N3C and OMOP

[Vojtech_Huser (Vojtech (Vojta) Huser)]

The N3C group adopted OMOP.
An interesting set of data ingestion issues is being tracked at this public github

repo https://github.com/National-COVID-Cohort-Collaborative/Data-Ingestion-and-Harmonization

issues link https://github.com/National-COVID-Cohort-Collaborative/Data-Ingestion-and-Harmonization/issues

[Christian_Reich]

Indeed, @Vojtech_Huser. Thanks for pointing that out. Who is helping them? You? Nobody?

[krfeeney (Kristin Kostka, MPH)]

A small army! So far I’ve seen @hripcsa @cukarthik @clairblacketer @Andrew @Vojtech_Huser @rtmill @mgkahn @benomark @jon_duke @Guoqian_Jiang on calls.

We’re going to present OHDSI’s involvement in N3C on the community call this coming Tuesday!

[Vojtech_Huser (Vojtech (Vojta) Huser)]

If there are other users of the Palantir platform, I would be glad to connect with them.

It seems the data in Palantir is offered as SparkDataFrame and the flavor of SQL used is SparkSQL. So yet another flavor for SqlRender.

[gregk (Gregory Klebanov)]

@Vojtech_Huser yes, we have been discussing SparkSQL for awhile now and I believe Ajit did even make some progress

Spark support: DatabaseConnector and SqlRender

Hello Developers, I have added Spark SQL support to the DatabaseConnector and SqlRender packages in the “spark” branch. If you have a Spark SQL environment, can you try these packages out? The branches are here: You can install using these commands: devtools::install_github("OHDSI/DatabaseConnector", ref = "spark") devtools::install_github("OHDSI/SqlRender", ref = "spark") Thank you @parisni for the initial SqlRender rules – I made some edits based on my environment. Thanks, Ajit

[Ajit_Londhe]

Yes, I do have a version of DatabaseConnector and SqlRender for Spark. Currently I’m using forked branches as I’ve needed to make changes to the JAR files:

alondhe/DatabaseConnector

alondhe/SqlRender

Please note, you will need to obtain the Spark JDBC driver to use this. We have it licensed through Databricks.

[Vojtech_Huser (Vojtech (Vojta) Huser)]

For advanced users of N3C data: Can I find out from you (or somehow publicly), whether N3C data have covid19 viral load data. (e.g., on at least several thousand patients, how common is viral load sarsCov2 quantitiative reporting. This lab test test: https://athena.ohdsi.org/search-terms/terms/715262 (LOINC code 94819-0).

[krfeeney (Kristin Kostka, MPH)]

Hi @Vojtech_Huser! Do you have a DUR in place? You can make a Contour of the Measurement table looking for that concept ID.

If you don’t have a DUR, have you joined one of the Domain teams? They have folks who could do this too.