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OMOP
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fixes #557

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Maxim Moinat 2023-03-30 16:00:23 +02:00
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rmd/sqlScripts.Rmd
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@ -404,10 +404,15 @@ SELECT * FROM #tmp_de;
### CDM_SOURCE Table
The script below is an example for how to fill in the CDM_SOURCE table. This table is required for the [Data Quality Dashboard](https://github.com/OHDSI/DataQualityDashboard) package to run. This was taken from the [ETL-Synthea](https://github.com/OHDSI/ETL-Synthea) package, a good example on how to write a complete extract-transform-load script from start to finish, including vocabulary import.
The script below is an example for how to fill in the CDM_SOURCE table.
This table is required for the [Data Quality Dashboard](https://github.com/OHDSI/DataQualityDashboard) package to run.
#### v5.3
This example was taken from the [ETL-Synthea](https://github.com/OHDSI/ETL-Synthea) package,
a good example on how to write a complete extract-transform-load script from start to finish, including vocabulary import.
```{sql eval = FALSE, echo = TRUE}
insert into @cdm_schema.cdm_source (
INSERT INTO @cdm_schema.cdm_source (
cdm_source_name,
cdm_source_abbreviation,
cdm_holder,
@ -419,7 +424,7 @@ cdm_release_date,
cdm_version,
vocabulary_version
)
select
SELECT
'Synthea synthetic health database',
'Synthea',
'OHDSI Community',
@ -430,8 +435,39 @@ getdate(), -- NB: Set this value to the day the source data was pulled
getdate(),
'v5.3',
vocabulary_version
from @cdm_schema.vocabulary
where vocabulary_id = 'None';
FROM @cdm_schema.vocabulary
WHERE vocabulary_id = 'None';
```
#### v5.4
```{sql eval = FALSE, echo = TRUE}
INSERT INTO @cdm_schema.cdm_source (
cdm_source_name,
cdm_source_abbreviation,
cdm_holder,
source_description,
source_documentation_reference,
cdm_etl_reference,
source_release_date,
cdm_release_date,
cdm_version,
vocabulary_version,
vocabulary_version_concept_id
)
SELECT
'<your_cdm_source_name>',
'<your_cdm_source_abbreviation>',
'<your_cdm_holder>',
'<your_source_description>',
'<your_source_documentation_reference>', -- e.g. link to source data dictionary
'<your_etl_reference>', -- e.g. link to ETL documentation
'<your_source_release_date>', -- when the source data was pulled
getdate(),
'v5.4',
vocabulary_version,
756265 -- OMOP CDM Version 5.4.0
FROM @cdm_schema.vocabulary
WHERE vocabulary_id = 'None';
```
## **Bonus Queries**