Many thanks Sean and Jeff. You guys must be both on the East Coast, because my coffee has only just kicked in enough to digest your lucid replies. Super helpful information. It sounds like the quick and dirty solution is to rebuild the dictionary without the OMIM and MTH vocabularies. So it’s not a case of a CUI being remapped - but that it’s being layered onto by a particular vocabulary adding a synonym (which in this case is probably very rarely used)
One question related to that - are the vocabulary & tui selections that one finds as defaults in the dictionary creator something set by the creator as a ctakes optimization, or are the defaults governed by information the creator reads from the UMLS release? And thanks for mentioning the capitalization project. I had been looking in vain for that functionality which I had assumed was already there. You can tell that these are still my first experiences with dictionary building. I appreciate how difficult it is to find the time to build enhancements to the product when one is so busy just using it. There’s an enhancement I’ve been prototyping for months which brings in some functionality from the Stanford NLP project. But just don’t have time or energy to productize it. It would have two completely different applications: a superior way of finding the values of findings and a way of validating/pruning the polarity status of concepts that are in an semi-grammatical or improperly punctuated sentence - such as “Denies headache, abdominal pain, temperature normal” Maybe one day.... Thanks again Peter Sent from my iPad > On Aug 2, 2020, at 06:25, Finan, Sean <sean.fi...@childrens.harvard.edu> > wrote: > > Hi Peter, > > I would guess that you are seeing things like "SOFT" because you new > dictionary has a vocabulary that was not included in sno_rx_16ab. > I don't remember if OMIM (which has the 'SOFT' synonym) was included in > sno_rx_16ab. Probably not, omim is a more -specialized- vocabulary for > genetics. > > The term is only in the omim (and mth) vocabularies in the 2016AB umls > release. > > https://uts.nlm.nih.gov/metathesaurus.html#C3542022;0;1;CUI;2016AB;WORD;CUI;*; > > > The term is in snomed in umls 2020AA, but only with the expanded full-text > synonym. It still has the abbreviation from omim. > https://uts.nlm.nih.gov/metathesaurus.html#SHORT%20STATURE,%20ONYCHODYSPLASIA,%20FACIAL%20DYSMORPHISM,%20AND%20HYPOTRICHOSIS;0;1;TERM;2020AA;WORD;TERM;*; > > As for finding terms in adjectives, the default parts of speech(pos) that are > checked for terms are: > VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB > > You can see what these are here: > https://www.ling.upenn.edu/courses/Fall_2003/ling001/penn_treebank_pos.html > > You can override this list. In your piper file, set the variable > "exclusionTags" > > // Default excluded parts of speech, plus various forms of adjective. > set > exclusionTags="ADJ,JJ,JJR,JJS,VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB" > > // Annotate concepts based upon default algorithms. > add DefaultJCasTermAnnotator > > > You'll notice that I threw in 'ADJ' for good measure. It should not break > anything. > > I have modified this list many times for various projects. In one I allow > verbs for lookup. For those notes the value of the true positives outweighed > the increased false negatives. In another I actually empty the entire list > to allow everything (set exclusionTags=""). I did this because there is a > lot of structured text in lists and tables, but the pos tagger is trying to > resolve prose text. The pos assigned on the structured text is all over the > place, and terms are missed left and right. > > So ... last but definitely not least, case-sensitivity. > I started working on this a while ago, but right now it sits unfinished. > > There is an additional table in the dictionary database, in which all > synonyms are all upper-case. > This second table is created with synonyms that exist in the umls as all > upper-case. > The first "classic" table is created using ONLY synonyms from the umls that > are lower and/or mixed case. > > When the annotator engine iterates over the text, it checks one table > (classic) or the other (caps) depending upon the case of the text in the note. > > It sounds like minor work, but it requires a new engine, new dictionary, and > new dictionary creator. None of this is difficult, but it requires time. > > Anyway, I hope that some of this helps. > > Sean > > > ________________________________________ > From: Peter Abramowitsch <pabramowit...@gmail.com> > Sent: Saturday, August 1, 2020 11:35 PM > To: dev@ctakes.apache.org > Subject: Re: With custom dictionary - over-eager resolution of acronyms > [EXTERNAL] > > * External Email - Caution * > > > 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 >>>> >>>> >>>> >>
