Hi Jeff thanks for your suggestions,
I spent some time in the script file and sure enough, my 2020 UMLS
extraction actually has these two entries:
INSERT INTO CUI_TERMS VALUES(3542022,0,1,'soft','soft')
INSERT INTO PREFTERM VALUES(3542022,'SHORT STATURE, ONYCHODYSPLASIA, FACIAL
DYSMORPHISM, AND HYPOTRICHOSIS SYNDROME')
It's unbelievable. the UMLS entry has got to be wrong or I'm missing
something to say that it only applies (as an acronym) if it's capitalized
In sno_rx there is neither a CUI 3542022 nor the definition of "soft" as a
solitary word, nor even a mention of ONYCHODYSPLASIA or HYPOTRICHOSIS
In any case, I would have thought that ctakes will only create an event
mention from a term tagged as NN or NP slot, not a ADJ as in "soft tissue"
Anyway Thanks! Now I will keep poking around.
Peter
On Sat, Aug 1, 2020 at 5:06 PM Jeffrey Miller <jeff...@gmail.com> wrote:
> 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
> >>
> >>
> >>
>
