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ATLAS QUESTION - concept set tab in cohort definition

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(Diana) #1

Hi @krfeeney ,
I have a basic question about Atlas. In the concept set tab of the cohort definition…for instance http://atlas-covid19.ohdsi.org/#/cohortdefinition/839.
image

There is a checkbox for descendants for each concept id in the concept name.

If you select the checkbox for descendants, does that select every descendant automatically even though the shopping carts aren’t highlighted?
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And if descendants is selected, will it also include the “descendants of the descendants” as well?
Thanks,
Diana


(Lisa Schilling) #2

@dir0417 @krfeeney @anthonysena. I have found this very confusing too, as you can see from Diana’s screenshots, there is one shopping cart that is orange, so why wouldn’t they all be orange? What does this one being orange mean. Also (we did not show this screenshot) but when you check the descendant box you do see the # of concepts increases, and the count equals the # of children, so in this case it would be 78. But then this begs the question of what about descendants of descendants (level 2 children) because those are NOT in the count, but when you select a level 1 desc and see the level 2 descendants - occasionally some of them will also have orange shopping carts but not all- so are they included or not. Thanks a ton for helping us understand this.


(Chris Knoll) #3

Quick answers:

Selecting the descendant checkbox will ‘pull in’ all descendants (including descendants of descendants, ie: the entire descendant line of a concept. When you look at the included concepts, you are seeing the entire set of concepts that are being ‘pulled in’ to the concept set. The orange ones represent those concepts that were specified in the concept set so you can see the difference between the ones that were in the included concepts via a descendant relationship, and those that are in the concept set because you specified them explicitly.

Right, same answer as above, just quoting you here so you know that’s the same deal: orange = ‘specified in concept set’, non-orange means ‘in the concept set from descendants’.

I do not think you are seeing it correctly: when you use ‘descendants’, it goes to CONCEPT_ANCESTOR and pulls in all the descendant_concept_ids associated to that concept set. It doesn’t do anything resembling ‘just the immediate children’. If you have a concept set for that specific example where you have a parent and a child in the concept set, and you select the descendants of the parent (which will include the child), but then when you include the descendants of the child, the number increases, you should share that with us, because descendants of parents includes all descendants of the child.

Additionally, we are planning on changing the way these shopping carts work in a future release of Atlas because of some of the confusion you are experiencing. For example: if you see a lit shopping cart in a search result, you know it’s used in the concept set expression somehow, but if you de-select the shopping cart (remove from concept set) and select it again (put it back in), you may have removed the concept as an ‘include desendant’ but it gets put back in as a ‘non-include descendant’. There are other sources of problems with the current design as well. To that end, we’ll be going to a check-box form of selection where you won’t accidentally remove a concept from your concept set and loose the concept set’s setting, as well as allow you to select a bunch of concepts at once and then decide how they should be added to the concept set: as descendants, as excludes, as exclude-desendants, etc.


(Lisa Schilling) #4

@Chris_Knoll thanks for the great explanation! My recap -checking/including descendants includes all descendants and all descendants of descendants. Those descendants (and desc of desc ) that are orange are so because they were specified in the original concept set.
(you are right, I was seeing it wrong). It will be a great addition to be able to add desc in total and them remove select desc.
@dir0417


(Chris Knoll) #5

You can do this (with a little effort) today: if you’re looking at included concepts (where there are grey and orange shopping carts), you can click on the grey shopping cart to ‘add’ it to your concept set, and then flip over to the concept set expression to find the concept to exclude. The challenge with this is finding the concept you clicked on under ‘Included Concepts’ back in your ‘Concept Set Expression’ tab: you might have many concepts already selected in your concept set, so finding the one out of many that you just added from Included Concepts involves a bit of ‘hunt-and-peck’.

The improvement we have planned will be that you can select a set of concepts from Included Concepts via check-boxes, and then add them to your concept as exclusions or exclusion + descendants.


(Diana) #6

@Chris_Knoll @schillil Thank you, this was very helpful!


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