CTV3 mapping requires term id for exact mapping (inferring details on code level)

[MaximMoinat]

Every CTV3 code has one or more terms. We only map the Preferred (P) term, which can have a different meaning than the others. For example two of the six terms of code Xa9Bs (DVT).

ctv3_conceptid	ctv3_termid	ctv3_termtype	snomed concept_id	snomed_name
Xa9Bs	Y20L6	P	443537	Deep venous thrombosis of lower extremity
Xa9Bs	Y20Kh	S	4133004	Deep venous thrombosis

The preferred term here is more specific than the others. In our mapping, all Xa9Bs codes will be mapped using the SNOMED of this more specific (preferred) term. This is adding a level of granularity that we don't have.

Ideally we also use the CTV3 term to do the mapping. This is not available.

While resolving issue #330 , we decided to go with the preferred one. It will be consistent with the rest of the mapping. Also, for the AESI study, both these concepts are included.

[spiros]

I agree that using the Preferred term is the right way to go here.

Some things to note:

1. Unlike Read version 2, where you have pairs of concept identifiers and concept term strings, CTV3 has different identifiers for concepts themselves and for the concept terms. So in your example above, the core concept is Xa9Bs and the preferred term identifier for it is Y20L6. As a rule of thing, all codes starting with Y are term identifiers.

2. Read codes are case-sensitive ! So in the example link you have in the issue, the results are incorrect ! You can tell by looking at them as they seem to mix DVT and glaucoma...! The DVT identifier is Xa9Bs while the glaucoma one is Xa9BS but the NHS Browser is doing a bad job and returns everything. It's worth doing a quick check in the code to make sure this case sensitivity is taken into consideration (i've learned the hard way).

3. Bioportal provides a decent browser

[MaximMoinat]

Thanks Spiros for the comments. I will leave the issue for awareness.

Our lookup should be case-sensitive, but still good to be aware of.