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External Study Database for participant demographics - best way to integrate with sample management and assays

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External Study Database for participant demographics - best way to integrate with sample management and assays steve harris  2017-06-30 01:51
Status: Closed
 
Hi

I have a whole genome study that has established case/participant/consent management facilities, but I would like to deploy Labkey for the registration of samples against the participants, and for the recording of assays (QC, DNA extraction results, sequencer run data) on the samples. I control the schema on the study management database and can co-locate it on the same postrgres instance as the labkey server installation.

I know how to register the external schema with labkey so I can presumably provide the samples list with a lookup to the participants in the management database. Can I integrate more closely with the LK data model and convince it that a view within the study management database is the demographics table and source of participant ids?

Hope that makes sense. thanks in advance

Steve
 
 
Jon (LabKey DevOps) responded:  2017-06-30 16:18
Hi Steve,

So in a nutshell, you want to know if you can take the data in your external database and have it look like it's apart of the LabKey study as a demographics dataset. Is that correct?

Regards,

Jon
 
steve harris responded:  2017-07-03 01:28
Hi Jon

Yes!

Steve
 
Jon (LabKey DevOps) responded:  2017-07-04 23:43
Thanks for confirming Steve.

You have a few options depending on whether the external schema is in the same DB as your LabKey schemas or in a different DB.

- If this external schema is within the same database as your LabKey schemas, you could configure a lookup or something similar after configuring this as an external schema.

- If this external schema is coming from a separate database, you could set it up as an external schema as well, but you would have no ability to do lookups.

https://www.labkey.org/Documentation/wiki-page.view?name=externalSchemas

But regardless of how the information is being presented to LabKey initially, neither of these options would allow it to just appear as a demographics dataset in a study.

In order to have that data appear as a demographics dataset, you would need to create an ETL module that would copy the data from the external schema and place it into the study schema's demographics dataset.

https://www.labkey.org/Documentation/wiki-page.view?name=etlModule

Regards,

Jon