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From Alaa al Barari <alaa.albar...@gmail.com>
Subject Re: passing information through pipleline.process
Date Tue, 14 Feb 2017 14:42:32 GMT
not really i want this in dynamic manner, sometimes I need icd9 and other
times I need 10. if there is a way to specify exactly which scheme it
should work with.

like I have a webservice that sometimes it should return icd9 and other
times icd10 based on the request. modifying the xml wont do the trick.

On Tue, Feb 14, 2017 at 4:33 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Go into resources/org/apache/ctakes/dictionary/lookup/fast/ and edit your
> xml configuration file.  Comment out the 2 lines that have icd9 listed as
> desired schemes.  That should do it.
>
> The configuration file basically tells ctakes what is in your dictionary
> database.  If you comment those lines then it will think that there is no
> icd9 table in your database.  It won't bother to look up icd9 codes or
> store icd9 codes in the cas.  So, icd9 codes will not be in the array - no
> filtering is necessary and the iteration is shorter.
>
> Sean
>
> -----Original Message-----
> From: Alaa al Barari [mailto:alaa.albarari@gmail.com]
> Sent: Tuesday, February 14, 2017 9:29 AM
> To: dev@ctakes.apache.org
> Subject: Re: passing information through pipleline.process
>
> Thanks for your answer!
>
> Do you want ctakes to never find codes from certain schemes during
> processing?  yes exactly this is what I am shooting for, if I dont need
> them at the moment I dont want them found. suppose I have icd10 and icd9, I
> want it to not find icd9 when I am looking for 10 and nice versa.
>
>
> On Tue, Feb 14, 2017 at 4:13 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Hi Alaa,
> >
> > I have a question for you.  Do you want ctakes to never find codes
> > from certain schemes during processing?  Or do you want it to find
> > them, but only return them when you request them explicitly after
> processing?
> >
> > > can I override process(final JCas jcas)
> > That depends.  If you are subclassing an AE that declares it final you
> > cannot override it. If it is declared final then there may be a
> > reason.  In that case use composition.  If you need help, web search
> > "composition over inheritance".  You may want to use composition anyway
> ...
> >
> > > its from UIMA library right
> > Very close.  Process( JCas ) is from UimaFit while process (CAS ) is
> > from uima.  Web search UimaFit or go to uima.apache.org for more
> information.
> >
> > > how can I pass an information like final ConceptCode ...
> > > createConcepts(
> > final Collection<Long> cuiCodes, final ConceptCode
> > conceptCode)
> > Now you are getting into the fast-dictionary-lookup code that is in
> > ctakes.  You probably don't want to override this.  Look at my
> > question above.  What I am getting at is, if you only want ctakes to
> > maintain a small list of schemes then you should just change the
> > dictionary configuration file instead of delving into coding.  The
> > configuration file is xml and lists the schemes in your database, one
> > per line.  Just comment out the schemes that you don't want.
> >
> > As for a faster way to get codes of a different scheme, you are pretty
> > much out of luck.  This is because the uima cas stores everything in
> > an array.  To get items of interest ctakes has to go through the array
> > and filter out whatever you don't want.  We try to do that as
> > efficiently as possible, but we are tied to this array storage mechanism.
> >
> > Sean
> >
> >
> >
> > -----Original Message-----
> > From: Alaa al Barari [mailto:alaa.albarari@gmail.com]
> > Sent: Monday, February 13, 2017 3:40 AM
> > To: dev@ctakes.apache.org
> > Subject: passing information through pipleline.process
> >
> > Hi,
> >
> > I have around 16 different schemes, and the way I see it through
> > ctakes, it gets the information for all schemes then filter the un
> > wanted ones afterwards, this is a performance concern for me, so I am
> > trying to modify ctakes to suite my needs.
> >
> > can I override process(final JCas jcas)  if yes then where and how ?
> > its from UIMA library right ? if not how can I pass an information
> > like final ConceptCode from pipeline.process to createConcepts, my
> > createConcepts now look like below :
> > createConcepts( final Collection<Long> cuiCodes, final ConceptCode
> > conceptCode) ?
> >
> > --
> > Eng Alaa Al-Barari
> > phone 0599297470
> >
>
>
>
> --
> Eng Alaa Al-Barari
> phone 0599297470
>



-- 
Eng Alaa Al-Barari
phone 0599297470

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