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ACHILLES installation questions

atlas

(MB) #1

Hi all,
I’m trying to install the ACHILLES for Atlas. I’m following the instructions below and have some questions. https://github.com/OHDSI/Achilles#getting-started

  1. Where do I download cdm v5.3? The link in the instruction is for CDM v6.0
  2. Where are the schemas below (cdm5_inst, results, vocab) coming from. I only see dbo schema if I run omop_ddl.sql.

achilles(connectionDetails,
cdmDatabaseSchema = “cdm5_inst”,
resultsDatabaseSchema=“results”,
vocabDatabaseSchema = “vocab”,
numThreads = 1,
sourceName = “My Source Name”,
cdmVersion = “5.3.0”,
runHeel = TRUE,
runCostAnalysis = TRUE)

Thanks,
MB


(Anna Karenina) #2

Hello @marzbuzz,

  1. Choose the appropriate git tag for the CDM version you need. For example, v5.3.0 docs and DDL are here.
  2. In your case, the value for cdmDatabaseSchema parameter would be ‘dbo’, not ‘cdm5_inst’. This is the schema where your CDM tables are stored. As for resultsDatabaseSchema and scratchDatabaseSchema, these are for Achilles results and various temporary stuff. You can either create a new schema to keep them separate from CDM, or just assign ‘dbo’ as well to have everything in one schema.

(MB) #3

Thanks Anna.

One more question…

Is vocabDatabaseSchema suppose to be the schema to hold the standardized vocabulary tables like concept, vocabulary, domain… tables and cdmDatabaseSchema suppose to be the schema to hold the standardized clinical data tables like person, visit_occurrence, procedure_occurrence… tables? I know I can just use dbo schema for all these tables above.

Thanks,
MB


(Anna Karenina) #4

@marzbuzz,

Yes, that’s correct. This allows for more flexibility is some cases, like when you have several instances of clinical CDM data, but they need to use the same set of standardized vocabularies.


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