Atlas now load info properly

Developers
1

Hi folks,

Here is my issue:

  1. I have cmd data ----- data is survey data and now in PERSON and OBSERVATION tables;
  2. I set up the webapi_source and source_daimon
  3. In Atlas I only have part of PERSON data showing up but gender info is nothing; Nothing for OBSERVATION at all.

I ran ACHILLES and it generated 4 tables that name starting with ‘achilles_XXXX’. What should I do to find out what I missed?

Please see the screenshots for what I meant.

Any suggests are appreciated and it’s going to be even better if you can list the steps.

image
image1116×667 124 KB

image
image1924×968 152 KB

Thank you,
Ray Z.

2

Hello @zohdsi,

Have you populated Observation Period table? According to the docs (ETL conventions and answer #3 here), each Person needs to have at least one observation period, which should represent time intervals with a high capture rate of clinical events.

Observation treemap in ATLAS uses data collected by analyses 800 and 801 from Achilles, both of which require the events to fall into a valid observation period for the patient. This is probably the reason why you are able to see the report for Person table but all others show ‘no data’.

3

Hi @rookie_crewkie ,

Thank you so much for your help. No, since the data are from survey/registry data, I did not realize that the an observation period is required for the CDM.

Issue is resolved.

Thanks gain,

Ray Z.