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
