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From "Murphy, Sean P." <Murphy.S...@mayo.edu>
Subject Re: How to use Drug NER
Date Wed, 12 Mar 2014 14:21:56 GMT
Glad you got it running.

Part of the SHARP initiative was to standardize/normalize the type systems used in medical
annotations.

http://www.healthit.gov/policy-researchers-implementers/strategic-health-it-advanced-research-projects-sharp

Regarding your second question I am not sure I understand your workaround scenario. I suggest
you repost your question to the cTAKES community again to see if they can provide an answer.
          Thanks.

Sent from my iPhone

On Mar 12, 2014, at 8:40 AM, "ravi garg" <ravigarg27@gmail.com<mailto:ravigarg27@gmail.com>>
wrote:

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<mailto: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<mailto: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<mailto:ravigarg27@gmail.com>]
Sent: Tuesday, March 11, 2014 11:17 AM

To: user@ctakes.apache.org<mailto: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<mailto: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<mailto:ravigarg27@gmail.com>]
Sent: Tuesday, March 11, 2014 10:15 AM

To: user@ctakes.apache.org<mailto: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<mailto: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<mailto:ravigarg27@gmail.com>]
Sent: Tuesday, March 11, 2014 2:38 AM

To: user@ctakes.apache.org<mailto: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<mailto: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<mailto: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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