667 lines
17 KiB
HTML
667 lines
17 KiB
HTML
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<div id="header">
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||
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<h1 class="title toc-ignore">Indices, Primary Keys and Foreign Key
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Constraints</h1>
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</div>
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<div id="overview" class="section level2">
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<h2>Overview</h2>
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<p>Database indices improve the performance of queries against a
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database by organizing the data in a way that increase query
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execution.</p>
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<p>This article was written to provide guidance on the setting of
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indices, primary and foreign keys for data that has been transformed
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into the Observational Medical Outcome Partnership (OMOP) Common Data
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Model (CDM). The community that supports the design and development of
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the OHDSI/CommonDataModel Github repository is a diverse collaborative
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of healthcare and technical profesisonals whom have limited data base
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adminstrative (DBA) experience. As a result, the comments below should
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be interpreted as suggestions and recommendations to help increase
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performance. Your teams needs may call for a modified configuration.</p>
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||
</div>
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||
<div id="general-recommendations" class="section level2">
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<h2>General Recommendations</h2>
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<p>Should your database of choice support indexing, the OMOP CDM Working
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Group recommends</p>
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<ul>
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<li>Indexing on all columns containing an “_id”
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(e.g. condition_occurrence_id, drug_exposure_id, measurement_id,
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procedure_occurrence_id, etc.)</li>
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<li>Indexing on primary and foreign keys</li>
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||
</ul>
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<p>For all databases, regardless of custom indice support, primary and
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foreign keys should be set. This is a step towards ensuring data
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||
integrity. Information on what table level attributes should be set as
|
||
primary and foreign keys can be found within the *_Field_Level.csv
|
||
file(s) located in the <a
|
||
href="https://github.com/OHDSI/CommonDataModel/tree/v5.4/inst/csv">INST/CSV
|
||
directory</a></p>
|
||
</div>
|
||
<div id="database-support" class="section level2">
|
||
<h2>Database support</h2>
|
||
<p>The OHDSI/CommonDataModel package leverages OHDSI/SQLRender and as a
|
||
result is only capable of supporting sources that are supported by
|
||
OHDSI/SQLRender. The following databases are currently supported.</p>
|
||
<div id="microsoft-sql-server" class="section level3">
|
||
<h3>Microsoft SQL Server</h3>
|
||
</div>
|
||
<div id="oracle" class="section level3">
|
||
<h3>Oracle</h3>
|
||
</div>
|
||
<div id="postgresql" class="section level3">
|
||
<h3>PostgreSQL</h3>
|
||
</div>
|
||
<div id="amazon-redshift" class="section level3">
|
||
<h3>Amazon Redshift</h3>
|
||
<p>On AWS Redshift it is important to ensure that your data is properly
|
||
distributed and sorted across nodes. Compression on certain columns may
|
||
also help. The designed DDL does set DISTKEYS in an effort to optimize
|
||
performance. This configuration can be seen within the <a
|
||
href="https://github.com/OHDSI/CommonDataModel/blob/v5.4/ddl/5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql">Redshift-specific
|
||
DDL</a>.</p>
|
||
</div>
|
||
<div id="impala" class="section level3">
|
||
<h3>Impala</h3>
|
||
</div>
|
||
<div id="ibm-netezza" class="section level3">
|
||
<h3>IBM Netezza</h3>
|
||
</div>
|
||
<div id="google-bigquery" class="section level3">
|
||
<h3>Google BigQuery</h3>
|
||
<p>Google BigQuery does not require manual optimization and/or sizing.
|
||
Google BigQuery does massive parallel full table scans and intensive
|
||
caching, all under the hood. <a
|
||
href="https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2">Reference</a></p>
|
||
</div>
|
||
<div id="microsoft-parallel-data-warehouse-pdw" class="section level3">
|
||
<h3>Microsoft Parallel Data Warehouse (PDW)</h3>
|
||
</div>
|
||
<div id="sqlite" class="section level3">
|
||
<h3>SQLite</h3>
|
||
</div>
|
||
<div id="databricks" class="section level3">
|
||
<h3>Databricks</h3>
|
||
<p>This database type is not yet supported but is actively being worked
|
||
on by a number of collaborators. For more informtion, please contact
|
||
Ajit Londhe of Amgen.</p>
|
||
</div>
|
||
</div>
|
||
<div id="references" class="section level2">
|
||
<h2>References</h2>
|
||
<p><a
|
||
href="https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2">ISO
|
||
Best Practices of CDM Indexing</a></p>
|
||
</div>
|
||
|
||
|
||
|
||
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|
||
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|
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