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From ravi garg <ravigar...@gmail.com>
Subject Re: How to use Drug NER
Date Wed, 12 Mar 2014 13:39:28 GMT
Hey,

I have got it working now. But I wanted to know, just out of curiosity, why
to remove all the drugner typesystem annotations.
Also can you please let me know if there is any workaround to get all the
annotations from the plain text in one output.xml file.

Regards,
Ravi


On Tue, Mar 11, 2014 at 10:21 PM, ravi garg <ravigarg27@gmail.com> wrote:

> 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
>



-- 
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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