Thank you very much I was not aware of this! :)
Although I am using the CasedAnnotationFinder not the JCasTermAnnotator so not
dealing with .xml but this is useful to understand properly and perhaps give it
a go in another test where I would be using that Annotator.
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com
-----Original Message-----
From: Kean Kaufmann <k...@recordsone.com>
Sent: 15 February 2021 15:17
To: dev@ctakes.apache.org
Subject: Re: Dictionary "bad" codes
FWIW, rather than editing the HSQLDB script, we use Sean's
BsvRareWordDictionary to add phrases with a BSV file:
cTakesHsql.xml:
<lookupSpecification>
<dictionaries>
<!-- phrases not in dictionary -->
<dictionary>
<name>AddPhrases</name>
<implementationName>org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary</implementationName>
<properties>
<property key="bsvPath"
value="org/apache/ctakes/dictionary/lookup/fast/custom2020ab/AddPhrases.bsv"/>
</properties>
</dictionary>
AddPhrases.bsv:
C1276061|nstemi
C1276061|non st elevation mi
C1276061|non-st elevation mi
C1536222|non-stemi
C1276061|non st elevation myocardial infarction non st elevated
C1276061|myocardial infarction non-st elevated myocardial infarction non
C1276061|st elevated mi non-st elevated mi
On Mon, Feb 15, 2021 at 10:09 AM Peter Abramowitsch <pabramowit...@gmail.com>
wrote:
> Hi Eugenia
> There may be better ways to do this, but I would insert these as
> Synonyms in the CUI_TERMS table. The concept is already there:
>
> insert this:
> INSERT INTO CUI_TERMS VALUES(1303258,0,1,'stemi','stemi')
>
> the concept is already declared here
> INSERT INTO PREFTERM VALUES(1303258,'Acute ST segment elevation
> myocardial infarction (disorder)')
>
>
>
>
>
>
> On Mon, Feb 15, 2021 at 3:46 PM Monogyiou, Eugenia <
> eugenia.monogy...@nttdata.com> wrote:
>
> > Hello,
> >
> > Peter we had a discussion quite some time ago about additions and
> removals
> > that would result into a good dictionary. I have a specific example
> > I
> would
> > ask for your help please (or anyone else that has an idea :) )
> >
> > So STEMI and NSTEMI are correctly annotated but "Code" and "Coding
> Scheme"
> > are null... when that happens in my tests it is usually because of a
> badly
> > formed term interpretation which is to be discarded anyway. I have
> > found similar cases mentioned as "ghost" terms in the UMLS
> > documentation; in
> this
> > case, however, they are valid interpretations and quite important to
> > my tests because I am working on heart attack and cardiac disease cohorts.
> >
> > I tried associating with the appropriate code by adding the
> > following inserts but it did not work ...
> >
> > INSERT INTO UPPER VALUES(1276061,'','NSTEMI','',31,1)
> > INSERT INTO UPPER VALUES(1303258,'','STEMI','',31,1)
> >
> > Any ideas please?
> >
> > Many thanks in advance,
> >
> > Kind Regards,
> >
> > Eugenia Monogyiou | NTT Data UK
> > Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
> >
> > Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com<mailto:
> > eugenia.monogy...@nttdata.com>
> >
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