mz-health/OMOP
mz-health
/
OMOP
mirror of https://github.com/OHDSI/CommonDataModel.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

fixes #557

This commit is contained in:
Maxim Moinat 2023-03-30 16:00:23 +02:00
parent eeb4f27985
commit f0637ad97d
No known key found for this signature in database
GPG Key ID: 94EA516FB6174455
1 changed files with 61 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

86
rmd/sqlScripts.Rmd
View File

@ -404,34 +404,70 @@ SELECT * FROM #tmp_de;
### CDM_SOURCE Table ### 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} ```{sql eval = FALSE, echo = TRUE}
insert into @cdm_schema.cdm_source ( INSERT INTO @cdm_schema.cdm_source (
cdm_source_name, cdm_source_name,
cdm_source_abbreviation, cdm_source_abbreviation,
cdm_holder, cdm_holder,
source_description, source_description,
source_documentation_reference, source_documentation_reference,
cdm_etl_reference, cdm_etl_reference,
source_release_date, source_release_date,
cdm_release_date, cdm_release_date,
cdm_version, cdm_version,
vocabulary_version vocabulary_version
) )
select SELECT
'Synthea synthetic health database', 'Synthea synthetic health database',
'Synthea', 'Synthea',
'OHDSI Community', 'OHDSI Community',
'SyntheaTM is a Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats.', 'SyntheaTM is a Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats.',
'https://synthetichealth.github.io/synthea/', 'https://synthetichealth.github.io/synthea/',
'https://github.com/OHDSI/ETL-Synthea', 'https://github.com/OHDSI/ETL-Synthea',
getdate(), -- NB: Set this value to the day the source data was pulled getdate(), -- NB: Set this value to the day the source data was pulled
getdate(), getdate(),
'v5.3', 'v5.3',
vocabulary_version vocabulary_version
from @cdm_schema.vocabulary FROM @cdm_schema.vocabulary
where vocabulary_id = 'None'; 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** ## **Bonus Queries**