OMOP/docs/cdm54ToolingSupport.html

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<h1 class="title toc-ignore"><strong>OMOP CDM v5.4 Detailed Tooling
Support</strong></h1>
</div>
<div id="introduction" class="section level1">
<h1>Introduction</h1>
<p>This tables below contain an overview of which standard OHDSI tools
make use of which OMOP CDM fields. The goal is to inform ETL developers,
tooling developers and CDM extensions.</p>
<ul>
<li>For ETL developers it helps to have guidance on which fields to
prioritise in the mapping. Most value will be gained from populating
fields support across the OHDSI tooling.</li>
<li>For OHDSI tooling developers, this page provides insight in the gaps
of support and can drive future development efforts.</li>
<li>For CDM extensions, it helps to known what it means for an OMOP CDM
table/field to be part of the standard. In other words: what OHDSI
tooling do we at least expect to support the new extensions?</li>
</ul>
<p>Currently four OHDSI tools have been evaluated: DataQualityDashboard,
Achilles, Atlas (Data Sources and Cohort creation) and Feature
Extraction.</p>
<div id="criteria" class="section level2">
<h2>Criteria</h2>
<table>
<colgroup>
<col width="33%" />
<col width="33%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th>Tool</th>
<th>Supports CDM Field if</th>
<th>Link to resource used</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>DataQualityDashboard</td>
<td>Part of Field Level checks</td>
<td><a
href="https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv"
class="uri">https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv</a></td>
</tr>
<tr class="even">
<td>Achilles</td>
<td>Covered by at least one Achilles analysis</td>
<td><a
href="https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv"
class="uri">https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv</a></td>
</tr>
<tr class="odd">
<td>Atlas Data Sources</td>
<td>A statistic based on the field is shown in a Data Sources
visualisation</td>
<td><a href="https://atlas-demo.ohdsi.org/"
class="uri">https://atlas-demo.ohdsi.org/</a></td>
</tr>
<tr class="even">
<td>Atlas Cohort</td>
<td>Used in te Atlas User Interface for cohort definition criteria
(directly, or via Add attribute)</td>
<td><a href="https://atlas-demo.ohdsi.org/"
class="uri">https://atlas-demo.ohdsi.org/</a></td>
</tr>
<tr class="odd">
<td>Feature Extraction</td>
<td>Used in one of the Feature Extraction analyses</td>
<td><a
href="https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/"
class="uri">https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/</a></td>
</tr>
</tbody>
</table>
<p>General criteria: - ✔️ if the field essential for OMOP CDM definition
(Primary Key, Foreign Key) e.g. person_id not explicitly used, but
essential. (if the PK is marked as False, it typically means the whole
table is not used in the tool e.g. <code>_source_value</code> fields
that are used for traceability in ETL) - ❗ if field is used by the
tool, but not in a meaningful way. e.g. <code>provider_id</code> in
Achilles only checked for a valid foreign key to the provider table.</p>
</div>
</div>
<div id="tooling-support-for-omop-fields" class="section level1">
<h1>Tooling Support for OMOP fields</h1>
<table>
<colgroup>
<col width="50%" />
<col width="50%" />
</colgroup>
<thead>
<tr class="header">
<th><strong>Abbreviations</strong></th>
<th> </th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><strong>PK</strong></td>
<td>Primary Key</td>
</tr>
<tr class="even">
<td><strong>SV</strong></td>
<td>Source Value (for data quality / etl validation)</td>
</tr>
<tr class="odd">
<td><strong>BC</strong></td>
<td>Backwards Compatibility, to support CDM &lt;v5.4</td>
</tr>
<tr class="even">
<td><strong>FC</strong></td>
<td>Forwards Compatibility, to easy support for CDM v6 in the
future.</td>
</tr>
</tbody>
</table>
<div id="person" class="section level2">
<h2>Person</h2>
<table>
<colgroup>
<col width="6%" />
<col width="6%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="6%" />
</colgroup>
<thead>
<tr class="header">
<th>cdmTableName</th>
<th>cdmFieldName</th>
<th align="center">Special Fields</th>
<th align="center">DQD (v1.0)</th>
<th align="center">Achilles (v1.7)</th>
<th align="center">Atlas Cohort (v2.10)</th>
<th align="center">Atlas Cohort (v2.12)</th>
<th align="center">Atlas Data Sources (v2.12)</th>
<th align="center">Feature Extraction (v3.2)</th>
<th>Comment</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>PERSON</td>
<td>person_id</td>
<td align="center">PK</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>gender_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="odd">
<td>PERSON</td>
<td>year_of_birth</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>month_of_birth</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>PERSON</td>
<td>day_of_birth</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>birth_datetime</td>
<td align="center">FC</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>PERSON</td>
<td>race_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>ethnicity_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="odd">
<td>PERSON</td>
<td>location_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td>Achilles only does FK check</td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>provider_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td>Achilles only does FK check</td>
</tr>
<tr class="odd">
<td>PERSON</td>
<td>care_site_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td>Achilles only does FK check</td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>person_source_value</td>
<td align="center">SV</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>PERSON</td>
<td>gender_source_value</td>
<td align="center">SV</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>gender_source_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>PERSON</td>
<td>race_source_value</td>
<td align="center">SV</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>race_source_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>PERSON</td>
<td>ethnicity_source_value</td>
<td align="center">SV</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>PERSON</td>
<td>ethnicity_source_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
</tbody>
</table>
</div>
<div id="observation-period" class="section level2">
<h2>Observation Period</h2>
<table>
<colgroup>
<col width="6%" />
<col width="6%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="6%" />
</colgroup>
<thead>
<tr class="header">
<th>cdmTableName</th>
<th>cdmFieldName</th>
<th align="center">Special Fields</th>
<th align="center">DQD (v1.0)</th>
<th align="center">Achilles (v1.7)</th>
<th align="center">Atlas Cohort (v2.10)</th>
<th align="center">Atlas Cohort (v2.12)</th>
<th align="center">Atlas Data Sources (v2.12)</th>
<th align="center">Feature Extraction (v3.2)</th>
<th>Comment</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>OBSERVATION_PERIOD</td>
<td>observation_period_id</td>
<td align="center">PK</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="even">
<td>OBSERVATION_PERIOD</td>
<td>person_id</td>
<td align="center">Pid</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="odd">
<td>OBSERVATION_PERIOD</td>
<td>observation_period_start_date</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="even">
<td>OBSERVATION_PERIOD</td>
<td>observation_period_end_date</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="odd">
<td>OBSERVATION_PERIOD</td>
<td>period_type_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
</tbody>
</table>
</div>
<div id="visit-occurrence" class="section level2">
<h2>Visit Occurrence</h2>
<table>
<colgroup>
<col width="6%" />
<col width="6%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="6%" />
</colgroup>
<thead>
<tr class="header">
<th>cdmTableName</th>
<th>cdmFieldName</th>
<th align="center">Special Fields</th>
<th align="center">DQD (v1.0)</th>
<th align="center">Achilles (v1.7)</th>
<th align="center">Atlas Cohort (v2.10)</th>
<th align="center">Atlas Cohort (v2.12)</th>
<th align="center">Atlas Data Sources (v2.12)</th>
<th align="center">Feature Extraction (v3.2)</th>
<th>Comment</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>visit_occurrence_id</td>
<td align="center">PK</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="even">
<td>VISIT_OCCURRENCE</td>
<td>person_id</td>
<td align="center">Pid</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>visit_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="even">
<td>VISIT_OCCURRENCE</td>
<td>visit_source_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>visit_source_value</td>
<td align="center">SV</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>VISIT_OCCURRENCE</td>
<td>visit_start_date</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td>Achilles check 1900</td>
</tr>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>visit_start_datetime</td>
<td align="center">FC</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>VISIT_OCCURRENCE</td>
<td>visit_end_date</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center">✔️</td>
<td></td>
</tr>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>visit_end_datetime</td>
<td align="center">FC</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>VISIT_OCCURRENCE</td>
<td>visit_type_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>provider_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td>Atlas uses provider.specialty_concept_id</td>
</tr>
<tr class="even">
<td>VISIT_OCCURRENCE</td>
<td>care_site_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td>Achilles only does FK check, Atlas uses
care_site.place_of_service_concept_id</td>
</tr>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>admitted_from_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>VISIT_OCCURRENCE</td>
<td>admitted_from_source_value</td>
<td align="center">SV</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td>Achilles check 1900</td>
</tr>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>discharged_to_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>VISIT_OCCURRENCE</td>
<td>discharged_to_source_value</td>
<td align="center">SV</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td>Achilles check 1900</td>
</tr>
<tr class="odd">
<td>VISIT_OCCURRENCE</td>
<td>preceding_visit_occurrence_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
</tbody>
</table>
</div>
<div id="episode" class="section level2">
<h2>Episode</h2>
<table>
<colgroup>
<col width="6%" />
<col width="6%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="11%" />
<col width="6%" />
</colgroup>
<thead>
<tr class="header">
<th>cdmTableName</th>
<th>cdmFieldName</th>
<th align="center">Special Fields</th>
<th align="center">DQD (v1.0)</th>
<th align="center">Achilles (v1.7)</th>
<th align="center">Atlas Cohort (v2.10)</th>
<th align="center">Atlas Cohort (v2.12)</th>
<th align="center">Atlas Data Sources (v2.12)</th>
<th align="center">Feature Extraction (v3.2)</th>
<th>Comment</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>EPISODE</td>
<td>episode_id</td>
<td align="center">PK</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>EPISODE</td>
<td>person_id</td>
<td align="center">Pid</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>EPISODE</td>
<td>episode_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>EPISODE</td>
<td>episode_start_date</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>EPISODE</td>
<td>episode_start_datetime</td>
<td align="center">FC</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>EPISODE</td>
<td>episode_end_date</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>EPISODE</td>
<td>episode_end_datetime</td>
<td align="center">FC</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>EPISODE</td>
<td>episode_parent_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>EPISODE</td>
<td>episode_number</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>EPISODE</td>
<td>episode_object_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>EPISODE</td>
<td>episode_type_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="even">
<td>EPISODE</td>
<td>episode_source_value</td>
<td align="center">SV</td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
<tr class="odd">
<td>EPISODE</td>
<td>episode_source_concept_id</td>
<td align="center"></td>
<td align="center">✔️</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td></td>
</tr>
</tbody>
</table>
<p>This was an effort by the CDM Working Group in 2022. *Credits: Clair
Blacketer, Maxim Moinat, Nitin Park</p>
</div>
</div>
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