Merge pull request #558 from OHDSI/fix-557
Documentation fix for cdm_source example sql
This commit is contained in:
clairblacketer
GitHub
commit
77831c5326
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@ -11,9 +11,9 @@
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<title>sqlScripts.knit</title>
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<title>SQL Scripts</title>
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<script src="site_libs/header-attrs-2.16/header-attrs.js"></script>
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<script src="site_libs/header-attrs-2.21/header-attrs.js"></script>
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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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@ -35,8 +35,8 @@
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<script src="site_libs/navigation-1.1/tabsets.js"></script>
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<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-6.2.1/css/all.min.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-6.2.1/css/v4-shims.min.css" rel="stylesheet" />
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<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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<style type="text/css">
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@ -185,8 +185,8 @@ $(document).ready(function () {
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border-radius: 4px;
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}
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.tabset-dropdown > .nav-tabs > li.active:before {
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content: "";
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.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
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content: "\e259";
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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@ -194,16 +194,9 @@ $(document).ready(function () {
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
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content: "";
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border: none;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
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content: "";
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content: "\e258";
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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border: none;
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}
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.tabset-dropdown > .nav-tabs > li.active {
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@ -402,6 +395,9 @@ div.tocify {
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<li>
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<a href="cdm54Changes.html">Changes from CDM v5.3</a>
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</li>
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<li>
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<a href="cdm54erd.html">Entity Relationships</a>
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</li>
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</ul>
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</li>
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</ul>
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@ -908,35 +904,69 @@ SELECT * FROM #tmp_de;</code></pre>
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<p>The script below is an example for how to fill in the CDM_SOURCE
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table. This table is required for the <a
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href="https://github.com/OHDSI/DataQualityDashboard">Data Quality
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Dashboard</a> package to run. This was taken from the <a
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Dashboard</a> package to run.</p>
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<div id="v5.3" class="section level4">
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<h4>v5.3</h4>
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<p>This example was taken from the <a
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href="https://github.com/OHDSI/ETL-Synthea">ETL-Synthea</a> package, a
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good example on how to write a complete extract-transform-load script
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from start to finish, including vocabulary import.</p>
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<pre class="sql"><code>insert into @cdm_schema.cdm_source (
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cdm_source_name,
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cdm_source_abbreviation,
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cdm_holder,
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source_description,
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source_documentation_reference,
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cdm_etl_reference,
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source_release_date,
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cdm_release_date,
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cdm_version,
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vocabulary_version
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<pre class="sql"><code>INSERT INTO @cdm_schema.cdm_source (
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cdm_source_name,
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cdm_source_abbreviation,
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cdm_holder,
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source_description,
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source_documentation_reference,
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cdm_etl_reference,
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source_release_date,
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cdm_release_date,
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cdm_version,
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vocabulary_version
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)
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select
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'Synthea synthetic health database',
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'Synthea',
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'OHDSI Community',
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'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.',
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'https://synthetichealth.github.io/synthea/',
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'https://github.com/OHDSI/ETL-Synthea',
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getdate(), -- NB: Set this value to the day the source data was pulled
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getdate(),
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'v5.3',
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vocabulary_version
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from @cdm_schema.vocabulary
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where vocabulary_id = 'None';</code></pre>
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SELECT
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'Synthea synthetic health database',
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'Synthea',
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'OHDSI Community',
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'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.',
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'https://synthetichealth.github.io/synthea/',
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'https://github.com/OHDSI/ETL-Synthea',
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getdate(), -- NB: Set this value to the day the source data was pulled
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getdate(),
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'v5.3',
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vocabulary_version
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FROM @cdm_schema.vocabulary
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WHERE vocabulary_id = 'None';</code></pre>
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</div>
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<div id="v5.4" class="section level4">
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<h4>v5.4</h4>
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<pre class="sql"><code>INSERT INTO @cdm_schema.cdm_source (
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cdm_source_name,
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cdm_source_abbreviation,
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cdm_holder,
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source_description,
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source_documentation_reference,
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cdm_etl_reference,
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source_release_date,
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cdm_release_date,
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cdm_version,
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vocabulary_version,
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vocabulary_version_concept_id
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)
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SELECT
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'<your_cdm_source_name>',
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'<your_cdm_source_abbreviation>',
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'<your_cdm_holder>',
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'<your_source_description>',
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'<your_source_documentation_reference>', -- e.g. link to source data dictionary
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'<your_etl_reference>', -- e.g. link to ETL documentation
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'<your_source_release_date>', -- when the source data was pulled
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getdate(), -- or the date of ETL run
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'v5.4',
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vocabulary_version,
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756265 -- 'OMOP CDM Version 5.4.0'
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FROM @cdm_schema.vocabulary
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WHERE vocabulary_id = 'None';</code></pre>
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</div>
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</div>
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</div>
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<div id="bonus-queries" class="section level2">
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@ -955,13 +985,13 @@ Details. For more information on how this can be done, please see the <a
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href="https://ohdsi.github.io/ETL-LambdaBuilder/Optum%20Clinformatics/Optum_visit_occurrence.html">Optum
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Extended ETL documentation</a>.</p>
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<pre class="sql"><code>SELECT concept_id, concept_name
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FROM concept
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LEFT JOIN concept_ancestor
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ON concept_id=descendant_concept_id
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AND ancestor_concept_id!=descendant_concept_id
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WHERE domain_id='Visit'
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AND standard_concept='S'
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AND ancestor_concept_id IS NULL</code></pre>
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FROM concept
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LEFT JOIN concept_ancestor
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ON concept_id=descendant_concept_id
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AND ancestor_concept_id!=descendant_concept_id
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WHERE domain_id='Visit'
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AND standard_concept='S'
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AND ancestor_concept_id IS NULL</code></pre>
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</div>
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</div>
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</div>
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@ -1,4 +1,5 @@
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---
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title: 'SQL Scripts'
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output:
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html_document:
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toc: TRUE
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@ -404,34 +405,70 @@ SELECT * FROM #tmp_de;
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### CDM_SOURCE Table
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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.
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The script below is an example for how to fill in the CDM_SOURCE table.
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This table is required for the [Data Quality Dashboard](https://github.com/OHDSI/DataQualityDashboard) package to run.
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#### v5.3
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This example was taken from the [ETL-Synthea](https://github.com/OHDSI/ETL-Synthea) package,
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a good example on how to write a complete extract-transform-load script from start to finish, including vocabulary import.
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```{sql eval = FALSE, echo = TRUE}
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insert into @cdm_schema.cdm_source (
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cdm_source_name,
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cdm_source_abbreviation,
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cdm_holder,
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source_description,
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source_documentation_reference,
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cdm_etl_reference,
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source_release_date,
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cdm_release_date,
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cdm_version,
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vocabulary_version
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INSERT INTO @cdm_schema.cdm_source (
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cdm_source_name,
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cdm_source_abbreviation,
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cdm_holder,
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source_description,
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source_documentation_reference,
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cdm_etl_reference,
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source_release_date,
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cdm_release_date,
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cdm_version,
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vocabulary_version
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)
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select
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'Synthea synthetic health database',
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'Synthea',
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'OHDSI Community',
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'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.',
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'https://synthetichealth.github.io/synthea/',
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'https://github.com/OHDSI/ETL-Synthea',
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getdate(), -- NB: Set this value to the day the source data was pulled
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getdate(),
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'v5.3',
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vocabulary_version
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from @cdm_schema.vocabulary
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where vocabulary_id = 'None';
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SELECT
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'Synthea synthetic health database',
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'Synthea',
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'OHDSI Community',
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'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.',
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'https://synthetichealth.github.io/synthea/',
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'https://github.com/OHDSI/ETL-Synthea',
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getdate(), -- NB: Set this value to the day the source data was pulled
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getdate(),
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'v5.3',
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vocabulary_version
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FROM @cdm_schema.vocabulary
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WHERE vocabulary_id = 'None';
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```
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#### v5.4
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```{sql eval = FALSE, echo = TRUE}
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INSERT INTO @cdm_schema.cdm_source (
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cdm_source_name,
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cdm_source_abbreviation,
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cdm_holder,
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source_description,
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source_documentation_reference,
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cdm_etl_reference,
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source_release_date,
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cdm_release_date,
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cdm_version,
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vocabulary_version,
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vocabulary_version_concept_id
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)
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SELECT
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'<your_cdm_source_name>',
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'<your_cdm_source_abbreviation>',
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'<your_cdm_holder>',
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'<your_source_description>',
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'<your_source_documentation_reference>', -- e.g. link to source data dictionary
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'<your_etl_reference>', -- e.g. link to ETL documentation
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'<your_source_release_date>', -- when the source data was pulled
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getdate(), -- or the date of ETL run
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'v5.4',
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vocabulary_version,
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756265 -- 'OMOP CDM Version 5.4.0'
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FROM @cdm_schema.vocabulary
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WHERE vocabulary_id = 'None';
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```
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## **Bonus Queries**
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@ -442,11 +479,11 @@ The query below will utilize the Visit Concept hierarcy to find the highest-leve
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```{sql eval=FALSE, echo=TRUE}
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SELECT concept_id, concept_name
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FROM concept
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LEFT JOIN concept_ancestor
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ON concept_id=descendant_concept_id
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AND ancestor_concept_id!=descendant_concept_id
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WHERE domain_id='Visit'
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AND standard_concept='S'
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AND ancestor_concept_id IS NULL
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FROM concept
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LEFT JOIN concept_ancestor
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ON concept_id=descendant_concept_id
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AND ancestor_concept_id!=descendant_concept_id
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WHERE domain_id='Visit'
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AND standard_concept='S'
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AND ancestor_concept_id IS NULL
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```
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