Peter says: the LabValueFinder. It has settings that allow it to clone procedures into > lab values or vice versa (I can't remember).
The former... at least, when I contributed it. For potential lab values, it filters by TUIs: some procedures, others medications. Sean says: The only immediate solution that I can offer is to look for a nearby lab > value - by number or by unit. If a value exists then you could assume that > it is a lab result. Yes, that's what the LabValueFinder does... In short, I think that you may be stuck. ...and that's why it does it; I couldn't come up with a better solution at scale. Eugenia asks: So is it fair to say that cTakes is not fully aligned with SNOMED? Is > there a rule on how such concepts may be merged under the same CUI? Fair to say that cTAKES uses UMLS, and UMLS isn't an ontology -- nor does it claim to be! The UMLS Metathesaurus is a loose affiliation of ontologies, which aren't always individually coherent and consistent. Mapping between them is catch-as-catch-can. Hard wall to hit. Good luck with it! On Thu, Dec 3, 2020 at 9:01 AM Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Eugenia, > > In short, I think that you may be stuck. > The only immediate solution that I can offer is to look for a nearby lab > value - by number or by unit. If a value exists then you could assume that > it is a lab result. > > Sean > ________________________________________ > From: Monogyiou, Eugenia <eugenia.monogy...@nttdata.com> > Sent: Thursday, December 3, 2020 8:22 AM > To: dev@ctakes.apache.org > Subject: Disambiguation --alignment with SNOMED [EXTERNAL] > > * External Email - Caution * > > > Hello, > > I think I have hit a wall in terms of applying disambiguation in the > cTakes context. I have come across the following example where what I > consider to be a lab result (Monocyte Count) is picked up as a procedure, > apparently, in alignment with UMLS > coding Scheme = SNOMED Code =67776007, CUI =C0200637 , TUI =T059 > , preferredText = " Monocyte Count Procedure" > coding Scheme = SNOMED Code =365631001, CUI =C0200637 , TUI =T059 , > preferredText = " Monocyte Count Procedure" > > While they share the CUI (at UMLS level, due to the reconciliation of > different ontologies), they are quite different concepts. 67776007 stands > for "Monocyte count (procedure)" while 365631001 stands for "Finding of > monocyte count (finding)". So is it fair to say that cTakes is not fully > aligned with SNOMED? Is there a rule on how such concepts may be merged > under the same CUI? Would using YTEX resolve similar issues? > > And also I'm using cTakes 4.0.0 and the YTEX installation guide appears to > be outdated - the patch download is missing , names of files missing etc. > If YTEX is the answer are there any updated instructions? If it is not are > you using other UIMA-friendly solutions? > > Many thanks in advance, > Eugenia > > 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. >
