Hi Jeff I thought I did load them all, but I'll go back and check.
When looking at my gene issue the result is that the lookup arbitrarily (seemingly anyway) flips between one and another when there are overlaps between vocabularies. Ie. I see that both Vocab A & B both contain geneX and geneY. Neither of these are in SNOMED. So in my output, I get one of the genes associated with Vocab A and another with Vocab B. When I remove Vocab B then obviously both are associated with Vocab A - which is what I wanted. If, for you, WBC is showing up as an anatomical location, rather than a T059 then probably it's not getting the correct SNOMED code though. Wouldn't that be a problem for your researchers? Peter On Wed, Aug 5, 2020 at 5:37 PM Jeffrey Miller <jeff...@gmail.com> wrote: > Hi Peter, > > If I create a dictionary using UMLS 2020aa with just snomed and rxnorm my > cTAKES dictionary still seems to have a CUI associated with the string > 'wbc' that links to the snomed term for Leukocyte (Cell). It is not mapping > to a lab result TUI, but rather an anatomical site, but it seems to be the > same CUI that 'wbc' resolves to in sno_rx_16ab. Maybe HGNC is conflicting > with that too? > > Just to double check, when you installed UMLS through Metamorphosys, did > you install all of the available vocabularies? > > Jeff > > On Wed, Aug 5, 2020 at 6:52 PM Peter Abramowitsch <pabramowit...@gmail.com > > > wrote: > > > Hi All > > > > I've been setting up a custom dictionary using UMLS with the goal of > simply > > adding a comprehensive genetic vocabulary HGNC to the latest UMLS SNOMED > > and RXNORM vocabularies in the hope of getting somewhere close to the > > cTakes default dictionary again. > > > > However, there are changes to concept vocabularies in UMLS2020AA that > > affect the ability of cTakes to work well with older notes and possibly > the > > note-writing practices of older physicians and labs. Some of the tried > > and true acronyms such as WBC for leukocytes, RBC, and EOS (eosinophil > > count) are no longer part of SNOMED. Probably this is because the > > components of these parameters are now broken out into more granular > > types. The other reason this may be is that a few of these acronyms now > > overlap the names of Genes. EOS is one of them. This is just > speculation. > > > > In order to have these common parameters re-included via their common lab > > acronyms, it is necessary to add another common US vocabulary such as > > HL7-V3.0 or NCI_CDISC. Of course one can remap back into SNOMED by > adding > > insert statements into the dictionary script, but it might be a > > non-scalable exercise. > > > > So my point here is that if, one day, we plan to create a new cTakes > > release, and with it, a new UMLS lookup, we may need to consider adding a > > third basic vocabulary into our current set of two. > > > > Thoughts? > > Peter > > >
