Thanks Sean and Eugenia, I'm glad that it's not just me. I'll do some stats on this. I also found another possible issue where there's no current snomed mapping for a CUI (perhaps one of them is obsolete), so what happens then that the CUI based entry remains in TUI and in CUI_TERMS, but there's none in either SNOMEDCT or in PREFTERM.
Peter On Thu, Mar 18, 2021 at 1:28 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Peter, Eugenia, > > I haven't noticed the occurrence, but can believe that this could happen. > I am not sure why or how. I suppose you could run two counts to find out > how many are missing - I don't want to know. > > There are probably a few things that could be done to 'cover' this > problem, but the best would be making the dictionary creator fill in the > blanks. > > Sean > ________________________________________ > From: Monogyiou, Eugenia <eugenia.monogy...@nttdata.com> > Sent: Thursday, March 18, 2021 6:34 AM > To: dev@ctakes.apache.org > Subject: RE: Issue with dictionary creator? [EXTERNAL] > > * External Email - Caution * > > > Just to clarify the cases I encountered were not valid conceptually but > appeared to be valid , i.e. had cui, tui and SNOMED code. I used today as > an example to show exactly that "conceptual" issue but it has been many > months since the last time I encountered this so I don't have any proper > examples to list at the moment. > > 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: Monogyiou, Eugenia > Sent: 18 March 2021 10:27 > To: dev@ctakes.apache.org > Subject: RE: Issue with dictionary creator? > > Hi Peter, > > Yes I have (before I started using the cased format) and it was only > medication indeed-- however it was drugs that should not be annotated as > such in the first place , e.g. today as an antibiotic which led me to think > it may have had something to do with broken links, even residuals from > efforts to "fix" certain entries perhaps? Our cohort was for heart attack > so not a very broad range of meds were present in the letters; perhaps I > did not encounter "valid" cases just out of luck because of the specific > cohort...? > > Kind Regards, > > Eugenia Monogyiou > > -----Original Message----- > From: Peter Abramowitsch <pabramowit...@gmail.com> > Sent: 18 March 2021 10:19 > To: dev@ctakes.apache.org > Subject: Issue with dictionary creator? > > Has anyone seen an issue where a dictionary is created from UMLS sources > where there is no entry in PREFTERM for a valid CUI that is present in TUI, > CUI_TERMS, and SNOMEDCT_US?. > > It seems to be happening in certain medication mentions where there is a > base drug instance and then various forms. It could be that one of the > form descriptions is obsolete, but that wouldn't explain why it was only > half-present in the resulting dictionary. > > for instance > > clobetasol CUI 8992 has an entry in every table clobetasol emollient CUI > 4520933 has all information in every table clobetasol topical CUI 3207574 > but is missing only in PREFTERM > > cui_term > '3207574','0','2','clobetasol topical','clobetasol' > '3207574','0','8','clobetasol - containing product in cutaneous dose > form','clobetasol' > > Tui > '3207574','200' > > Snomed > '3207574','771278006' > > Prefterm > Blank. > > Peter > Disclaimer: This email and any attachments are sent in strictest > confidence for the sole use of the addressee and may contain legally > privileged, confidential, and proprietary data. If you are not the intended > recipient, please advise the sender by replying promptly to this email and > then delete and destroy this email and any attachments without any further > use, copying or forwarding. >
