Hey, Thanks I will look in to it and let you know if I run into any trouble. Thank you once again for the help.
On Tue, Mar 11, 2014 at 9:54 PM, Murphy, Sean P. <[email protected]>wrote: > The source code containing the lines to be modified are in > ctakes-drug-ner\src\main\java\org\apache\ctakes\drugner\ae\DrugMentionAnnotator.java > . > > > > I had it backwards in that the lines need to be commented out to enable > the annotations to be generated again. Specifically, lines ~ 275 to 290 > have the actual types that can be commented out to be included (e.g. > org.apache.ctakes.drugner.type.SubSectionAnnotation.type is already > commented out thus should already be included in existing annotations). > Or by commenting out line 264 < removeDrugNerTypes(jcas, > intermediateTypesToRemove)> all legacy types should be included. > > Thanks, > > ~Sean > > > > > > *From:* ravi garg [mailto:[email protected]] > *Sent:* Tuesday, March 11, 2014 11:17 AM > > *To:* [email protected] > *Subject:* Re: How to use Drug NER > > > > Hey, > > Yes, It is populated with the medication. I was actually getting that > before too but not the drug ner type system part.. Also when I browse the > inner annotations of MedicationMention, I can finally see other annotations > too like medicationFrequency, medicationRoute etc in the refsem typesystem. > Thank you very much for the help. I would try to uncomment the code you are > referring and try to rebuild that part.Just one final help can you please > kindly point me to the code you are talking about. > > Thanks, > > Ravi > > > > On Tue, Mar 11, 2014 at 9:18 PM, Murphy, Sean P. <[email protected]> > wrote: > > Ravi, > > Can you look at the list of IdentifiedAnnotation to see if > the entities include the drugs in question. Specifically, the > 'ctakes.typesystem.type.textsem.MedicationMention' should be populated. > Additionally, there should be the missing drug related annotations, such as > strength in that list. > > The problem is that the drug ner was migrated to use the > new type system a release or two back. However, the old type system format > was allowed to remain in the event that someone required that legacy > handling. These can actually be populated by uncommenting some code that > exists in the DrugMention source code and rerunning. > > I had forgotten about these changes. Hopefully, that > explains what you're seeing. > > Thanks, > > ~Sean > > > > *From:* ravi garg [mailto:[email protected]] > *Sent:* Tuesday, March 11, 2014 10:15 AM > > > *To:* [email protected] > *Subject:* Re: How to use Drug NER > > > > 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 > > > > > -- > > 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
