Re: cTakes drug ner problems..

[Pei Chen <ch...@apache.org>]

[Moved to dev@ list as these seem to be more developer centric]
Hi,
> I have so many clarifications to be solved. Can I post them frequently ?
How often can I ask questions on the average ?
Feel free to post to the mailing lists- just keep in mind that ASF is an
all volunteer organization. See http://www.apache.org/dev/#mail for general
mailing list info.

>a) Can anyone help me with drug ner module ? I have downloaded and
integrated the UMLS corpus with cTakes. But when I run the drug ner module
for DrugAggregatePlantextUMLSProcessor.xml, I am not able to detect the
drugs.
Would you mind attaching a sample text and save/export the xmi file?

>b) Also I am getting lots of false positives like "performed" as
medication. Can anyone help me with the problem. Also when I load the xml
DrugAggregateCDAUMLSProcessor.xml, I am getting problem following problem.
"org.apache.uima.analysis_engine.AnalysisEngineProcessException"/ Is this
because of UMLS or something ?
Would you mind attaching a sample text and save/export the xmi file?  In
particular, what IdentifiedAnnotation objects are returned. (just wanted to
make sure we are viewing the correct output types.)

>c) How secured it is when we authenticate for UMLS credentials with our
documents ? Will my data be shared ?
The UMLS validation just makes a simple https rest call to the umls license
service to ensure your license exists.
No data is shared (the code is actually open source, so you should be able
to see exactly what it is doing.)

>d) Also does cTakes also use ICD9 tagging ? I am not able to see clear
documentation. But if we need can I contribute for this.
It can normalize to IC9 in addition to SNOMED/RxNorm codes...  But would
need a bit more information in what you are trying to achieve here.

>e) For classification problem, have anyone tried using classifier from
other machine learning libraries and then add-on plugin to the cTakes.
Examples?

Thanks,
Pei





On Thu, Mar 27, 2014 at 1:27 AM, Prasanna Bala
<ba...@gmail.com>wrote:

> Hi,
> I have list of doubts to be asked.
>
>
> a) Can anyone help me with drug ner module ? I have downloaded and
> integrated the UMLS corpus with cTakes. But when I run the drug ner module
> for DrugAggregatePlantextUMLSProcessor.xml, I am not able to detect the
> drugs.
>
> b) Also I am getting lots of false positives like "performed" as
> medication. Can anyone help me with the problem. Also when I load the xml
> DrugAggregateCDAUMLSProcessor.xml, I am getting problem following problem.
> "org.apache.uima.analysis_engine.AnalysisEngineProcessException"/ Is this
> because of UMLS or something ?
>
> c) How secured it is when we authenticate for UMLS credentials with our
> documents ? Will my data be shared ?
>
> d) Also does cTakes also use ICD9 tagging ? I am not able to see clear
> documentation. But if we need can I contribute for this.
>
> e) For classification problem, have anyone tried using classifier from
> other machine learning libraries and then add-on plugin to the cTakes.
>
> I have so many clarifications to be solved. Can I post them frequently ?
> How often can I ask questions on the average ?
>
> Regards,
> Prasanna.
>