Merge branch 'v5.4' into v5.4
This commit is contained in:
Alan Andryc
GitHub
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d73a0f426d
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||||
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||||
<h1 class="title toc-ignore">Indices, Primary Keys and Foreign Key Constraints</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<div id="to-do" class="section level3">
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||||
<h3>To Do</h3>
|
||||
<ul>
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||||
<li>Need something for hashing</li>
|
||||
<li>What about constraints that aren’t foreign keys</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="overview" class="section level2">
|
||||
<h2>Overview</h2>
|
||||
<p>Database indices improve the performance of queries against a database by organizing the data in a way that increase query execution.</p>
|
||||
<p>This article was written to provide guidance on the setting of indices, primary and foreign keys for data that has been transformed into the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM). The community that supports the design and development of the OHDSI/CommonDataModel Github repository is a diverse collaborative of healthcare and technical profesisonals whom have limited data base adminstrative (DBA) experience. As a result, the comments below should be interpreted as suggestions and recommendations to help increase performance. Your teams needs may call for a modified configuration.</p>
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||||
</div>
|
||||
<div id="general-recommendations" class="section level2">
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||||
<h2>General Recommendations</h2>
|
||||
<p>Should your database of choice support indexing, the OMOP CDM Working Group recommends</p>
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||||
<ul>
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||||
<li>Indexing on all columns containing an "_id" (e.g. condition_occurrence_id, drug_exposure_id, measurement_id, procedure_occurrence_id, etc.)</li>
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||||
<li>Indexing on primary and foreign keys</li>
|
||||
</ul>
|
||||
<p>For all databases, regardless of custom indice support, primary and foreign keys should be set. This is a step towards ensuring data integrity.</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">
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<h3>Microsoft SQL Server</h3>
|
||||
</div>
|
||||
<div id="oracle" class="section level3">
|
||||
<h3>Oracle</h3>
|
||||
</div>
|
||||
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|
||||
<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>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
|
||||
<script>
|
||||
|
||||
// add bootstrap table styles to pandoc tables
|
||||
function bootstrapStylePandocTables() {
|
||||
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
|
||||
}
|
||||
$(document).ready(function () {
|
||||
bootstrapStylePandocTables();
|
||||
});
|
||||
|
||||
|
||||
</script>
|
||||
|
||||
<!-- tabsets -->
|
||||
|
||||
<script>
|
||||
$(document).ready(function () {
|
||||
window.buildTabsets("TOC");
|
||||
});
|
||||
|
||||
$(document).ready(function () {
|
||||
$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
||||
$(this).parent().toggleClass('nav-tabs-open');
|
||||
});
|
||||
});
|
||||
</script>
|
||||
|
||||
<!-- code folding -->
|
||||
|
||||
<script>
|
||||
$(document).ready(function () {
|
||||
|
||||
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
|
||||
$('.unlisted.unnumbered').addClass('toc-ignore')
|
||||
|
||||
// move toc-ignore selectors from section div to header
|
||||
$('div.section.toc-ignore')
|
||||
.removeClass('toc-ignore')
|
||||
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
|
||||
|
||||
// establish options
|
||||
var options = {
|
||||
selectors: "h1,h2,h3,h4,h5",
|
||||
theme: "bootstrap3",
|
||||
context: '.toc-content',
|
||||
hashGenerator: function (text) {
|
||||
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
|
||||
},
|
||||
ignoreSelector: ".toc-ignore",
|
||||
scrollTo: 0
|
||||
};
|
||||
options.showAndHide = true;
|
||||
options.smoothScroll = true;
|
||||
|
||||
// tocify
|
||||
var toc = $("#TOC").tocify(options).data("toc-tocify");
|
||||
});
|
||||
</script>
|
||||
|
||||
<!-- dynamically load mathjax for compatibility with self-contained -->
|
||||
<script>
|
||||
(function () {
|
||||
var script = document.createElement("script");
|
||||
script.type = "text/javascript";
|
||||
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
|
||||
document.getElementsByTagName("head")[0].appendChild(script);
|
||||
})();
|
||||
</script>
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -23,7 +23,6 @@ window.initializeCodeFolding = function(show) {
|
|||
// create a collapsable div to wrap the code in
|
||||
var div = $('<div class="collapse r-code-collapse"></div>');
|
||||
var showThis = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide');
|
||||
if (showThis) div.addClass('in');
|
||||
var id = 'rcode-643E0F36' + currentIndex++;
|
||||
div.attr('id', id);
|
||||
$(this).before(div);
|
||||
|
|
@ -31,7 +30,7 @@ window.initializeCodeFolding = function(show) {
|
|||
|
||||
// add a show code button right above
|
||||
var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
|
||||
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs code-folding-btn pull-right"></button>');
|
||||
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
|
||||
showCodeButton.append(showCodeText);
|
||||
showCodeButton
|
||||
.attr('data-toggle', 'collapse')
|
||||
|
|
@ -47,13 +46,27 @@ window.initializeCodeFolding = function(show) {
|
|||
|
||||
div.before(buttonRow);
|
||||
|
||||
// show the div if necessary
|
||||
if (showThis) div.collapse('show');
|
||||
|
||||
// update state of button on show/hide
|
||||
div.on('hidden.bs.collapse', function () {
|
||||
// * Change text
|
||||
// * add a class for intermediate states styling
|
||||
div.on('hide.bs.collapse', function () {
|
||||
showCodeText.text('Code');
|
||||
showCodeButton.addClass('btn-collapsing');
|
||||
});
|
||||
div.on('hidden.bs.collapse', function () {
|
||||
showCodeButton.removeClass('btn-collapsing');
|
||||
});
|
||||
div.on('show.bs.collapse', function () {
|
||||
showCodeText.text('Hide');
|
||||
showCodeButton.addClass('btn-expanding');
|
||||
});
|
||||
div.on('shown.bs.collapse', function () {
|
||||
showCodeButton.removeClass('btn-expanding');
|
||||
});
|
||||
|
||||
});
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -176,7 +176,7 @@
|
|||
self._setEventHandlers();
|
||||
|
||||
// Binding to the Window load event to make sure the correct scrollTop is calculated
|
||||
$(window).load(function() {
|
||||
$(window).on("load", function() {
|
||||
|
||||
// Sets the active TOC item
|
||||
self._setActiveElement(true);
|
||||
|
|
|
|||
|
|
@ -361,11 +361,13 @@ Condition.",,No,No,,,,,
|
|||
CONDITION_ERA,condition_occurrence_count,No,integer,"The number of individual Condition
|
||||
Occurrences used to construct the
|
||||
condition era.",,No,No,,,,,
|
||||
METADATA,metadata_id,Yes,integer,The unique key given to a Metadata record.,Attribute value is auto-generated,Yes,No,,,,,
|
||||
METADATA,metadata_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
METADATA,metadata_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
METADATA,name,Yes,varchar(250),,,No,No,,,,,
|
||||
METADATA,value_as_string,No,varchar(250),,,No,No,,,,,
|
||||
METADATA,value_as_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
METADATA,value_as_number,No,float,"This is the numerical value of the Result of the Metadata, if applicable and available. It is not expected that all Metadata will have numeric results, rather, this field is here to house values should they exist. ",,No,No,,,,,
|
||||
METADATA,metadata_date,No,date,,,No,No,,,,,
|
||||
METADATA,metadata_datetime,No,datetime,,,No,No,,,,,
|
||||
CDM_SOURCE,cdm_source_name,Yes,varchar(255),The name of the CDM instance.,,No,No,,,,,
|
||||
|
|
|
|||
|
|
|
@ -27,10 +27,10 @@ navbar:
|
|||
menu:
|
||||
- text: "CDM v3.0"
|
||||
href: cdm30.html
|
||||
- text: "CDM v5.3.1"
|
||||
href: cdm531.html
|
||||
- text: "CDM v5.3"
|
||||
href: cdm53.html
|
||||
- text: "CDM v5.4"
|
||||
href: cdm531.html
|
||||
href: cdm54.html
|
||||
- text: "CDM v6.0"
|
||||
href: cdm60.html
|
||||
- text: "Proposals"
|
||||
|
|
|
|||
|
|
@ -0,0 +1,109 @@
|
|||
---
|
||||
output:
|
||||
# pdf_document:
|
||||
# toc: yes
|
||||
# toc_depth: '5'
|
||||
html_document:
|
||||
toc: yes
|
||||
toc_depth: 5
|
||||
toc_float: yes
|
||||
---
|
||||
|
||||
```{r setup, include=FALSE, eval=TRUE}
|
||||
|
||||
#todo figure out how to get the document dynamically without specifying the name
|
||||
library(rmarkdown)
|
||||
library(knitr)
|
||||
library(kableExtra)
|
||||
library(magrittr)
|
||||
library(dplyr)
|
||||
library(stringr)
|
||||
|
||||
```
|
||||
|
||||
# **OMOP CDM v5.3**
|
||||
|
||||
Below is the specification document for the OMOP Common Data Model, v5.3 (previously v5.3.1). Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page.
|
||||
|
||||
*__Special Note__ This documentation previously referenced v5.3.1. During the OHDSI/CommonDataModel Hack-A-Thon that occurred on August 18, 2021 the decision was made to align documentation with the minor releases. Hot fixes and minor.minor release can be found through the searching of tags.*
|
||||
|
||||
--after regeneration of DDLs
|
||||
link to csv of cdm
|
||||
link to pdf of cdm documentation
|
||||
link to forum on doc page
|
||||
|
||||
```{r docLoop53, echo=FALSE, results='asis'}
|
||||
tableSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3_Table_Level.csv", stringsAsFactors = FALSE)
|
||||
cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3_Field_Level.csv", stringsAsFactors = FALSE)
|
||||
|
||||
tables <- tableSpecs$cdmTableName
|
||||
|
||||
cdmSpecsClean <- cdmSpecs %>%
|
||||
dplyr::select(`CDM Table` = cdmTableName,
|
||||
`CDM Field` = cdmFieldName,
|
||||
`User Guide` = userGuidance,
|
||||
`ETL Conventions` = etlConventions,
|
||||
`Datatype` = cdmDatatype,
|
||||
`Required` = isRequired,
|
||||
`Primary Key` = isPrimaryKey,
|
||||
`Foreign Key` = isForeignKey,
|
||||
`FK Table` = fkTableName,
|
||||
`FK Domain` = fkDomain
|
||||
)
|
||||
|
||||
cdmSpecsClean[is.na(cdmSpecsClean)] <- ""
|
||||
|
||||
for(tb in tables) {
|
||||
|
||||
if(tb == 'PERSON'){
|
||||
cat("## **Clinical Data Tables**\n\n")
|
||||
}
|
||||
|
||||
if(tb == 'LOCATION'){
|
||||
cat("## **Health System Data Tables**\n\n")
|
||||
}
|
||||
|
||||
if(tb == 'PAYER_PLAN_PERIOD'){
|
||||
cat("## **Health Economics Data Tables**\n\n")
|
||||
}
|
||||
|
||||
if(tb == 'DRUG_ERA'){
|
||||
cat("## **Standardized Derived Elements**\n\n")
|
||||
}
|
||||
|
||||
if(tb == 'METADATA'){
|
||||
cat("## **Metadata Tables**\n\n")
|
||||
}
|
||||
if(tb == 'CONCEPT'){
|
||||
cat("## **Vocabulary Tables**\n\n")
|
||||
}
|
||||
|
||||
cat("###", tb, "{.tabset .tabset-pills} \n\n")
|
||||
|
||||
tableInfo <- subset(tableSpecs, cdmTableName == tb)
|
||||
cat("**Table Description**\n\n",tableInfo[,"tableDescription"], "\n\n")
|
||||
|
||||
if(!isTRUE(tableInfo[,"userGuidance"]=="")){
|
||||
cat("**User Guide**\n\n",tableInfo[,"userGuidance"],"\n\n")
|
||||
}
|
||||
|
||||
if(!isTRUE(tableInfo[,"etlConventions"]=="")){
|
||||
cat("**ETL Conventions**\n\n",tableInfo[,"etlConventions"],"\n\n")
|
||||
}
|
||||
|
||||
loopTable <- subset(cdmSpecsClean, `CDM Table` == tb)
|
||||
loopTable <- subset(loopTable, select = -c(1))
|
||||
|
||||
print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html", escape = FALSE) %>%
|
||||
column_spec(1, bold = T) %>%
|
||||
column_spec(2, width = "3in", include_thead = T) %>%
|
||||
column_spec(3, width = "4in", include_thead = T) %>%
|
||||
column_spec(4:9, width = "1in", include_thead = T) %>%
|
||||
kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13))
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
```
|
||||
|
|
@ -21,9 +21,9 @@ library(stringr)
|
|||
|
||||
```
|
||||
|
||||
# **OMOP CDM v5.3.1**
|
||||
# **OMOP CDM v5.4**
|
||||
|
||||
Below is the specification document for the OMOP Common Data Model, v5.3.1. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page.
|
||||
Below is the specification document for the OMOP Common Data Model, v5.4. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page.
|
||||
|
||||
--after regeneration of DDLs
|
||||
link to csv of cdm
|
||||
|
|
@ -31,8 +31,8 @@ link to pdf of cdm documentation
|
|||
link to forum on doc page
|
||||
|
||||
```{r docLoop53, echo=FALSE, results='asis'}
|
||||
tableSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3.1_Table_Level.csv", stringsAsFactors = FALSE)
|
||||
cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3.1_Field_Level.csv", stringsAsFactors = FALSE)
|
||||
tableSpecs <- read.csv("../inst/csv/OMOP_CDMv5.4_Table_Level.csv", stringsAsFactors = FALSE)
|
||||
cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv5.4_Field_Level.csv", stringsAsFactors = FALSE)
|
||||
|
||||
tables <- tableSpecs$cdmTableName
|
||||
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
---
|
||||
title: "Indices, Primary Keys and Foreign Key Constraints"
|
||||
output:
|
||||
html_document:
|
||||
toc: true
|
||||
toc_depth: 5
|
||||
toc_float: true
|
||||
---
|
||||
|
||||
## Overview
|
||||
Database indices improve the performance of queries against a database by organizing the data in a way that increase query execution.
|
||||
|
||||
This article was written to provide guidance on the setting of indices, primary and foreign keys for data that has been transformed into the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM). The community that supports the design and development of the OHDSI/CommonDataModel Github repository is a diverse collaborative of healthcare and technical profesisonals whom have limited data base adminstrative (DBA) experience. As a result, the comments below should be interpreted as suggestions and recommendations to help increase performance. Your teams needs may call for a modified configuration.
|
||||
|
||||
## General Recommendations
|
||||
Should your database of choice support indexing, the OMOP CDM Working Group recommends
|
||||
|
||||
* Indexing on all columns containing an "_id" (e.g. condition_occurrence_id, drug_exposure_id, measurement_id, procedure_occurrence_id, etc.)
|
||||
* Indexing on primary and foreign keys
|
||||
|
||||
For all databases, regardless of custom indice support, primary and foreign keys should be set. This is a step towards ensuring data 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 [INST/CSV directory](https://github.com/OHDSI/CommonDataModel/tree/v5.4/inst/csv)
|
||||
|
||||
## Database support
|
||||
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.
|
||||
|
||||
### Microsoft SQL Server
|
||||
### Oracle
|
||||
### PostgreSQL
|
||||
|
||||
### Amazon Redshift
|
||||
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 [Redshift-specific DDL](https://github.com/OHDSI/CommonDataModel/blob/v5.4/ddl/5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql).
|
||||
|
||||
### Impala
|
||||
### IBM Netezza
|
||||
### Google BigQuery
|
||||
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.
|
||||
[Reference](https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2)
|
||||
|
||||
### Microsoft Parallel Data Warehouse (PDW)
|
||||
### SQLite
|
||||
|
||||
### Databricks
|
||||
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.
|
||||
|
||||
## References
|
||||
|
||||
[ISO Best Practices of CDM Indexing](https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2)
|
||||
|
||||
Loading…
Reference in New Issue