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SQL Lite and OHDSI tools


(Jose Posada) #1

Dear Community,

Is there anything that cannot be done using SQL Lite? Is there any tool we are aware that will not run (e.g. ATLAS). I know the amazing work in Eunomia, and I wonder if there are any constraints in terms of SQL dialect that the community is aware of.

Thanks,

@schuemie, @Ajit_Londhe, @anthonysena, @Adam_Black, @Chris_Knoll


(Vojtech Huser) #2

I also like SQL Lite and plan to release (or aim for) MIMIC3 and MIMIC4 data just like Eunomia does. Eunomia is super nice! I am not aware of any limits.

In some my prior work - I noticed that concept queries take time. If you figure out indexing inside SQL Lite file, please post it to a github somewhere.


(Jose Posada) #3

hi @Vojtech_Huser,

I think this will copy the entire database with the index


(Martijn Schuemie) #4

SQLite is pretty amazing indeed. There are some limitations for you to consider:

  1. SQLite is for single user only
  2. I don’t think it can support very large databases (e.g. > 1 TB)
  3. It doesn’t support DATE and DATETIME types and operations, although SqlRender is doing its best to make it look like it does. (This does require field names end in ‘_date’ and ‘_datetime’)

Furthermore, the current released version of RSQLite (2.2.0) contains an older version of SQLite which does not correctly support a specific windowing function used in all ATLAS-generated cohort definitions. So in order to run those you’ll need the develop version from GitHub.


(Jose Posada) #5

hi @schuemie,

Thank you for your response. This is indeed great to know. Google failed me in replying this question :slight_smile:

Jose


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