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From Phan Hồng Phúc <phanhongphu...@gmail.com>
Subject Re: Clinical Element Model normalization component
Date Wed, 10 Feb 2016 18:55:18 GMT
Hi Jessica,

I start from MedicationMention now.

Thank you,
- Phúc

2016-02-10 21:27 GMT+07:00 Jessica Glover <glover.jessica.m@gmail.com>:

> Hi,
> I saw that it does come with DrugNER, but I also find that isn't picking up
> Tylenol as an ner type annotation. I'm curious to know whether DrugNER
> worked prior to 3.2 . I will keep digging. In the meantime I hope you find
> MedicationMention in the IdentifiedAnnotations. I don't think the
> attributes like dosage, etc. get populated, but it does pick up Tylenol for
> me.
>
> - Jessica
> On Feb 10, 2016 4:30 AM, "Phan Hồng Phúc" <phanhongphucit@gmail.com>
> wrote:
>
> > Thanks Jessica, looking forward to you..
> > Just an information that from this email
> >
> >
> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201508.mbox/%3CCOL130-W826156991F6C8E4085DA7AFB7D0@phx.gbl%3E
> > Chenpei said that AggregatePlaintextFastUMLSProcessor.xml should already
> > have
> > the Drug NER included.
> >
> > Regards,
> > - Phúc
> >
> >
> >
> >
> > 2016-02-10 3:51 GMT+07:00 Jessica Glover <glover.jessica.m@gmail.com>:
> >
> > > I believe you need to add an annotator like DrugAggregateCDAProcessor
> to
> > > the pipeline to get the annotations you seek. I will investigate and
> > write
> > > more soon.
> > >
> > > - Jessica G.
> > > On Feb 9, 2016 2:31 PM, "Miller, Timothy" <
> > > Timothy.Miller@childrens.harvard.edu> wrote:
> > >
> > > > I'm not that familiar with that module but I can confirm that I was
> > able
> > > > to replicate your output on this example.
> > > > If it helps at all the MedicationMention type does have a span for
> the
> > > > tylenol mention, but obviously doesn't help with all the dosage,
> route,
> > > > etc. information you might want.
> > > > Hopefully one of the devs/maintainers of that module will have some
> > idea.
> > > > Tim
> > > >
> > > >
> > > > On 02/09/2016 02:19 PM, Phan HôÌng Phuìc wrote:
> > > > > Hi all,
> > > > >
> > > > > I try to run the sample to get the drug name.
> > > > > Let me describe my steps:
> > > > > - runctakesCVD.bat
> > > > > - Load AE:
> > > > >
> > > >
> > >
> >
> apache-ctakes-3.2.2\desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor
> > > > > - Add sample text: "*He is taking 500mg of tylenol, twice a day"*
> > > > > *- *After run, I see a list of result but all type
> > > > > org.apache.ctakes.drugner.type.* are [0]
> > > > >
> > > > > I think it should contain at least drug name "tylenol" in the
> result.
> > > > >
> > > > > Do I miss something?
> > > > >
> > > > > Thank you,
> > > > > - Phúc
> > > > >
> > > >
> > > >
> > >
> >
>

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