Hi all, I’m trying to build a cohort of the Antibiotic-Acne study in the OHDSI.org/web/atlas- but Atlas is persistently slow/not functioning. I had a lot of problems even creating the concept sets due to the same problem. Question-is this just bad luck or is there something I could alter to improve the function on my end? Also I could try using a local instance but then I need to move all the concept sets. I can export to CSV, but not sure how to import that, I tried the copy clipboard feature- but that wasn’t working. Also, what I can export and what I can import don’t line up one-to-one (export: Concept Set Expression JSON, Concept Identifier List, Included Concept Identifier List; import: concept identifiers, concept set expression JSON). It may not matter b/c as it stands now the copy to clipboard feature isn’t working (it timed out on entering the word ‘Age’ to the criteria definition). Any help and suggestions are greatly appreciated!!! Lisa
Hi @schillil can you provide the steps needed to reproduce the problem on the OHDSI.org ATLAS site and I’ll investigate. Thanks.
Thanks Lee. I’m not sure it was a specific error. For example, in typing in a criteria definition- it would take 5 min or more, than time out just to show that I had entered the letter ‘A’. An import of a concept set would time, and then when it imported, and I saved it, it would be not truly be saved, and I had have to start from scratch. This is all when using the OHDSI web version.
@schillil I did some investigation and it looks like there were cohorts being generated on the OHDSI.org ATLAS site on Sunday evening that could have been using significant server/database resources. The OHDSI.org database backup was also running around that time. There could also have been transient network related issues with traffic to/from the AWS hosted server but I didn’t see any evidence of that on the AWS server side. I didn’t see any errors in the OHDSI.org Atlas/WebAPI log.
The OHDSI.org Atlas site seems to be performing normally (yesterday and this morning). Let me know if you are still experiencing this issue and I can work with you to investigate further.
@lee_evans
Do you any advice on the concept export and import, I want to export the concept sets and see if I can import them to a local atlas-OMOP instance. This part of the original questions is copied here:
Thanks!
Lisa
In general it should be possible to export/import a cohort definition (including the concept sets created within the cohort definition) as json on the cohort definition JSON tab. Import the cohort definition on the JSON tab by command-v or control-v pasting the cohort definition json text (replacing any existing json text) and pressing the reload button.
@Chris_Knoll is there a way to export and import concept sets created outside of a cohort definition?
@Chris_Knoll are there any constraints/limitations around exporting/importing cohort definitions/concept sets between two different instances of ATLAS? (assuming they both have the same cdm and omop vocabulary data loaded - in this case the synpuf data).
To export: open the concept set -> Go to Export tab -> click the ‘copy to clipboard’ icon button next to Concept Set Expression JSON
To import:
Close any open concept set -> go to Vocabulary Search -> click ‘Import’ tab, click ‘Concept Set’ pill -> paste concept set JSON in text box -> Click import concept set expression.
Note: after you perform the import, you will have an unsaved, ‘active’ concept set which you can add/remove additional concepts to the concept set through the normal vocabulary search workflow.
There are no constraints or limitations: if your vocabulary of your source system matches the vocabulary of the target system, the cohort definition /concept sets will import properly.