I have this issue a lot. There are many moving parts. Sometimes it can be resolved by using the widest window in the DictionaryLookup or sometimes the TermOverlap lookup annotator. Sometimes you need to further customize your dictionary.
The problem arises when there isn't enough context to whittle down the lookup to the correct SNOMED entity. Or there isn't a synonym entry in the Dictionary that maps to the widest context in your texts. If you look at how the UMLS SNO_RX dictionary is structured you'll see how it can happen. For starters, look at the raw XMI and see all the entries in the UmlsArray that were selected even if later, only the wrong one entry surfaced. Another issue is the LabValueFinder. It has settings that allow it to clone procedures into lab values or vice versa (I can't remember). This can lead to a lot of duplication Peter On Thu, Dec 3, 2020 at 2:23 PM Monogyiou, Eugenia < eugenia.monogy...@nttdata.com> wrote: > 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 be outdated - the patch download is missing , names of files missing etc.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. >
