Thanks Sean. Interesting. I will have a look. Then have a look in the creator code.
I should work through emails from older to newer. Just responded to Gandhi. On Fri, Aug 14, 2020, 4:53 AM Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Peter, > > I don't have an answer but I do have a question: > > In your mrconso.rrf, do you see a snomed line item for "SOB" or only "SOB > -Shortness of breath" ? > > I think that the simple "SOB" and "sob" entries might be from other > vocabularies. > > There is (was?) logic in the dictionary creator to multiply things like > "SOB - Shortness of breath", "SOB (Shortness of breath)" etc. and create 3 > synonym entries: full, left and right. There is a requirement that the > left side be all caps and a fitting acronym for the right side. However, I > vacillated on the correctness of this behavior as almost all terms already > had the 3 entries. I am not sure what the current version of the creator > does. > > Dictionary creation is indeed a touchy operation. > > Sean > ________________________________________ > From: Peter Abramowitsch <pabramowit...@gmail.com> > Sent: Thursday, August 13, 2020 11:57 PM > To: dev@ctakes.apache.org > Subject: Need a little more help on dictionaries [EXTERNAL] > > * External Email - Caution * > > > Hi All > > I'm able to create a subset with the UMLS mmsys tool, use the dictionary > creator on the full UMLS release, create, install and tweak the scripts > adding or removing aliases etc. My goal is simply to add HUGO gene terms > to SNOMED and RXNORM. > > However I must be missing some bit of information on the use of mmsys or > the dictionary creator, because some very common terms are missing from my > dictionary but present in the released sno_rx > > As an example, the acronym SOB > in mmsys, the term SOB is present in my subset, and it is mapped into > SNOMED with the expected CUI 13404 and SNOMEDIDs same as sno_rx > I see the cui_tui mapping it into the correct TUI for a finding INSERT > INTO TUI VALUES(13404,184) > I see the cui and the preferred term "dyspnea" in my *script file, and I > can resolve it in a note using the default consumer and obtaining the > correct SNOMED ID > I see lots of cui_term entries for the same CUI, and I can resolve them > too. but SOB is not present in my cui terms. > How did it get there? > > So either - I am not using one of the tools correctly, or in creating > SNO_RX, someone has added SOB by hand rather than using the creator. And > if they have, they have probably also done other tweaks. > > Sean, Ghandi or Jeff > Can you explain this? > > Peter >
