Hi Everyone,
We are new to cTakes so please bear with our questions. We are using cTakes to
annotate things like encounter diagnoses and referral notes and are especially
interested with the SNOMED CT encodings. But we are not sure how to make sense
of all the outputs.
Example #1
In the example below, “cancer of colon, lung and liver” has been encoded with
SNOMED CT and additional concepts that do not apply have been removed (e.g.,
general “cancer” concept, lung, colon and liver structures, etc). They have
been plotted out by the begin/end positions. If the terms to do not align, its
probably because the email only accepts plain text and a mono-spaced font is
not the default.
cancer of colon, lung and liver
cancer of colon, lung and liver 93870000|Malignant neoplasm of liver
(disorder)|
cancer of colon, lung 363358000|Malignant tumor of lung (disorder)|
cancer of colon 363406005|Malignant tumor of colon (disorder)|
Question (1) – We had to do quite a bit of post-processing to remove inactive
concepts, subtype concepts, concepts that are part of the defining attributes,
etc. Are there a set of guidelines to help sort out the CUI or SNOMED CT codes
that have been identified?
Question (2) – How can we determine that “93870000|Malignant neoplasm of liver
(disorder)|” refers to “cancer of liver” as opposed to using the begin/end
string, which points to “cancer of colon, lung and liver”? Certainly we can
try to do additional parsing but there are a lot of different scenarios to take
into account.
Question (3) – This relates to question 2, are we able to identify the original
terms that were used for the concept matching or the exact description that was
returned in the UMLS? While the CUI is helpful, the CUI can refer to tens or
even hundreds of descriptions.
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Example #2
Switching the position of colon, lung and liver can result in different
encodings. Once again, after removing additional concepts not needed (i.e.,
“cancer” and “colon structure”), we get the following. What happened to liver
and lung cancer?
cancer of colon, liver and lung
cancer of colon 363406005|Malignant tumor of colon (disorder)|
lung 39607008|Lung structure (body structure)|
We have more questions but will start with these. Thank you in advance.
Regards,
Dennis
