First of all, thank you for this impressive work! That was a joy to follow phenotype phebruary from the very first day.
However, I think that there is an issue we have in this phenotype resulting from combination of Atlas behaviour and Vocabulary hierarchy. Using phenotype 1 with conditions only, I noticed that in Atlas included source codes, there are a few concepts with type 1 diabetes.
There are none of type 1 diabetes in included standard concepts, which suggests erroneous mapping. Lets take one code as example and see:
E10.10 Type 1 diabetes mellitus with ketoacidosis without coma is mapped to 2 conditions: 201254 Type 1 diabetes mellitus and 4009303 Diabetic ketoacidosis without coma, which is neither connected to Type 1, nor to type 2 diabetes, which is true, because any type of diabetes may result in diabetic ketoacidosis without coma. What is not true is that patients are included in Type 2 diabetes cohort despite explicit exlusion of Type 1 diabetes from the concept set. These codes were included by 442793 Complication due to diabetes mellitus and not excluded by 201254 Type 1 diabetes mellitus, which I think is a bit tricky of Atlas.
The pretty close issue is discussed right now in another topic.
We excluded Type 1 concepts by source code and the cohort was limited to only Type 2 DM patients.
So is it the expected behavior of Atlas and it just should be kept in mind or should be changed?
Am I missing something? Thoughts?
@Gowtham_Rao @Patrick_Ryan @Christian_Reich @Chris_Knoll @aostropolets @Alexdavv