646 lines
18 KiB
HTML
646 lines
18 KiB
HTML
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<div id="header">
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<h1 class="title toc-ignore">Oncology Extension</h1>
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</div>
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<div id="omop-common-data-model-oncology-extension-documentation"
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class="section level2">
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<h2>OMOP Common Data Model Oncology Extension Documentation</h2>
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<p>This documentation details the ratified proposal of adding an
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oncology extension to the OMOP CDM. These tables and fields will become
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part of the next release (v6.1) of the Common Data Model. Below are
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their descriptions; showing <em>additions</em> to the model only. For
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example, two fields were added to the MEASUREMENT table as part of this
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extension so only those two fields are listed below for MEASUREMENT
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instead of the entire table. For more information, please see the <a
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href="https://github.com/OHDSI/OncologyWG/wiki">OMOP Oncology wiki
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site</a>.</p>
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<p>The DDLs for these tables are located on the Oncology github, as
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detailed in the <a
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href="https://github.com/OHDSI/OncologyWG/wiki/Oncology-CDM-Extension-Installation">installation
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instructions</a>.</p>
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<pre><code>## Warning in read.table(file = file, header = header, sep = sep, quote = quote, :
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## incomplete final line found by readTableHeader on
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## '../inst/csv/OMOP_CDM_Oncology_Ex_Table_Level.csv'</code></pre>
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<div id="episode" class="section level3 tabset tabset-pills">
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<h3 class="tabset tabset-pills">EPISODE</h3>
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<p><strong>Table Description</strong></p>
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<p>The EPISODE table aggregates lower-level clinical events
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(VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE)
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||
into a higher-level abstraction representing clinically and analytically
|
||
relevant disease phases,outcomes and treatments. The EPISODE_EVENT table
|
||
connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE,
|
||
PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry.
|
||
For example cancers including their development over time, their
|
||
treatment, and final resolution.</p>
|
||
<p><strong>User Guide</strong></p>
|
||
<p>Valid Episode Concepts belong to the ‘Episode’ domain. For cancer
|
||
episodes please see [article], for non-cancer episodes please see
|
||
[article]. If your source data does not have all episodes that are
|
||
relevant to the therapeutic area, write only those you can easily derive
|
||
from the data. It is understood that that table is not currently
|
||
expected to be comprehensive.</p>
|
||
</div>
|
||
<div id="episode_event" class="section level3 tabset tabset-pills">
|
||
<h3 class="tabset tabset-pills">EPISODE_EVENT</h3>
|
||
<p><strong>Table Description</strong></p>
|
||
<p>The EPISODE_EVENT table connects qualifying clinical events (such as
|
||
CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT)
|
||
to the appropriate EPISODE entry. For example, linking the precise
|
||
location of the metastasis (cancer modifier in MEASUREMENT) to the
|
||
disease episode.</p>
|
||
<p><strong>User Guide</strong></p>
|
||
<p>This connecting table is used instead of the FACT_RELATIONSHIP table
|
||
for linking low-level events to abstracted Episodes.</p>
|
||
<p><strong>ETL Conventions</strong></p>
|
||
<p>Some episodes may not have links to any underlying clinical events.
|
||
For such episodes, the EPISODE_EVENT table is not populated.</p>
|
||
</div>
|
||
<div id="measurement" class="section level3 tabset tabset-pills">
|
||
<h3 class="tabset tabset-pills">MEASUREMENT</h3>
|
||
<p><strong>Table Description</strong></p>
|
||
<p>The MEASUREMENT table contains records of Measurement,
|
||
i.e. structured values (numerical or categorical) obtained through
|
||
systematic and standardized examination or testing of a Person or
|
||
Person’s sample. The MEASUREMENT table contains both orders and results
|
||
of such Measurements as laboratory tests, vital signs, quantitative
|
||
findings from pathology reports, etc. Measurements are stored as
|
||
attribute value pairs, with the attribute as the Measurement Concept and
|
||
the value representing the result. The value can be a Concept (stored in
|
||
VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit
|
||
(UNIT_CONCEPT_ID).</p>
|
||
<p><strong>User Guide</strong></p>
|
||
<p>Measurements differ from Observations in that they require a
|
||
standardized test or some other activity to generate a quantitative or
|
||
qualitative result.</p>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
</div>
|
||
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|
||
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|
||
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