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From ravi garg <ravigar...@gmail.com>
Subject Re: How to use Drug NER
Date Tue, 11 Mar 2014 16:51:32 GMT
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. <Murphy.Sean@mayo.edu>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:ravigarg27@gmail.com]
> *Sent:* Tuesday, March 11, 2014 11:17 AM
>
> *To:* user@ctakes.apache.org
> *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. <Murphy.Sean@mayo.edu>
> 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:ravigarg27@gmail.com]
> *Sent:* Tuesday, March 11, 2014 10:15 AM
>
>
> *To:* user@ctakes.apache.org
> *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. <Murphy.Sean@mayo.edu>
> 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:ravigarg27@gmail.com]
> *Sent:* Tuesday, March 11, 2014 2:38 AM
>
>
> *To:* user@ctakes.apache.org
> *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 <ravigarg27@gmail.com> 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 <huangxy@cs.wisc.edu>
> 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

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