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Updated drug_era ingredient class convention

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Clair Blacketer 2023-09-28 11:29:02 -04:00
parent 55c4d7a934
commit a3aa5af76a
19 changed files with 10456 additions and 134 deletions
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@ -13,7 +13,7 @@
<title>OMOP CDM v5.3</title> <title>OMOP CDM v5.3</title>
<script src="site_libs/header-attrs-2.16/header-attrs.js"></script> <script src="site_libs/header-attrs-2.21/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script> <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
@ -35,8 +35,8 @@
<script src="site_libs/navigation-1.1/tabsets.js"></script> <script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" /> <link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script> <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" /> <link href="site_libs/font-awesome-6.2.1/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" /> <link href="site_libs/font-awesome-6.2.1/css/v4-shims.min.css" rel="stylesheet" />
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' /> <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
<style type="text/css"> <style type="text/css">
@ -185,8 +185,8 @@ $(document).ready(function () {
border-radius: 4px; border-radius: 4px;
} }
.tabset-dropdown > .nav-tabs > li.active:before { .tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: ""; content: "\e259";
font-family: 'Glyphicons Halflings'; font-family: 'Glyphicons Halflings';
display: inline-block; display: inline-block;
padding: 10px; padding: 10px;
@ -194,16 +194,9 @@ $(document).ready(function () {
} }
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "&#xe258;"; content: "\e258";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings'; font-family: 'Glyphicons Halflings';
display: inline-block; border: none;
padding: 10px;
border-right: 1px solid #ddd;
} }
.tabset-dropdown > .nav-tabs > li.active { .tabset-dropdown > .nav-tabs > li.active {
@ -402,6 +395,9 @@ div.tocify {
<li> <li>
<a href="cdm54Changes.html">Changes from CDM v5.3</a> <a href="cdm54Changes.html">Changes from CDM v5.3</a>
</li> </li>
<li>
<a href="cdm54erd.html">Entity Relationships</a>
</li>
</ul> </ul>
</li> </li>
</ul> </ul>
@ -510,12 +506,10 @@ referenced v5.3.1. During the OHDSI/CommonDataModel Hack-A-Thon that
occurred on August 18, 2021 the decision was made to align documentation 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 with the minor releases. Hot fixes and minor.minor release can be found
through the searching of tags.</em></p> through the searching of tags.</em></p>
<p>–after regeneration of DDLs link to csv of cdm link to pdf of cdm
documentation link to forum on doc page</p>
<div id="clinical-data-tables" class="section level2"> <div id="clinical-data-tables" class="section level2">
<h2><strong>Clinical Data Tables</strong></h2> <h2><strong>Clinical Data Tables</strong></h2>
<div id="person" class="section level3 tabset tabset-pills"> <div id="person" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">PERSON</h3> <h3 class="tabset tabset-pills">person</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table serves as the central identity management for all Persons <p>This table serves as the central identity management for all Persons
in the database. It contains records that uniquely identify each person in the database. It contains records that uniquely identify each person
@ -1125,7 +1119,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="observation_period" class="section level3 tabset tabset-pills"> <div id="observation_period" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">OBSERVATION_PERIOD</h3> <h3 class="tabset tabset-pills">observation_period</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table contains records which define spans of time during which <p>This table contains records which define spans of time during which
two conditions are expected to hold: (i) Clinical Events that happened two conditions are expected to hold: (i) Clinical Events that happened
@ -1359,7 +1353,7 @@ Type Concept
</table> </table>
</div> </div>
<div id="visit_occurrence" class="section level3 tabset tabset-pills"> <div id="visit_occurrence" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">VISIT_OCCURRENCE</h3> <h3 class="tabset tabset-pills">visit_occurrence</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table contains Events where Persons engage with the healthcare <p>This table contains Events where Persons engage with the healthcare
system for a duration of time. They are often also called “Encounters”. system for a duration of time. They are often also called “Encounters”.
@ -2032,7 +2026,7 @@ VISIT_OCCURRENCE
</table> </table>
</div> </div>
<div id="visit_detail" class="section level3 tabset tabset-pills"> <div id="visit_detail" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">VISIT_DETAIL</h3> <h3 class="tabset tabset-pills">visit_detail</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The VISIT_DETAIL table is an optional table used to represents <p>The VISIT_DETAIL table is an optional table used to represents
details of each record in the parent VISIT_OCCURRENCE table. A good details of each record in the parent VISIT_OCCURRENCE table. A good
@ -2702,7 +2696,7 @@ VISIT_OCCURRENCE
</div> </div>
<div id="condition_occurrence" <div id="condition_occurrence"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONDITION_OCCURRENCE</h3> <h3 class="tabset tabset-pills">condition_occurrence</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table contains records of Events of a Person suggesting the <p>This table contains records of Events of a Person suggesting the
presence of a disease or medical condition stated as a diagnosis, a presence of a disease or medical condition stated as a diagnosis, a
@ -3285,7 +3279,7 @@ No
</table> </table>
</div> </div>
<div id="drug_exposure" class="section level3 tabset tabset-pills"> <div id="drug_exposure" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DRUG_EXPOSURE</h3> <h3 class="tabset tabset-pills">drug_exposure</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table captures records about the exposure to a Drug ingested or <p>This table captures records about the exposure to a Drug ingested or
otherwise introduced into the body. A Drug is a biochemical substance otherwise introduced into the body. A Drug is a biochemical substance
@ -4095,7 +4089,7 @@ No
</div> </div>
<div id="procedure_occurrence" <div id="procedure_occurrence"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">PROCEDURE_OCCURRENCE</h3> <h3 class="tabset tabset-pills">procedure_occurrence</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table contains records of activities or processes ordered by, or <p>This table contains records of activities or processes ordered by, or
carried out by, a healthcare provider on the patient with a diagnostic carried out by, a healthcare provider on the patient with a diagnostic
@ -4602,7 +4596,7 @@ No
</table> </table>
</div> </div>
<div id="device_exposure" class="section level3 tabset tabset-pills"> <div id="device_exposure" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DEVICE_EXPOSURE</h3> <h3 class="tabset tabset-pills">device_exposure</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The Device domain captures information about a person’s exposure to a <p>The Device domain captures information about a person’s exposure to a
foreign physical object or instrument which is used for diagnostic or foreign physical object or instrument which is used for diagnostic or
@ -5100,7 +5094,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="measurement" class="section level3 tabset tabset-pills"> <div id="measurement" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">MEASUREMENT</h3> <h3 class="tabset tabset-pills">measurement</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The MEASUREMENT table contains records of Measurements, <p>The MEASUREMENT table contains records of Measurements,
i.e. structured values (numerical or categorical) obtained through i.e. structured values (numerical or categorical) obtained through
@ -5828,7 +5822,7 @@ No
</table> </table>
</div> </div>
<div id="observation" class="section level3 tabset tabset-pills"> <div id="observation" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">OBSERVATION</h3> <h3 class="tabset tabset-pills">observation</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The OBSERVATION table captures clinical facts about a Person obtained <p>The OBSERVATION table captures clinical facts about a Person obtained
in the context of examination, questioning or a procedure. Any data that in the context of examination, questioning or a procedure. Any data that
@ -6469,13 +6463,17 @@ No
</table> </table>
</div> </div>
<div id="death" class="section level3 tabset tabset-pills"> <div id="death" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DEATH</h3> <h3 class="tabset tabset-pills">death</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The death domain contains the clinical event for how and when a <p>The death domain contains the clinical event for how and when a
Person dies. A person can have up to one record if the source system Person dies. A person can have up to one record if the source system
contains evidence about the Death, such as: Condition in an contains evidence about the Death, such as: Condition in an
administrative claim, status of enrollment into a health plan, or administrative claim, status of enrollment into a health plan, or
explicit record in EHR data.</p> explicit record in EHR data.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -6712,12 +6710,14 @@ CONCEPT
</table> </table>
</div> </div>
<div id="note" class="section level3 tabset tabset-pills"> <div id="note" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">NOTE</h3> <h3 class="tabset tabset-pills">note</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The NOTE table captures unstructured information that was recorded by <p>The NOTE table captures unstructured information that was recorded by
a provider about a patient in free text (in ASCII, or preferably in UTF8 a provider about a patient in free text (in ASCII, or preferably in UTF8
format) notes on a given date. The type of note_text is CLOB or format) notes on a given date. The type of note_text is CLOB or
varchar(MAX) depending on RDBMS.</p> varchar(MAX) depending on RDBMS.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>HL7/LOINC CDO is a standard for consistent naming of documents to <p>HL7/LOINC CDO is a standard for consistent naming of documents to
support a range of use cases: retrieval, organization, display, and support a range of use cases: retrieval, organization, display, and
@ -7174,10 +7174,14 @@ No
</table> </table>
</div> </div>
<div id="note_nlp" class="section level3 tabset tabset-pills"> <div id="note_nlp" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">NOTE_NLP</h3> <h3 class="tabset tabset-pills">note_nlp</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The NOTE_NLP table encodes all output of NLP on clinical notes. Each <p>The NOTE_NLP table encodes all output of NLP on clinical notes. Each
row represents a single extracted term from a note.</p> row represents a single extracted term from a note.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -7598,10 +7602,12 @@ No
</table> </table>
</div> </div>
<div id="specimen" class="section level3 tabset tabset-pills"> <div id="specimen" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">SPECIMEN</h3> <h3 class="tabset tabset-pills">specimen</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The specimen domain contains the records identifying biological <p>The specimen domain contains the records identifying biological
samples from a person.</p> samples from a person.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Anatomic site is coded at the most specific level of granularity <p>Anatomic site is coded at the most specific level of granularity
possible, such that higher level classifications can be derived using possible, such that higher level classifications can be derived using
@ -8051,7 +8057,7 @@ No
</table> </table>
</div> </div>
<div id="fact_relationship" class="section level3 tabset tabset-pills"> <div id="fact_relationship" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">FACT_RELATIONSHIP</h3> <h3 class="tabset tabset-pills">fact_relationship</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The FACT_RELATIONSHIP table contains records about the relationships <p>The FACT_RELATIONSHIP table contains records about the relationships
between facts stored as records in any table of the CDM. Relationships between facts stored as records in any table of the CDM. Relationships
@ -8064,6 +8070,8 @@ indication relationship (between drug exposures and associated
conditions), usage relationships (of devices during the course of an conditions), usage relationships (of devices during the course of an
associated procedure), or facts derived from one another (measurements associated procedure), or facts derived from one another (measurements
derived from an associated specimen).</p> derived from an associated specimen).</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>All relationships are directional, and each relationship is <p>All relationships are directional, and each relationship is
represented twice symmetrically within the FACT_RELATIONSHIP table. For represented twice symmetrically within the FACT_RELATIONSHIP table. For
@ -8239,10 +8247,12 @@ CONCEPT
<div id="health-system-data-tables" class="section level2"> <div id="health-system-data-tables" class="section level2">
<h2><strong>Health System Data Tables</strong></h2> <h2><strong>Health System Data Tables</strong></h2>
<div id="location" class="section level3 tabset tabset-pills"> <div id="location" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">LOCATION</h3> <h3 class="tabset tabset-pills">location</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The LOCATION table represents a generic way to capture physical <p>The LOCATION table represents a generic way to capture physical
location or address information of Persons and Care Sites.</p> location or address information of Persons and Care Sites.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Each address or Location is unique and is present only once in the <p>Each address or Location is unique and is present only once in the
table. Locations do not contain names, such as the name of a hospital. table. Locations do not contain names, such as the name of a hospital.
@ -8499,11 +8509,13 @@ No
</table> </table>
</div> </div>
<div id="care_site" class="section level3 tabset tabset-pills"> <div id="care_site" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CARE_SITE</h3> <h3 class="tabset tabset-pills">care_site</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CARE_SITE table contains a list of uniquely identified <p>The CARE_SITE table contains a list of uniquely identified
institutional (physical or organizational) units where healthcare institutional (physical or organizational) units where healthcare
delivery is practiced (offices, wards, hospitals, clinics, etc.).</p> delivery is practiced (offices, wards, hospitals, clinics, etc.).</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Care site is a unique combination of location_id and <p>Care site is a unique combination of location_id and
place_of_service_source_value. Care site does not take into account the place_of_service_source_value. Care site does not take into account the
@ -8726,7 +8738,7 @@ No
</table> </table>
</div> </div>
<div id="provider" class="section level3 tabset tabset-pills"> <div id="provider" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">PROVIDER</h3> <h3 class="tabset tabset-pills">provider</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The PROVIDER table contains a list of uniquely identified healthcare <p>The PROVIDER table contains a list of uniquely identified healthcare
providers. These are individuals providing hands-on healthcare to providers. These are individuals providing hands-on healthcare to
@ -8738,6 +8750,8 @@ institutional providers. The PROVIDER table contains the individual
providers. If the source, instead of uniquely identifying individual providers. If the source, instead of uniquely identifying individual
providers, only provides limited information such as specialty, generic providers, only provides limited information such as specialty, generic
or ‘pooled’ Provider records are listed in the PROVIDER table.</p> or ‘pooled’ Provider records are listed in the PROVIDER table.</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -9166,7 +9180,7 @@ CONCEPT
<div id="health-economics-data-tables" class="section level2"> <div id="health-economics-data-tables" class="section level2">
<h2><strong>Health Economics Data Tables</strong></h2> <h2><strong>Health Economics Data Tables</strong></h2>
<div id="payer_plan_period" class="section level3 tabset tabset-pills"> <div id="payer_plan_period" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">PAYER_PLAN_PERIOD</h3> <h3 class="tabset tabset-pills">payer_plan_period</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The PAYER_PLAN_PERIOD table captures details of the period of time <p>The PAYER_PLAN_PERIOD table captures details of the period of time
that a Person is continuously enrolled under a specific health Plan that a Person is continuously enrolled under a specific health Plan
@ -9187,6 +9201,8 @@ table. For example, medical and drug coverage in the US can be
represented by two Payer_Plan_Periods. The details of the benefit represented by two Payer_Plan_Periods. The details of the benefit
structure of the Plan is rarely known, the idea is just to identify that structure of the Plan is rarely known, the idea is just to identify that
the Plans are different.</p> the Plans are different.</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -9716,7 +9732,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="cost" class="section level3 tabset tabset-pills"> <div id="cost" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">COST</h3> <h3 class="tabset tabset-pills">cost</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The COST table captures records containing the cost of any medical <p>The COST table captures records containing the cost of any medical
event recorded in one of the OMOP clinical event tables such as event recorded in one of the OMOP clinical event tables such as
@ -10347,7 +10363,7 @@ No
<div id="standardized-derived-elements" class="section level2"> <div id="standardized-derived-elements" class="section level2">
<h2><strong>Standardized Derived Elements</strong></h2> <h2><strong>Standardized Derived Elements</strong></h2>
<div id="drug_era" class="section level3 tabset tabset-pills"> <div id="drug_era" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DRUG_ERA</h3> <h3 class="tabset tabset-pills">drug_era</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>A Drug Era is defined as a span of time when the Person is assumed to <p>A Drug Era is defined as a span of time when the Person is assumed to
be exposed to a particular active ingredient. A Drug Era is not the same be exposed to a particular active ingredient. A Drug Era is not the same
@ -10355,6 +10371,8 @@ as a Drug Exposure: Exposures are individual records corresponding to
the source when Drug was delivered to the Person, while successive the source when Drug was delivered to the Person, while successive
periods of Drug Exposures are combined under certain rules to produce periods of Drug Exposures are combined under certain rules to produce
continuous Drug Eras.</p> continuous Drug Eras.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>The SQL script for generating DRUG_ERA records can be found <a <p>The SQL script for generating DRUG_ERA records can be found <a
href="https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras">here</a>.</p> href="https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras">here</a>.</p>
@ -10450,6 +10468,9 @@ drug_concept_id
The Concept Id representing the specific drug ingredient. The Concept Id representing the specific drug ingredient.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
The drug_concept_id should conform to the concept class ‘ingredient’ as
the drug_era is an era of time where a person is exposed to a particular
drug ingredient.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer
@ -10599,10 +10620,12 @@ No
</table> </table>
</div> </div>
<div id="dose_era" class="section level3 tabset tabset-pills"> <div id="dose_era" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DOSE_ERA</h3> <h3 class="tabset tabset-pills">dose_era</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>A Dose Era is defined as a span of time when the Person is assumed to <p>A Dose Era is defined as a span of time when the Person is assumed to
be exposed to a constant dose of a specific active ingredient.</p> be exposed to a constant dose of a specific active ingredient.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Dose Eras will be derived from records in the DRUG_EXPOSURE table and <p>Dose Eras will be derived from records in the DRUG_EXPOSURE table and
the Dose information from the DRUG_STRENGTH table using a standardized the Dose information from the DRUG_STRENGTH table using a standardized
@ -10835,7 +10858,7 @@ No
</table> </table>
</div> </div>
<div id="condition_era" class="section level3 tabset tabset-pills"> <div id="condition_era" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONDITION_ERA</h3> <h3 class="tabset tabset-pills">condition_era</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>A Condition Era is defined as a span of time when the Person is <p>A Condition Era is defined as a span of time when the Person is
assumed to have a given condition. Similar to Drug Eras, Condition Eras assumed to have a given condition. Similar to Drug Eras, Condition Eras
@ -10855,6 +10878,8 @@ provides the appropriate treatment to resolve the condition. These two
independent doctor visits should be aggregated into one Condition independent doctor visits should be aggregated into one Condition
Era.</li> Era.</li>
</ul> </ul>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Each Condition Era corresponds to one or many Condition Occurrence <p>Each Condition Era corresponds to one or many Condition Occurrence
records that form a continuous interval. The condition_concept_id field records that form a continuous interval. The condition_concept_id field
@ -11073,10 +11098,14 @@ No
<div id="metadata-tables" class="section level2"> <div id="metadata-tables" class="section level2">
<h2><strong>Metadata Tables</strong></h2> <h2><strong>Metadata Tables</strong></h2>
<div id="metadata" class="section level3 tabset tabset-pills"> <div id="metadata" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">METADATA</h3> <h3 class="tabset tabset-pills">metadata</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The METADATA table contains metadata information about a dataset that <p>The METADATA table contains metadata information about a dataset that
has been transformed to the OMOP Common Data Model.</p> has been transformed to the OMOP Common Data Model.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -11292,11 +11321,15 @@ No
</table> </table>
</div> </div>
<div id="cdm_source" class="section level3 tabset tabset-pills"> <div id="cdm_source" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CDM_SOURCE</h3> <h3 class="tabset tabset-pills">cdm_source</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CDM_SOURCE table contains detail about the source database and <p>The CDM_SOURCE table contains detail about the source database and
the process used to transform the data into the OMOP Common Data the process used to transform the data into the OMOP Common Data
Model.</p> Model.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -11594,7 +11627,7 @@ No
<div id="vocabulary-tables" class="section level2"> <div id="vocabulary-tables" class="section level2">
<h2><strong>Vocabulary Tables</strong></h2> <h2><strong>Vocabulary Tables</strong></h2>
<div id="concept" class="section level3 tabset tabset-pills"> <div id="concept" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT</h3> <h3 class="tabset tabset-pills">concept</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The Standardized Vocabularies contains records, or Concepts, that <p>The Standardized Vocabularies contains records, or Concepts, that
uniquely identify each fundamental unit of meaning used to express uniquely identify each fundamental unit of meaning used to express
@ -11616,6 +11649,10 @@ associated morphology, etc.).</p>
national or international vocabularies such as SNOMED-CT, RxNorm, and national or international vocabularies such as SNOMED-CT, RxNorm, and
LOINC, or custom Concepts defined to cover various aspects of LOINC, or custom Concepts defined to cover various aspects of
observational data analysis.</p> observational data analysis.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -11931,13 +11968,17 @@ No
</table> </table>
</div> </div>
<div id="vocabulary" class="section level3 tabset tabset-pills"> <div id="vocabulary" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">VOCABULARY</h3> <h3 class="tabset tabset-pills">vocabulary</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The VOCABULARY table includes a list of the Vocabularies collected <p>The VOCABULARY table includes a list of the Vocabularies collected
from various sources or created de novo by the OMOP community. This from various sources or created de novo by the OMOP community. This
reference table is populated with a single record for each Vocabulary reference table is populated with a single record for each Vocabulary
source and includes a descriptive name and other associated attributes source and includes a descriptive name and other associated attributes
for the Vocabulary.</p> for the Vocabulary.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12110,7 +12151,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="domain" class="section level3 tabset tabset-pills"> <div id="domain" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DOMAIN</h3> <h3 class="tabset tabset-pills">domain</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The DOMAIN table includes a list of OMOP-defined Domains the Concepts <p>The DOMAIN table includes a list of OMOP-defined Domains the Concepts
of the Standardized Vocabularies can belong to. A Domain defines the set of the Standardized Vocabularies can belong to. A Domain defines the set
@ -12120,6 +12161,10 @@ condition of a patient, and these Concepts can only be stored in the
condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA
tables. This reference table is populated with a single record for each tables. This reference table is populated with a single record for each
Domain and includes a descriptive name for the Domain.</p> Domain and includes a descriptive name for the Domain.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12237,12 +12282,16 @@ CONCEPT
</table> </table>
</div> </div>
<div id="concept_class" class="section level3 tabset tabset-pills"> <div id="concept_class" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT_CLASS</h3> <h3 class="tabset tabset-pills">concept_class</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CONCEPT_CLASS table is a reference table, which includes a list <p>The CONCEPT_CLASS table is a reference table, which includes a list
of the classifications used to differentiate Concepts within a given of the classifications used to differentiate Concepts within a given
Vocabulary. This reference table is populated with a single record for Vocabulary. This reference table is populated with a single record for
each Concept Class.</p> each Concept Class.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12361,12 +12410,16 @@ CONCEPT
</div> </div>
<div id="concept_relationship" <div id="concept_relationship"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT_RELATIONSHIP</h3> <h3 class="tabset tabset-pills">concept_relationship</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CONCEPT_RELATIONSHIP table contains records that define direct <p>The CONCEPT_RELATIONSHIP table contains records that define direct
relationships between any two Concepts and the nature or type of the relationships between any two Concepts and the nature or type of the
relationship. Each type of a relationship is defined in the RELATIONSHIP relationship. Each type of a relationship is defined in the RELATIONSHIP
table.</p> table.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12565,11 +12618,15 @@ No
</table> </table>
</div> </div>
<div id="relationship" class="section level3 tabset tabset-pills"> <div id="relationship" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">RELATIONSHIP</h3> <h3 class="tabset tabset-pills">relationship</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The RELATIONSHIP table provides a reference list of all types of <p>The RELATIONSHIP table provides a reference list of all types of
relationships that can be used to associate any two concepts in the relationships that can be used to associate any two concepts in the
CONCEPT_RELATIONSHP table.</p> CONCEPT_RELATIONSHP table.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12769,10 +12826,14 @@ CONCEPT
</table> </table>
</div> </div>
<div id="concept_synonym" class="section level3 tabset tabset-pills"> <div id="concept_synonym" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT_SYNONYM</h3> <h3 class="tabset tabset-pills">concept_synonym</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CONCEPT_SYNONYM table is used to store alternate names and <p>The CONCEPT_SYNONYM table is used to store alternate names and
descriptions for Concepts.</p> descriptions for Concepts.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12887,7 +12948,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="concept_ancestor" class="section level3 tabset tabset-pills"> <div id="concept_ancestor" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT_ANCESTOR</h3> <h3 class="tabset tabset-pills">concept_ancestor</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CONCEPT_ANCESTOR table is designed to simplify observational <p>The CONCEPT_ANCESTOR table is designed to simplify observational
analysis by providing the complete hierarchical relationships between analysis by providing the complete hierarchical relationships between
@ -12902,6 +12963,10 @@ descendants of a hierarchical concept. For example, drug ingredients and
drug products are all descendants of a drug class ancestor.</p> drug products are all descendants of a drug class ancestor.</p>
<p>This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP <p>This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP
and RELATIONSHIP tables.</p> and RELATIONSHIP tables.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13052,7 +13117,7 @@ No
</div> </div>
<div id="source_to_concept_map" <div id="source_to_concept_map"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">SOURCE_TO_CONCEPT_MAP</h3> <h3 class="tabset tabset-pills">source_to_concept_map</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The source to concept map table is a legacy data structure within the <p>The source to concept map table is a legacy data structure within the
OMOP Common Data Model, recommended for use in ETL processes to maintain OMOP Common Data Model, recommended for use in ETL processes to maintain
@ -13062,6 +13127,10 @@ code into a Standard Concept as target_concept_ids that can be used to
populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table
is no longer populated with content within the Standardized Vocabularies is no longer populated with content within the Standardized Vocabularies
published to the OMOP community.</p> published to the OMOP community.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13346,12 +13415,16 @@ No
</table> </table>
</div> </div>
<div id="drug_strength" class="section level3 tabset tabset-pills"> <div id="drug_strength" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DRUG_STRENGTH</h3> <h3 class="tabset tabset-pills">drug_strength</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The DRUG_STRENGTH table contains structured content about the amount <p>The DRUG_STRENGTH table contains structured content about the amount
or concentration and associated units of a specific ingredient contained or concentration and associated units of a specific ingredient contained
within a particular drug product. This table is supplemental information within a particular drug product. This table is supplemental information
to support standardized analysis of drug utilization.</p> to support standardized analysis of drug utilization.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13719,7 +13792,7 @@ No
</table> </table>
</div> </div>
<div id="cohort_definition" class="section level3 tabset tabset-pills"> <div id="cohort_definition" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">COHORT_DEFINITION</h3> <h3 class="tabset tabset-pills">cohort_definition</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The COHORT_DEFINITION table contains records defining a Cohort <p>The COHORT_DEFINITION table contains records defining a Cohort
derived from the data through the associated description and syntax and derived from the data through the associated description and syntax and
@ -13730,6 +13803,10 @@ provides a standardized structure for maintaining the rules governing
the inclusion of a subject into a cohort, and can store operational the inclusion of a subject into a cohort, and can store operational
programming code to instantiate the cohort within the OMOP Common Data programming code to instantiate the cohort within the OMOP Common Data
Model.</p> Model.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13955,7 +14032,7 @@ No
</div> </div>
<div id="attribute_definition" <div id="attribute_definition"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">ATTRIBUTE_DEFINITION</h3> <h3 class="tabset tabset-pills">attribute_definition</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The ATTRIBUTE_DEFINITION table contains records to define each <p>The ATTRIBUTE_DEFINITION table contains records to define each
attribute through an associated description and syntax. Attributes are attribute through an associated description and syntax. Attributes are
@ -13965,6 +14042,10 @@ structure for maintaining the rules governing the calculation of
covariates for a subject in a cohort, and can store operational covariates for a subject in a cohort, and can store operational
programming code to instantiate the attributes for a given cohort within programming code to instantiate the attributes for a given cohort within
the OMOP Common Data Model.</p> the OMOP Common Data Model.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>

187
docs/cdm54.html
View File

@ -13,7 +13,7 @@
<title>OMOP CDM v5.4</title> <title>OMOP CDM v5.4</title>
<script src="site_libs/header-attrs-2.16/header-attrs.js"></script> <script src="site_libs/header-attrs-2.21/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script> <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
@ -35,8 +35,8 @@
<script src="site_libs/navigation-1.1/tabsets.js"></script> <script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" /> <link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script> <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" /> <link href="site_libs/font-awesome-6.2.1/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" /> <link href="site_libs/font-awesome-6.2.1/css/v4-shims.min.css" rel="stylesheet" />
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' /> <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
<style type="text/css"> <style type="text/css">
@ -185,8 +185,8 @@ $(document).ready(function () {
border-radius: 4px; border-radius: 4px;
} }
.tabset-dropdown > .nav-tabs > li.active:before { .tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: ""; content: "\e259";
font-family: 'Glyphicons Halflings'; font-family: 'Glyphicons Halflings';
display: inline-block; display: inline-block;
padding: 10px; padding: 10px;
@ -194,16 +194,9 @@ $(document).ready(function () {
} }
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "&#xe258;"; content: "\e258";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings'; font-family: 'Glyphicons Halflings';
display: inline-block; border: none;
padding: 10px;
border-right: 1px solid #ddd;
} }
.tabset-dropdown > .nav-tabs > li.active { .tabset-dropdown > .nav-tabs > li.active {
@ -402,6 +395,9 @@ div.tocify {
<li> <li>
<a href="cdm54Changes.html">Changes from CDM v5.3</a> <a href="cdm54Changes.html">Changes from CDM v5.3</a>
</li> </li>
<li>
<a href="cdm54erd.html">Entity Relationships</a>
</li>
</ul> </ul>
</li> </li>
</ul> </ul>
@ -621,7 +617,7 @@ main github page.</p>
<div id="clinical-data-tables" class="section level2"> <div id="clinical-data-tables" class="section level2">
<h2><strong>Clinical Data Tables</strong></h2> <h2><strong>Clinical Data Tables</strong></h2>
<div id="person" class="section level3 tabset tabset-pills"> <div id="person" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">PERSON</h3> <h3 class="tabset tabset-pills">person</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table serves as the central identity management for all Persons <p>This table serves as the central identity management for all Persons
in the database. It contains records that uniquely identify each person in the database. It contains records that uniquely identify each person
@ -1231,7 +1227,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="observation_period" class="section level3 tabset tabset-pills"> <div id="observation_period" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">OBSERVATION_PERIOD</h3> <h3 class="tabset tabset-pills">observation_period</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table contains records which define spans of time during which <p>This table contains records which define spans of time during which
two conditions are expected to hold: (i) Clinical Events that happened two conditions are expected to hold: (i) Clinical Events that happened
@ -1468,7 +1464,7 @@ Type Concept
</table> </table>
</div> </div>
<div id="visit_occurrence" class="section level3 tabset tabset-pills"> <div id="visit_occurrence" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">VISIT_OCCURRENCE</h3> <h3 class="tabset tabset-pills">visit_occurrence</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table contains Events where Persons engage with the healthcare <p>This table contains Events where Persons engage with the healthcare
system for a duration of time. They are often also called “Encounters”. system for a duration of time. They are often also called “Encounters”.
@ -2152,7 +2148,7 @@ VISIT_OCCURRENCE
</table> </table>
</div> </div>
<div id="visit_detail" class="section level3 tabset tabset-pills"> <div id="visit_detail" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">VISIT_DETAIL</h3> <h3 class="tabset tabset-pills">visit_detail</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The VISIT_DETAIL table is an optional table used to represents <p>The VISIT_DETAIL table is an optional table used to represents
details of each record in the parent VISIT_OCCURRENCE table. A good details of each record in the parent VISIT_OCCURRENCE table. A good
@ -2833,7 +2829,7 @@ VISIT_OCCURRENCE
</div> </div>
<div id="condition_occurrence" <div id="condition_occurrence"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONDITION_OCCURRENCE</h3> <h3 class="tabset tabset-pills">condition_occurrence</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table contains records of Events of a Person suggesting the <p>This table contains records of Events of a Person suggesting the
presence of a disease or medical condition stated as a diagnosis, a presence of a disease or medical condition stated as a diagnosis, a
@ -3419,7 +3415,7 @@ No
</table> </table>
</div> </div>
<div id="drug_exposure" class="section level3 tabset tabset-pills"> <div id="drug_exposure" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DRUG_EXPOSURE</h3> <h3 class="tabset tabset-pills">drug_exposure</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table captures records about the exposure to a Drug ingested or <p>This table captures records about the exposure to a Drug ingested or
otherwise introduced into the body. A Drug is a biochemical substance otherwise introduced into the body. A Drug is a biochemical substance
@ -4232,7 +4228,7 @@ No
</div> </div>
<div id="procedure_occurrence" <div id="procedure_occurrence"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">PROCEDURE_OCCURRENCE</h3> <h3 class="tabset tabset-pills">procedure_occurrence</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>This table contains records of activities or processes ordered by, or <p>This table contains records of activities or processes ordered by, or
carried out by, a healthcare provider on the patient with a diagnostic carried out by, a healthcare provider on the patient with a diagnostic
@ -4796,7 +4792,7 @@ No
</table> </table>
</div> </div>
<div id="device_exposure" class="section level3 tabset tabset-pills"> <div id="device_exposure" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DEVICE_EXPOSURE</h3> <h3 class="tabset tabset-pills">device_exposure</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The Device domain captures information about a person’s exposure to a <p>The Device domain captures information about a person’s exposure to a
foreign physical object or instrument which is used for diagnostic or foreign physical object or instrument which is used for diagnostic or
@ -5427,7 +5423,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="measurement" class="section level3 tabset tabset-pills"> <div id="measurement" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">MEASUREMENT</h3> <h3 class="tabset tabset-pills">measurement</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The MEASUREMENT table contains records of Measurements, <p>The MEASUREMENT table contains records of Measurements,
i.e. structured values (numerical or categorical) obtained through i.e. structured values (numerical or categorical) obtained through
@ -6254,7 +6250,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="observation" class="section level3 tabset tabset-pills"> <div id="observation" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">OBSERVATION</h3> <h3 class="tabset tabset-pills">observation</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The OBSERVATION table captures clinical facts about a Person obtained <p>The OBSERVATION table captures clinical facts about a Person obtained
in the context of examination, questioning or a procedure. Any data that in the context of examination, questioning or a procedure. Any data that
@ -6994,13 +6990,17 @@ CONCEPT
</table> </table>
</div> </div>
<div id="death" class="section level3 tabset tabset-pills"> <div id="death" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DEATH</h3> <h3 class="tabset tabset-pills">death</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The death domain contains the clinical event for how and when a <p>The death domain contains the clinical event for how and when a
Person dies. A person can have up to one record if the source system Person dies. A person can have up to one record if the source system
contains evidence about the Death, such as: Condition in an contains evidence about the Death, such as: Condition in an
administrative claim, status of enrollment into a health plan, or administrative claim, status of enrollment into a health plan, or
explicit record in EHR data.</p> explicit record in EHR data.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -7240,12 +7240,14 @@ CONCEPT
</table> </table>
</div> </div>
<div id="note" class="section level3 tabset tabset-pills"> <div id="note" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">NOTE</h3> <h3 class="tabset tabset-pills">note</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The NOTE table captures unstructured information that was recorded by <p>The NOTE table captures unstructured information that was recorded by
a provider about a patient in free text (in ASCII, or preferably in UTF8 a provider about a patient in free text (in ASCII, or preferably in UTF8
format) notes on a given date. The type of note_text is CLOB or format) notes on a given date. The type of note_text is CLOB or
varchar(MAX) depending on RDBMS.</p> varchar(MAX) depending on RDBMS.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>HL7/LOINC CDO is a standard for consistent naming of documents to <p>HL7/LOINC CDO is a standard for consistent naming of documents to
support a range of use cases: retrieval, organization, display, and support a range of use cases: retrieval, organization, display, and
@ -7764,10 +7766,14 @@ CONCEPT
</table> </table>
</div> </div>
<div id="note_nlp" class="section level3 tabset tabset-pills"> <div id="note_nlp" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">NOTE_NLP</h3> <h3 class="tabset tabset-pills">note_nlp</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The NOTE_NLP table encodes all output of NLP on clinical notes. Each <p>The NOTE_NLP table encodes all output of NLP on clinical notes. Each
row represents a single extracted term from a note.</p> row represents a single extracted term from a note.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -8188,10 +8194,12 @@ No
</table> </table>
</div> </div>
<div id="specimen" class="section level3 tabset tabset-pills"> <div id="specimen" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">SPECIMEN</h3> <h3 class="tabset tabset-pills">specimen</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The specimen domain contains the records identifying biological <p>The specimen domain contains the records identifying biological
samples from a person.</p> samples from a person.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Anatomic site is coded at the most specific level of granularity <p>Anatomic site is coded at the most specific level of granularity
possible, such that higher level classifications can be derived using possible, such that higher level classifications can be derived using
@ -8644,7 +8652,7 @@ No
</table> </table>
</div> </div>
<div id="fact_relationship" class="section level3 tabset tabset-pills"> <div id="fact_relationship" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">FACT_RELATIONSHIP</h3> <h3 class="tabset tabset-pills">fact_relationship</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The FACT_RELATIONSHIP table contains records about the relationships <p>The FACT_RELATIONSHIP table contains records about the relationships
between facts stored as records in any table of the CDM. Relationships between facts stored as records in any table of the CDM. Relationships
@ -8657,6 +8665,8 @@ indication relationship (between drug exposures and associated
conditions), usage relationships (of devices during the course of an conditions), usage relationships (of devices during the course of an
associated procedure), or facts derived from one another (measurements associated procedure), or facts derived from one another (measurements
derived from an associated specimen).</p> derived from an associated specimen).</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>All relationships are directional, and each relationship is <p>All relationships are directional, and each relationship is
represented twice symmetrically within the FACT_RELATIONSHIP table. For represented twice symmetrically within the FACT_RELATIONSHIP table. For
@ -8832,7 +8842,7 @@ CONCEPT
<div id="health-system-data-tables" class="section level2"> <div id="health-system-data-tables" class="section level2">
<h2><strong>Health System Data Tables</strong></h2> <h2><strong>Health System Data Tables</strong></h2>
<div id="location" class="section level3 tabset tabset-pills"> <div id="location" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">LOCATION</h3> <h3 class="tabset tabset-pills">location</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The LOCATION table represents a generic way to capture physical <p>The LOCATION table represents a generic way to capture physical
location or address information of Persons and Care Sites.</p> location or address information of Persons and Care Sites.</p>
@ -9205,11 +9215,13 @@ No
</table> </table>
</div> </div>
<div id="care_site" class="section level3 tabset tabset-pills"> <div id="care_site" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CARE_SITE</h3> <h3 class="tabset tabset-pills">care_site</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CARE_SITE table contains a list of uniquely identified <p>The CARE_SITE table contains a list of uniquely identified
institutional (physical or organizational) units where healthcare institutional (physical or organizational) units where healthcare
delivery is practiced (offices, wards, hospitals, clinics, etc.).</p> delivery is practiced (offices, wards, hospitals, clinics, etc.).</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Care site is a unique combination of location_id and <p>Care site is a unique combination of location_id and
place_of_service_source_value. Care site does not take into account the place_of_service_source_value. Care site does not take into account the
@ -9433,7 +9445,7 @@ No
</table> </table>
</div> </div>
<div id="provider" class="section level3 tabset tabset-pills"> <div id="provider" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">PROVIDER</h3> <h3 class="tabset tabset-pills">provider</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The PROVIDER table contains a list of uniquely identified healthcare <p>The PROVIDER table contains a list of uniquely identified healthcare
providers. These are individuals providing hands-on healthcare to providers. These are individuals providing hands-on healthcare to
@ -9445,6 +9457,8 @@ institutional providers. The PROVIDER table contains the individual
providers. If the source, instead of uniquely identifying individual providers. If the source, instead of uniquely identifying individual
providers, only provides limited information such as specialty, generic providers, only provides limited information such as specialty, generic
or ‘pooled’ Provider records are listed in the PROVIDER table.</p> or ‘pooled’ Provider records are listed in the PROVIDER table.</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -9873,7 +9887,7 @@ CONCEPT
<div id="health-economics-data-tables" class="section level2"> <div id="health-economics-data-tables" class="section level2">
<h2><strong>Health Economics Data Tables</strong></h2> <h2><strong>Health Economics Data Tables</strong></h2>
<div id="payer_plan_period" class="section level3 tabset tabset-pills"> <div id="payer_plan_period" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">PAYER_PLAN_PERIOD</h3> <h3 class="tabset tabset-pills">payer_plan_period</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The PAYER_PLAN_PERIOD table captures details of the period of time <p>The PAYER_PLAN_PERIOD table captures details of the period of time
that a Person is continuously enrolled under a specific health Plan that a Person is continuously enrolled under a specific health Plan
@ -9894,6 +9908,8 @@ table. For example, medical and drug coverage in the US can be
represented by two Payer_Plan_Periods. The details of the benefit represented by two Payer_Plan_Periods. The details of the benefit
structure of the Plan is rarely known, the idea is just to identify that structure of the Plan is rarely known, the idea is just to identify that
the Plans are different.</p> the Plans are different.</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -10423,7 +10439,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="cost" class="section level3 tabset tabset-pills"> <div id="cost" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">COST</h3> <h3 class="tabset tabset-pills">cost</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The COST table captures records containing the cost of any medical <p>The COST table captures records containing the cost of any medical
event recorded in one of the OMOP clinical event tables such as event recorded in one of the OMOP clinical event tables such as
@ -11054,7 +11070,7 @@ No
<div id="standardized-derived-elements" class="section level2"> <div id="standardized-derived-elements" class="section level2">
<h2><strong>Standardized Derived Elements</strong></h2> <h2><strong>Standardized Derived Elements</strong></h2>
<div id="drug_era" class="section level3 tabset tabset-pills"> <div id="drug_era" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DRUG_ERA</h3> <h3 class="tabset tabset-pills">drug_era</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>A Drug Era is defined as a span of time when the Person is assumed to <p>A Drug Era is defined as a span of time when the Person is assumed to
be exposed to a particular active ingredient. A Drug Era is not the same be exposed to a particular active ingredient. A Drug Era is not the same
@ -11062,6 +11078,8 @@ as a Drug Exposure: Exposures are individual records corresponding to
the source when Drug was delivered to the Person, while successive the source when Drug was delivered to the Person, while successive
periods of Drug Exposures are combined under certain rules to produce periods of Drug Exposures are combined under certain rules to produce
continuous Drug Eras.</p> continuous Drug Eras.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>The SQL script for generating DRUG_ERA records can be found <a <p>The SQL script for generating DRUG_ERA records can be found <a
href="https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras">here</a>.</p> href="https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras">here</a>.</p>
@ -11157,6 +11175,9 @@ drug_concept_id
The Concept Id representing the specific drug ingredient. The Concept Id representing the specific drug ingredient.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
The drug_concept_id should conform to the concept class ‘ingredient’ as
the drug_era is an era of time where a person is exposed to a particular
drug ingredient.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer
@ -11306,10 +11327,12 @@ No
</table> </table>
</div> </div>
<div id="dose_era" class="section level3 tabset tabset-pills"> <div id="dose_era" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DOSE_ERA</h3> <h3 class="tabset tabset-pills">dose_era</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>A Dose Era is defined as a span of time when the Person is assumed to <p>A Dose Era is defined as a span of time when the Person is assumed to
be exposed to a constant dose of a specific active ingredient.</p> be exposed to a constant dose of a specific active ingredient.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Dose Eras will be derived from records in the DRUG_EXPOSURE table and <p>Dose Eras will be derived from records in the DRUG_EXPOSURE table and
the Dose information from the DRUG_STRENGTH table using a standardized the Dose information from the DRUG_STRENGTH table using a standardized
@ -11542,7 +11565,7 @@ No
</table> </table>
</div> </div>
<div id="condition_era" class="section level3 tabset tabset-pills"> <div id="condition_era" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONDITION_ERA</h3> <h3 class="tabset tabset-pills">condition_era</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>A Condition Era is defined as a span of time when the Person is <p>A Condition Era is defined as a span of time when the Person is
assumed to have a given condition. Similar to Drug Eras, Condition Eras assumed to have a given condition. Similar to Drug Eras, Condition Eras
@ -11562,6 +11585,8 @@ provides the appropriate treatment to resolve the condition. These two
independent doctor visits should be aggregated into one Condition independent doctor visits should be aggregated into one Condition
Era.</li> Era.</li>
</ul> </ul>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Each Condition Era corresponds to one or many Condition Occurrence <p>Each Condition Era corresponds to one or many Condition Occurrence
records that form a continuous interval. The condition_concept_id field records that form a continuous interval. The condition_concept_id field
@ -11777,7 +11802,7 @@ No
</table> </table>
</div> </div>
<div id="episode" class="section level3 tabset tabset-pills"> <div id="episode" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">EPISODE</h3> <h3 class="tabset tabset-pills">episode</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The EPISODE table aggregates lower-level clinical events <p>The EPISODE table aggregates lower-level clinical events
(VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE)
@ -11794,6 +11819,8 @@ episodes please see [article], for non-cancer episodes please see
relevant to the therapeutic area, write only those you can easily derive relevant to the therapeutic area, write only those you can easily derive
from the data. It is understood that that table is not currently from the data. It is understood that that table is not currently
expected to be comprehensive.</p> expected to be comprehensive.</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12219,7 +12246,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="episode_event" class="section level3 tabset tabset-pills"> <div id="episode_event" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">EPISODE_EVENT</h3> <h3 class="tabset tabset-pills">episode_event</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The EPISODE_EVENT table connects qualifying clinical events (such as <p>The EPISODE_EVENT table connects qualifying clinical events (such as
CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT) CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT)
@ -12362,10 +12389,14 @@ Metadata
<div id="metadata-tables" class="section level2"> <div id="metadata-tables" class="section level2">
<h2><strong>Metadata Tables</strong></h2> <h2><strong>Metadata Tables</strong></h2>
<div id="metadata" class="section level3 tabset tabset-pills"> <div id="metadata" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">METADATA</h3> <h3 class="tabset tabset-pills">metadata</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The METADATA table contains metadata information about a dataset that <p>The METADATA table contains metadata information about a dataset that
has been transformed to the OMOP Common Data Model.</p> has been transformed to the OMOP Common Data Model.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12636,11 +12667,15 @@ No
</table> </table>
</div> </div>
<div id="cdm_source" class="section level3 tabset tabset-pills"> <div id="cdm_source" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CDM_SOURCE</h3> <h3 class="tabset tabset-pills">cdm_source</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CDM_SOURCE table contains detail about the source database and <p>The CDM_SOURCE table contains detail about the source database and
the process used to transform the data into the OMOP Common Data the process used to transform the data into the OMOP Common Data
Model.</p> Model.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -12970,7 +13005,7 @@ No
<div id="vocabulary-tables" class="section level2"> <div id="vocabulary-tables" class="section level2">
<h2><strong>Vocabulary Tables</strong></h2> <h2><strong>Vocabulary Tables</strong></h2>
<div id="concept" class="section level3 tabset tabset-pills"> <div id="concept" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT</h3> <h3 class="tabset tabset-pills">concept</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The Standardized Vocabularies contains records, or Concepts, that <p>The Standardized Vocabularies contains records, or Concepts, that
uniquely identify each fundamental unit of meaning used to express uniquely identify each fundamental unit of meaning used to express
@ -12992,6 +13027,10 @@ associated morphology, etc.).</p>
national or international vocabularies such as SNOMED-CT, RxNorm, and national or international vocabularies such as SNOMED-CT, RxNorm, and
LOINC, or custom Concepts defined to cover various aspects of LOINC, or custom Concepts defined to cover various aspects of
observational data analysis.</p> observational data analysis.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13307,13 +13346,17 @@ No
</table> </table>
</div> </div>
<div id="vocabulary" class="section level3 tabset tabset-pills"> <div id="vocabulary" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">VOCABULARY</h3> <h3 class="tabset tabset-pills">vocabulary</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The VOCABULARY table includes a list of the Vocabularies collected <p>The VOCABULARY table includes a list of the Vocabularies collected
from various sources or created de novo by the OMOP community. This from various sources or created de novo by the OMOP community. This
reference table is populated with a single record for each Vocabulary reference table is populated with a single record for each Vocabulary
source and includes a descriptive name and other associated attributes source and includes a descriptive name and other associated attributes
for the Vocabulary.</p> for the Vocabulary.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13486,7 +13529,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="domain" class="section level3 tabset tabset-pills"> <div id="domain" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DOMAIN</h3> <h3 class="tabset tabset-pills">domain</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The DOMAIN table includes a list of OMOP-defined Domains the Concepts <p>The DOMAIN table includes a list of OMOP-defined Domains the Concepts
of the Standardized Vocabularies can belong to. A Domain defines the set of the Standardized Vocabularies can belong to. A Domain defines the set
@ -13496,6 +13539,10 @@ condition of a patient, and these Concepts can only be stored in the
condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA
tables. This reference table is populated with a single record for each tables. This reference table is populated with a single record for each
Domain and includes a descriptive name for the Domain.</p> Domain and includes a descriptive name for the Domain.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13613,12 +13660,16 @@ CONCEPT
</table> </table>
</div> </div>
<div id="concept_class" class="section level3 tabset tabset-pills"> <div id="concept_class" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT_CLASS</h3> <h3 class="tabset tabset-pills">concept_class</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CONCEPT_CLASS table is a reference table, which includes a list <p>The CONCEPT_CLASS table is a reference table, which includes a list
of the classifications used to differentiate Concepts within a given of the classifications used to differentiate Concepts within a given
Vocabulary. This reference table is populated with a single record for Vocabulary. This reference table is populated with a single record for
each Concept Class.</p> each Concept Class.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13737,12 +13788,16 @@ CONCEPT
</div> </div>
<div id="concept_relationship" <div id="concept_relationship"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT_RELATIONSHIP</h3> <h3 class="tabset tabset-pills">concept_relationship</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CONCEPT_RELATIONSHIP table contains records that define direct <p>The CONCEPT_RELATIONSHIP table contains records that define direct
relationships between any two Concepts and the nature or type of the relationships between any two Concepts and the nature or type of the
relationship. Each type of a relationship is defined in the RELATIONSHIP relationship. Each type of a relationship is defined in the RELATIONSHIP
table.</p> table.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -13941,11 +13996,15 @@ No
</table> </table>
</div> </div>
<div id="relationship" class="section level3 tabset tabset-pills"> <div id="relationship" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">RELATIONSHIP</h3> <h3 class="tabset tabset-pills">relationship</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The RELATIONSHIP table provides a reference list of all types of <p>The RELATIONSHIP table provides a reference list of all types of
relationships that can be used to associate any two concepts in the relationships that can be used to associate any two concepts in the
CONCEPT_RELATIONSHP table.</p> CONCEPT_RELATIONSHP table.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -14145,10 +14204,14 @@ CONCEPT
</table> </table>
</div> </div>
<div id="concept_synonym" class="section level3 tabset tabset-pills"> <div id="concept_synonym" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT_SYNONYM</h3> <h3 class="tabset tabset-pills">concept_synonym</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CONCEPT_SYNONYM table is used to store alternate names and <p>The CONCEPT_SYNONYM table is used to store alternate names and
descriptions for Concepts.</p> descriptions for Concepts.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -14263,7 +14326,7 @@ CONCEPT
</table> </table>
</div> </div>
<div id="concept_ancestor" class="section level3 tabset tabset-pills"> <div id="concept_ancestor" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">CONCEPT_ANCESTOR</h3> <h3 class="tabset tabset-pills">concept_ancestor</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The CONCEPT_ANCESTOR table is designed to simplify observational <p>The CONCEPT_ANCESTOR table is designed to simplify observational
analysis by providing the complete hierarchical relationships between analysis by providing the complete hierarchical relationships between
@ -14278,6 +14341,10 @@ descendants of a hierarchical concept. For example, drug ingredients and
drug products are all descendants of a drug class ancestor.</p> drug products are all descendants of a drug class ancestor.</p>
<p>This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP <p>This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP
and RELATIONSHIP tables.</p> and RELATIONSHIP tables.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -14428,7 +14495,7 @@ No
</div> </div>
<div id="source_to_concept_map" <div id="source_to_concept_map"
class="section level3 tabset tabset-pills"> class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">SOURCE_TO_CONCEPT_MAP</h3> <h3 class="tabset tabset-pills">source_to_concept_map</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The source to concept map table is a legacy data structure within the <p>The source to concept map table is a legacy data structure within the
OMOP Common Data Model, recommended for use in ETL processes to maintain OMOP Common Data Model, recommended for use in ETL processes to maintain
@ -14438,6 +14505,10 @@ code into a Standard Concept as target_concept_ids that can be used to
populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table
is no longer populated with content within the Standardized Vocabularies is no longer populated with content within the Standardized Vocabularies
published to the OMOP community.</p> published to the OMOP community.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -14722,12 +14793,16 @@ No
</table> </table>
</div> </div>
<div id="drug_strength" class="section level3 tabset tabset-pills"> <div id="drug_strength" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">DRUG_STRENGTH</h3> <h3 class="tabset tabset-pills">drug_strength</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The DRUG_STRENGTH table contains structured content about the amount <p>The DRUG_STRENGTH table contains structured content about the amount
or concentration and associated units of a specific ingredient contained or concentration and associated units of a specific ingredient contained
within a particular drug product. This table is supplemental information within a particular drug product. This table is supplemental information
to support standardized analysis of drug utilization.</p> to support standardized analysis of drug utilization.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>
@ -15095,7 +15170,7 @@ No
</table> </table>
</div> </div>
<div id="cohort" class="section level3 tabset tabset-pills"> <div id="cohort" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">COHORT</h3> <h3 class="tabset tabset-pills">cohort</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The COHORT table contains records of subjects that satisfy a given <p>The COHORT table contains records of subjects that satisfy a given
set of criteria for a duration of time. The definition of the cohort is set of criteria for a duration of time. The definition of the cohort is
@ -15105,6 +15180,8 @@ well as tools such as ATLAS need to be able to write to. The CDM and
Vocabulary tables are all read-only so it is suggested that the COHORT Vocabulary tables are all read-only so it is suggested that the COHORT
and COHORT_DEFINTION tables are kept in a separate schema to alleviate and COHORT_DEFINTION tables are kept in a separate schema to alleviate
confusion.</p> confusion.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p> <p><strong>ETL Conventions</strong></p>
<p>Cohorts typically include patients diagnosed with a specific <p>Cohorts typically include patients diagnosed with a specific
condition, patients exposed to a particular drug, but can also be condition, patients exposed to a particular drug, but can also be
@ -15256,7 +15333,7 @@ No
</table> </table>
</div> </div>
<div id="cohort_definition" class="section level3 tabset tabset-pills"> <div id="cohort_definition" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">COHORT_DEFINITION</h3> <h3 class="tabset tabset-pills">cohort_definition</h3>
<p><strong>Table Description</strong></p> <p><strong>Table Description</strong></p>
<p>The COHORT_DEFINITION table contains records defining a Cohort <p>The COHORT_DEFINITION table contains records defining a Cohort
derived from the data through the associated description and syntax and derived from the data through the associated description and syntax and
@ -15267,6 +15344,10 @@ provides a standardized structure for maintaining the rules governing
the inclusion of a subject into a cohort, and can store operational the inclusion of a subject into a cohort, and can store operational
programming code to instantiate the cohort within the OMOP Common Data programming code to instantiate the cohort within the OMOP Common Data
Model.</p> Model.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;"> <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead> <thead>
<tr> <tr>

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@ -0,0 +1,12 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

2
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@ -316,7 +316,7 @@ cost,drg_concept_id,No,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
cost,drg_source_value,No,varchar(3),Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups.,NA,No,No,NA,NA,NA,NA,NA cost,drg_source_value,No,varchar(3),Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups.,NA,No,No,NA,NA,NA,NA,NA
drug_era,drug_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA drug_era,drug_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA
drug_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA drug_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
drug_era,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,NA,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,NA drug_era,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,The drug_concept_id should conform to the concept class 'ingredient' as the drug_era is an era of time where a person is exposed to a particular drug ingredient.,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,NA
drug_era,drug_era_start_date,Yes,date,NA,"The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure.",No,No,NA,NA,NA,NA,NA drug_era,drug_era_start_date,Yes,date,NA,"The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure.",No,No,NA,NA,NA,NA,NA
drug_era,drug_era_end_date,Yes,date,NA,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules: drug_era,drug_era_end_date,Yes,date,NA,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:
For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information. For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information.

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
316 cdm_source cdm_source_abbreviation No varchar(25) The abbreviation of the CDM instance. NA No No NA NA NA NA NA
317 cdm_source cdm_holder No varchar(255) The holder of the CDM instance. NA No No NA NA NA NA NA
318 cdm_source source_description No varchar(MAX) The description of the CDM instance. NA No No NA NA NA NA NA
319 cdm_source source_documentation_reference No varchar(255) NA NA No No NA NA NA NA NA
320 cdm_source cdm_etl_reference No varchar(255) NA Put the link to the CDM version used. No No NA NA NA NA NA
321 cdm_source source_release_date No date The release date of the source data. NA No No NA NA NA NA NA
322 cdm_source cdm_release_date No date The release data of the CDM instance. NA No No NA NA NA NA NA

2
inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -334,7 +334,7 @@ cost,drg_concept_id,No,integer,NA,NA,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
cost,drg_source_value,No,varchar(3),Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups.,NA,No,No,NA,NA,NA,NA,NA cost,drg_source_value,No,varchar(3),Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups.,NA,No,No,NA,NA,NA,NA,NA
drug_era,drug_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA drug_era,drug_era_id,Yes,integer,NA,NA,Yes,No,NA,NA,NA,NA,NA
drug_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA drug_era,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
drug_era,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,NA,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,NA drug_era,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,The drug_concept_id should conform to the concept class 'ingredient' as the drug_era is an era of time where a person is exposed to a particular drug ingredient.,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient,NA
drug_era,drug_era_start_date,Yes,date,NA,"The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure.",No,No,NA,NA,NA,NA,NA drug_era,drug_era_start_date,Yes,date,NA,"The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure.",No,No,NA,NA,NA,NA,NA
drug_era,drug_era_end_date,Yes,date,NA,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules: drug_era,drug_era_end_date,Yes,date,NA,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:
For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information. For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information.

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
334 episode episode_number No integer For sequences of episodes, this is used to indicate the order the episodes occurred. For example, lines of treatment could be indicated here. Please see [article] for the details of how to count episodes. No No NA NA NA NA NA
335 episode episode_object_concept_id Yes integer A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists. For example, if the EPISODE_CONCEPT_ID is [treatment regimen](https://athena.ohdsi.org/search-terms/terms/32531) then the EPISODE_OBJECT_CONCEPT_ID should contain the chemotherapy regimen concept, like [Afatinib monotherapy](https://athena.ohdsi.org/search-terms/terms/35804392). Episode entries from the 'Disease Episode' concept class should have an episode_object_concept_id that comes from the Condition domain. Episode entries from the 'Treatment Episode' concept class should have an episode_object_concept_id that scome from the 'Procedure' domain or 'Regimen' concept class. No Yes CONCEPT CONCEPT_ID Procedure, Regimen NA NA
336 episode episode_type_concept_id Yes integer This field can be used to determine the provenance of the Episode record, as in whether the episode was from an EHR system, insurance claim, registry, or other sources. Choose the EPISODE_TYPE_CONCEPT_ID that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept NA NA
337 episode episode_source_value No varchar(50) The source code for the Episdoe as it appears in the source data. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. NA No No NA NA NA NA NA
338 episode episode_source_concept_id No integer A foreign key to a Episode Concept that refers to the code used in the source. Given that the Episodes are user-defined it is unlikely that there will be a Source Concept available. If that is the case then set this field to zero. No Yes CONCEPT CONCEPT_ID NA NA NA
339 episode_event episode_id Yes integer Use this field to link the EPISODE_EVENT record to its EPISODE. Put the EPISODE_ID that subsumes the EPISODE_EVENT record here. No Yes EPISODE EPISODE_ID NA NA NA
340 episode_event event_id Yes integer This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the CONDITION_OCCURRENCE_ID of the linked record goes in this field. Put the primary key of the linked record here. No No NA NA NA NA NA

20
rmd/cdm53.Rmd
View File

@ -5,6 +5,9 @@ output:
toc: yes toc: yes
toc_depth: 5 toc_depth: 5
toc_float: yes toc_float: yes
pdf_document:
toc: yes
toc_depth: 5
--- ---
```{r setup, include=FALSE, eval=TRUE} ```{r setup, include=FALSE, eval=TRUE}
@ -23,11 +26,6 @@ Below is the specification document for the OMOP Common Data Model, v5.3 (previo
*__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.* *__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'} ```{r docLoop53, echo=FALSE, results='asis'}
tableSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3_Table_Level.csv", stringsAsFactors = FALSE) 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) cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3_Field_Level.csv", stringsAsFactors = FALSE)
@ -51,26 +49,26 @@ cdmSpecsClean[is.na(cdmSpecsClean)] <- ""
for(tb in tables) { for(tb in tables) {
if(tb == 'PERSON'){ if(tb == 'person'){
cat("## **Clinical Data Tables**\n\n") cat("## **Clinical Data Tables**\n\n")
} }
if(tb == 'LOCATION'){ if(tb == 'location'){
cat("## **Health System Data Tables**\n\n") cat("## **Health System Data Tables**\n\n")
} }
if(tb == 'PAYER_PLAN_PERIOD'){ if(tb == 'payer_plan_period'){
cat("## **Health Economics Data Tables**\n\n") cat("## **Health Economics Data Tables**\n\n")
} }
if(tb == 'DRUG_ERA'){ if(tb == 'drug_era'){
cat("## **Standardized Derived Elements**\n\n") cat("## **Standardized Derived Elements**\n\n")
} }
if(tb == 'METADATA'){ if(tb == 'metadata'){
cat("## **Metadata Tables**\n\n") cat("## **Metadata Tables**\n\n")
} }
if(tb == 'CONCEPT'){ if(tb == 'concept'){
cat("## **Vocabulary Tables**\n\n") cat("## **Vocabulary Tables**\n\n")
} }

30
rmd/cdm54.Rmd
View File

@ -23,20 +23,20 @@ This is the specification document for the OMOP Common Data Model, v5.4. **This
### Current Support for CDM v5.4 ### Current Support for CDM v5.4
The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green check `r emo::ji("white heavy check mark")` indicates that the support level for the listed tool is in place, has been tested, and released. A warning sign `r emo::ji("warning")` indicates that the support level for the listed tool has been initiated but has not yet been tested and released. The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green check `r emoji::emoji('check_mark_button')` indicates that the support level for the listed tool is in place, has been tested, and released. A warning sign `r emoji::emoji('warning')` indicates that the support level for the listed tool has been initiated but has not yet been tested and released.
<br> <br>
|**Tool**|**Description**|**Legacy Support**|**Feature Support**| |**Tool**|**Description**|**Legacy Support**|**Feature Support**|
|--|--|--|--| |--|--|--|--|
|**CDM R package**|This package can be downloaded from [https://github.com/OHDSI/CommonDataModel/](https://github.com/OHDSI/CommonDataModel/). It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. |`r emo::ji("white heavy check mark")`|`r emo::ji("white heavy check mark")` |**CDM R package**|This package can be downloaded from [https://github.com/OHDSI/CommonDataModel/](https://github.com/OHDSI/CommonDataModel/). It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. |`r emoji::emoji('check_mark_button')`|`r emoji::emoji('check_mark_button')`
|**Data Quality Dashboard**|This package can be downloaded from [https://github.com/OHDSI/DataQualityDashboard](https://github.com/OHDSI/DataQualityDashboard). It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.|`r emo::ji("white heavy check mark")`| `r emo::ji("warning")` |**Data Quality Dashboard**|This package can be downloaded from [https://github.com/OHDSI/DataQualityDashboard](https://github.com/OHDSI/DataQualityDashboard). It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.|`r emoji::emoji('check_mark_button')`| `r emoji::emoji('warning')`
|**Achilles**|This package can be downloaded from [https://github.com/OHDSI/Achilles](https://github.com/OHDSI/Achilles), performing a set of broad database characterizations agains an OMOP CDM instance. |`r emo::ji("white heavy check mark")`|`r emo::ji("warning")` |**Achilles**|This package can be downloaded from [https://github.com/OHDSI/Achilles](https://github.com/OHDSI/Achilles), performing a set of broad database characterizations agains an OMOP CDM instance. |`r emoji::emoji('check_mark_button')`|`r emoji::emoji('warning')`
|**ARES**|This package can be downloaded from [https://github.com/OHDSI/Ares](https://github.com/OHDSI/Ares) and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.|`r emo::ji("white heavy check mark")`|`r emo::ji("warning")` |**ARES**|This package can be downloaded from [https://github.com/OHDSI/Ares](https://github.com/OHDSI/Ares) and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.|`r emoji::emoji('check_mark_button')`|`r emoji::emoji('warning')`
|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](http://atlas-demo.ohdsi.org/) |`r emo::ji("white heavy check mark")`|`r emo::ji("warning")` |**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](http://atlas-demo.ohdsi.org/) |`r emoji::emoji('check_mark_button')`|`r emoji::emoji('warning')`
|**Rabbit-In-A-Hat**|This package can be downloaded from [https://github.com/OHDSI/WhiteRabbit](https://github.com/OHDSI/WhiteRabbit) and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.|`r emo::ji("white heavy check mark")`|`r emo::ji("white heavy check mark")` |**Rabbit-In-A-Hat**|This package can be downloaded from [https://github.com/OHDSI/WhiteRabbit](https://github.com/OHDSI/WhiteRabbit) and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.|`r emoji::emoji('check_mark_button')`|`r emoji::emoji('check_mark_button')`
|**Feature Extraction**|This package can be downloaded from [https://github.com/OHDSI/FeatureExtraction](https://github.com/OHDSI/FeatureExtraction). It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. |`r emo::ji("white heavy check mark")`|`r emo::ji("white heavy check mark")`* |**Feature Extraction**|This package can be downloaded from [https://github.com/OHDSI/FeatureExtraction](https://github.com/OHDSI/FeatureExtraction). It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. |`r emoji::emoji('check_mark_button')`|`r emoji::emoji('check_mark_button')`*
|**Cohort Diagnostics**|This package can be downloaded from [https://github.com/OHDSI/CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) and is used to critically evaluate cohort phenotypes. |`r emo::ji("white heavy check mark")`|`r emo::ji("warning")` |**Cohort Diagnostics**|This package can be downloaded from [https://github.com/OHDSI/CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) and is used to critically evaluate cohort phenotypes. |`r emoji::emoji('check_mark_button')`|`r emoji::emoji('warning')`
<br> <br>
\* The **Feature Extraction** package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates. \* The **Feature Extraction** package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates.
@ -67,26 +67,26 @@ cdmSpecsClean[is.na(cdmSpecsClean)] <- ""
for(tb in tables) { for(tb in tables) {
if(tb == 'PERSON'){ if(tb == 'person'){
cat("## **Clinical Data Tables**\n\n") cat("## **Clinical Data Tables**\n\n")
} }
if(tb == 'LOCATION'){ if(tb == 'location'){
cat("## **Health System Data Tables**\n\n") cat("## **Health System Data Tables**\n\n")
} }
if(tb == 'PAYER_PLAN_PERIOD'){ if(tb == 'payer_plan_period'){
cat("## **Health Economics Data Tables**\n\n") cat("## **Health Economics Data Tables**\n\n")
} }
if(tb == 'DRUG_ERA'){ if(tb == 'drug_era'){
cat("## **Standardized Derived Elements**\n\n") cat("## **Standardized Derived Elements**\n\n")
} }
if(tb == 'METADATA'){ if(tb == 'metadata'){
cat("## **Metadata Tables**\n\n") cat("## **Metadata Tables**\n\n")
} }
if(tb == 'CONCEPT'){ if(tb == 'concept'){
cat("## **Vocabulary Tables**\n\n") cat("## **Vocabulary Tables**\n\n")
} }