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Cohort data

(Scott Fischbein) #1

Hi all - we have a local ATLAS implementation that we just released to some of our end users for data quality and user testing and there have been some questions from the researchers about how to use Cohort data that I can’t answer (I’m just a developer, after all!)

We’re wondering if there’s a way to get more information about a particular set of patients returned in a cohort - is there any way to get at a “patient level” view of the returned results? I’ve looked a bit at Characterizations and while I don’t understand the full toolset yet, I see that you can get demographic type information that way, but they’re looking for a more granular view. Is anything like that available?

Thanks for any information/suggestions.

Scott Fischbein
UC Davis School of Veterinary Medicine

(Chris Knoll) #2

Yes, there is a patient profile viewer, but it’s very hard to access. If you do a quick analysis under the Reporting tab of cohort definitions, you will get a ‘tornado report’ which lets you pick a demographic group and view a profile.

However, we are planning on releasing an update in Atlas 2.8 where you are able to fetch a sample of people from a cohort, and then see the timeline of patient level data. Stand by for this new feature, as it greatly simplifies the process of viewing a subset of the cohort.

Tagging @MaximMoinat.

(Scott Fischbein) #3

Thanks Chris,
The cohort “report” functionality doesn’t seem to work for our dataset (perhaps we’re missing something from the data we’ve imported, or from the Achilles metadata - there’s a reference to Heracles when the report is generated, so perhaps that’s where the problem lies?) I’ll work on getting this running and look forward to the upcoming update.


(Chris Knoll) #4

I’d look in your logs maybe it is a table that isn’t created properly, but this will be greatly simplified in the next release, so don’t pull out too many hairs trying to figure it out.

(Scott Fischbein) #5

Hi Chris - Following up on this with another question from the boss: When you say that the new update will allow fetching “a sample of people from a cohort” - what does that mean - is it a (definable) subset of the cohort ? And what data will be provided?

What we’re really looking for is something like this: Generate a cohort, and then access a report that shows Patient IDs for that cohort, so that we can tie back to our external medical records to gather information about the cohort that is not being imported into the OHDSI tools. Not sure if this is/will be possible or if we’ll need to create something from scratch, but appreciate any information you can provide.


(Chris Knoll) #6

After you generate a cohort, you are presented the option to grab a sample. The sample is random, except you can specify demographic criteria (age (range) and gender). You specify a number of people to sample, and you’ll be presented with the set of patient IDs. Clicking on the patient ID will send you to the patient profile viewer. I guess it’s technically possible to specify a sample size that is equal to your cohort size, but that’s not the intent of the ‘sample’ functionality.

(Maxim Moinat) #7

Hi @scottf2. At The Hyve, we have been working together with UCB to develop exactly the feature you describe: New Atlas features: Cohort Sample and Profile timeline

We have also created a short video presenting the features: https://youtu.be/etC9EONnMow