Thank you all for the support!
Sean, Kean the labValueFinder works as described so thanks for pointing that
out!
Peter, I will ask for your help with the LookupWindow if you could please spare
a bit more time... I have located the UmlsOverlapLookupAnnotator file, thank
you for that.
I have located in the UmlsLookupAnnotator (in ctakes-dictionary-lookup-fast)
<name>windowAnnotations</name>
<value>
<!-- LookupWindowAnnotation is supposed to be a refined Noun
Phrase -->
<!--<string>org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</string>-->
<!-- In some instances LookupWindowAnnotation is missing tokens
and Sentence can be used -->
<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
</value>
I have gone through various java and typesystem files but I am not sure where I
can find all the potential options for the Lookup Window and where/how I can
set these. Also, if you could please let me know where in the code it is
possible to see what symbols are considered "end-of sentence". I have noticed
that ":" sometimes defines the end of a sentence but I haven't located anything
relevant in the code ...
Peter says :
> > Sometimes you need to further customize your dictionary. (can you please
> > elaborate ?)
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
-----Original Message-----
From: Peter Abramowitsch <pabramowit...@gmail.com>
Sent: 03 December 2020 18:54
To: dev@ctakes.apache.org
Subject: Re: Disambiguation --alignment with SNOMED
I have this issue a lot. There are many moving parts. Sometimes it can
be resolved by using the widest window in the DictionaryLookup or sometimes the
TermOverlap lookup annotator. Sometimes you need to further customize your
dictionary.
The problem arises when there isn't enough context to whittle down the lookup
to the correct SNOMED entity. Or there isn't a synonym entry in the
Dictionary that maps to the widest context in your texts. If you look at
how the UMLS SNO_RX dictionary is structured you'll see how it can happen.
For starters, look at the raw XMI and see all the entries in the UmlsArray that
were selected even if later, only the wrong one entry surfaced.
Another issue is the LabValueFinder. It has settings that allow it to clone
procedures into lab values or vice versa (I can't remember). This can lead to
a lot of duplication
Peter
On Thu, Dec 3, 2020 at 2:23 PM Monogyiou, Eugenia <
eugenia.monogy...@nttdata.com> wrote:
> Hello,
>
> I think I have hit a wall in terms of applying disambiguation in the
> cTakes context. I have come across the following example where what I
> consider to be a lab result (Monocyte Count) is picked up as a
> procedure, apparently, in alignment with UMLS
> coding Scheme = SNOMED Code =67776007, CUI =C0200637 , TUI =T059
> , preferredText = " Monocyte Count Procedure"
> coding Scheme = SNOMED Code =365631001, CUI =C0200637 , TUI =T059 ,
> preferredText = " Monocyte Count Procedure"
>
> While they share the CUI (at UMLS level, due to the reconciliation of
> different ontologies), they are quite different concepts. 67776007
> stands for "Monocyte count (procedure)" while 365631001 stands for
> "Finding of monocyte count (finding)". So is it fair to say that
> cTakes is not fully aligned with SNOMED? Is there a rule on how such
> concepts may be merged under the same CUI? Would using YTEX resolve similar
> issues?
>
> And also I'm using cTakes 4.0.0 and the YTEX installation guide
> appears to be outdated - the patch download is missing , names of files
> missing etc.
> If YTEX is the answer are there any updated instructions? If it is not
> are you using other UIMA-friendly solutions?
>
> Many thanks in advance,
> Eugenia
>
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