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]<mailto:[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]<mailto:[email protected]>]
Sent: Tuesday, March 11, 2014 2:38 AM
To: [email protected]<mailto:[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]<mailto:[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]<mailto:[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
