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Date: Mon, 22 Sep 2014 02:17:20 -0400
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Subject: Re: ctakes not capturing all meds/rxnorm IDs
From: EM Gladiators <emgladiators@gmail.com>
To: user@ctakes.apache.org
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Pei,  I am not seeing anything being filtered in the logs.  I checked both
the output in the terminal and also I set the log in the software to log
everything.  How do I go about suppressing the OrangeBook filter and use
only Rxnorm?  I'm still not sure the filtering is the problem, because
aspirin is also found in OrangeBook.  But, removing the OrgangeBook filter
would be a good place to start to see if it improves the medication name
recognition.

Thank you,

James

On Sun, Sep 21, 2014 at 10:30 PM, Pei Chen <chenpei@apache.org> wrote:

> In the logs, do you see something like "Filtered out xyz"?
> I think the default configuration has a OrangeBook Filter consumer
> applied.  That is only RxNorm concepts that also exist in the
> OrangeBook are returned.  I'm not sure if this is causing some of your
> drugs to be missed, but worth taking out OrangeBook filter out to
> confirm.
> We should probably default all RxNorm to be returned and make the
> OrangeBook filter optional in the future release.
>
> On Sun, Sep 21, 2014 at 5:53 PM, EM Gladiators <emgladiators@gmail.com>
> wrote:
> > I have recently installed ctakes.  I am using the
> > AggregatePlaintextUMLSProcessor.  When running the CVD, it is not
> accurately
> > annotating all medication names.  Specific medication names that it
> > annotates correctly are metformin and nifedipine.  Specific medications
> it
> > fails to annotate are aspirin and simvastatin.  It is unclear why some
> names
> > would be annotated correctly and some not, even though all medication
> names
> > are found in rxnorm.  I am afraid that it is not correctly using the
> rxnorm
> > files.  Is there a way to check to see if the full rxnorm is being
> searched?
> >
> > I have not had a problem with snomed CT terms, ctakes does appear to be
> > capturing these correctly.
> >
> > Thank you,
> >
> > James Foster
> >
> > My setup is as follows...
> >
> > Mac OS 10.9.4
> > Java version 1.8.0_20
> > ctakes version 3.2.0 with optional resources package
>

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<div dir=3D"ltr">Pei, =C2=A0I am not seeing anything being filtered in the =
logs.=C2=A0 I checked both the output in the terminal and also I set the lo=
g in the software to log everything.=C2=A0 How do I go about suppressing th=
e OrangeBook filter and use only Rxnorm?=C2=A0 I&#39;m still not sure the f=
iltering is the problem, because aspirin is also found in OrangeBook.=C2=A0=
 But, removing the OrgangeBook filter would be a good place to start to see=
 if it improves the medication name recognition.<div><br></div><div>Thank y=
ou,</div><div><br></div><div>James</div></div><div class=3D"gmail_extra"><b=
r><div class=3D"gmail_quote">On Sun, Sep 21, 2014 at 10:30 PM, Pei Chen <sp=
an dir=3D"ltr">&lt;<a href=3D"mailto:chenpei@apache.org" target=3D"_blank">=
chenpei@apache.org</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quot=
e" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">=
In the logs, do you see something like &quot;Filtered out xyz&quot;?<br>
I think the default configuration has a OrangeBook Filter consumer<br>
applied.=C2=A0 That is only RxNorm concepts that also exist in the<br>
OrangeBook are returned.=C2=A0 I&#39;m not sure if this is causing some of =
your<br>
drugs to be missed, but worth taking out OrangeBook filter out to<br>
confirm.<br>
We should probably default all RxNorm to be returned and make the<br>
OrangeBook filter optional in the future release.<br>
<div class=3D"HOEnZb"><div class=3D"h5"><br>
On Sun, Sep 21, 2014 at 5:53 PM, EM Gladiators &lt;<a href=3D"mailto:emglad=
iators@gmail.com">emgladiators@gmail.com</a>&gt; wrote:<br>
&gt; I have recently installed ctakes.=C2=A0 I am using the<br>
&gt; AggregatePlaintextUMLSProcessor.=C2=A0 When running the CVD, it is not=
 accurately<br>
&gt; annotating all medication names.=C2=A0 Specific medication names that =
it<br>
&gt; annotates correctly are metformin and nifedipine.=C2=A0 Specific medic=
ations it<br>
&gt; fails to annotate are aspirin and simvastatin.=C2=A0 It is unclear why=
 some names<br>
&gt; would be annotated correctly and some not, even though all medication =
names<br>
&gt; are found in rxnorm.=C2=A0 I am afraid that it is not correctly using =
the rxnorm<br>
&gt; files.=C2=A0 Is there a way to check to see if the full rxnorm is bein=
g searched?<br>
&gt;<br>
&gt; I have not had a problem with snomed CT terms, ctakes does appear to b=
e<br>
&gt; capturing these correctly.<br>
&gt;<br>
&gt; Thank you,<br>
&gt;<br>
&gt; James Foster<br>
&gt;<br>
&gt; My setup is as follows...<br>
&gt;<br>
&gt; Mac OS 10.9.4<br>
&gt; Java version 1.8.0_20<br>
&gt; ctakes version 3.2.0 with optional resources package<br>
</div></div></blockquote></div><br></div>

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