi Garg > 4th Year > MSc (hons) Biological Sciences > B.E (hons) Computer Science and Engineering > BITS Pilani KK Birla Goa Campus > -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus
