Sorry, I meant suggest to search for 'soft' in the dictionary file not
'short'
grep -i ,\'soft\', *.script
On Sat, Aug 1, 2020 at 7:47 PM Jeffrey Miller <jeff...@gmail.com> wrote:
> Hi Peter,
>
> To my knowledge, there isn't any drastic difference in the behavior of the
> dictionary gui creator and the way the sno_rx dictionary was created. I
> originally thought there was, but I realized the difference was that I had
> not installed all of UMLS to my machine (just the vocabularies I was
> interested in) and I was missing synonyms. The first thing I would check,
> are you able to find a matching entry in the .script file for your ctakes
> dictionary when you do this:
>
> grep -i ,\'short\', *.script
>
> That would confirm whether or not you have a term in your dictionary made
> up only of 'short' and whether it mapped to the CUI equal to "SHORT
> STATURE, ONYCHODYSPLASIA, FACIAL DYSMORPHISM, AND HYPOTRICHOSIS SYNDROME".
> If it's not in there, something else is going on. You could do the same for
> 'bed'.
>
> If not, another thing I might check is that I noticed you are using
> the OverlapJCasTermAnnotator in your prior e-mail. I don't have much
> experience with it, and I don't think it should cause this behavior, but I
> wonder if that could be making the difference (as compared
> to DefaultJCasTermAnnotator).
>
> Jeff
>
> On Sat, Aug 1, 2020 at 5:27 PM Peter Abramowitsch <pabramowit...@gmail.com>
> wrote:
>
>>
>> Hi All
>>
>> Having created a new dictionary from the 2020AA UMLS and added Genes and
>> Receptors to the dictionary-creator's default selections, I have a curious
>> problem where cTakes now assigns the most bizarre acronyms to ordinary
>> words used in POS contexts where it shouldn't find <XXX>Mentions.
>>
>> Here are two examples:
>>
>> 1. soft (in "soft tissue...")
>> becomes "SHORT STATURE, ONYCHODYSPLASIA, FACIAL DYSMORPHISM, AND
>> HYPOTRICHOSIS SYNDROME",
>>
>> 2. bed in ("The wound bed was...")
>> becomes "BORNHOLM EYE DISEASE"
>>
>> I have not changed the TermConsumer type in the descriptor XML.
>>
>> Are the DictionaryCreator's defaults, the equivalent to the default
>> sno_rx that's delivered with the app?
>>
>> Attached is the vocab subsets list I used
>>
>>
>> Peter
>>
>>
>>
