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From "Dennis Lee Hon Kit" <d...@uvic.ca>
Subject Concept annotation questions
Date Wed, 21 Aug 2013 18:09:31 GMT
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.


--------------------------------------------------------------------------------

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
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