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Fix dead 5.3.1 CDM links #718

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Mar 6, 2025
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Fix dead 5.3.1 CDM links #718

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c840423
fix: dead links for 5.4 docs source csvs
lawrenceadams Oct 2, 2024
080816f
fix: deadlinks in 5.4 rendered docs
lawrenceadams Oct 2, 2024
720b548
fix: data model conventions dead links
lawrenceadams Oct 2, 2024
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24 changes: 12 additions & 12 deletions docs/cdm54.html
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Original file line number Diff line number Diff line change
Expand Up @@ -715,7 +715,7 @@ <h3 class="tabset tabset-pills">person</h3>
Use the gender or sex value present in the data under the assumption
that it is the biological sex at birth. If the source data captures
gender identity it should be stored in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#observation">OBSERVATION</a>
table. <a
href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
gender concepts</a>. Please refer to the <a
Expand Down Expand Up @@ -939,7 +939,7 @@ <h3 class="tabset tabset-pills">person</h3>
</td>
<td style="text-align:left;">
Put the location_id from the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#location">LOCATION</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#location">LOCATION</a>
table here that represents the most granular location information for
the person. For additional information on how to populate this field,
please refer to the <a
Expand Down Expand Up @@ -974,7 +974,7 @@ <h3 class="tabset tabset-pills">person</h3>
</td>
<td style="text-align:left;">
Put the provider_id from the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#provider">PROVIDER</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#provider">PROVIDER</a>
table of the last known general practitioner of the person. If there are
multiple providers, it is up to the ETL to decide which to put here.
</td>
Expand Down Expand Up @@ -1379,7 +1379,7 @@ <h3 class="tabset tabset-pills">observation_period</h3>
time period the Person is enrolled with a payer. If a Person switches
plans but stays with the same payer, and therefore capturing of data
continues, that change would be captured in <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period">PAYER_PLAN_PERIOD</a>.
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#payer_plan_period">PAYER_PLAN_PERIOD</a>.
</td>
<td style="text-align:left;">
date
Expand Down Expand Up @@ -1879,7 +1879,7 @@ <h3 class="tabset tabset-pills">visit_occurrence</h3>
If there are multiple providers associated with a visit, you will need
to choose which one to put here. The additional providers can be stored
in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#visit_detail">VISIT_DETAIL</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#visit_detail">VISIT_DETAIL</a>
table.
</td>
<td style="text-align:left;">
Expand Down Expand Up @@ -2858,21 +2858,21 @@ <h3 class="tabset tabset-pills">condition_occurrence</h3>
Record all conditions as they exist in the source data. Any decisions
about diagnosis/phenotype definitions would be done through cohort
specifications. These cohorts can be housed in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period">COHORT</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#payer_plan_period">COHORT</a>
table. Conditions span a time interval from start to end, but are
typically recorded as single snapshot records with no end date. The
reason is twofold: (i) At the time of the recording the duration is not
known and later not recorded, and (ii) the Persons typically cease
interacting with the healthcare system when they feel better, which
leads to incomplete capture of resolved Conditions. The <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#condition_era">CONDITION_ERA</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#condition_era">CONDITION_ERA</a>
table addresses this issue. Family history and past diagnoses (‘history
of’) are not recorded in this table. Instead, they are listed in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#observation">OBSERVATION</a>
table. Codes written in the process of establishing the diagnosis, such
as ‘question of’ of and ‘rule out’, should not represented here.
Instead, they should be recorded in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#observation">OBSERVATION</a>
table, if they are used for analyses. However, this information is not
always available.</p>
<p><strong>ETL Conventions</strong></p>
Expand Down Expand Up @@ -13178,7 +13178,7 @@ <h3 class="tabset tabset-pills">concept</h3>
</td>
<td style="text-align:left;">
A foreign key to the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#domain">DOMAIN</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#domain">DOMAIN</a>
table the Concept belongs to.
</td>
<td style="text-align:left;">
Expand Down Expand Up @@ -13207,7 +13207,7 @@ <h3 class="tabset tabset-pills">concept</h3>
</td>
<td style="text-align:left;">
A foreign key to the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#vocabulary">VOCABULARY</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#vocabulary">VOCABULARY</a>
table indicating from which source the Concept has been adapted.
</td>
<td style="text-align:left;">
Expand Down Expand Up @@ -14256,7 +14256,7 @@ <h3 class="tabset tabset-pills">relationship</h3>
</td>
<td style="text-align:left;">
A foreign key that refers to an identifier in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept">CONCEPT</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept">CONCEPT</a>
table for the unique relationship concept.
</td>
<td style="text-align:left;">
Expand Down
22 changes: 11 additions & 11 deletions docs/dataModelConventions.html
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Original file line number Diff line number Diff line change
Expand Up @@ -603,7 +603,7 @@ <h3>Concepts</h3>
<li>A descriptive name for each Concept is stored as the Concept Name as
part of the CONCEPT table. Additional names and descriptions for the
Concept are stored as Synonyms in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym">CONCEPT_SYNONYM</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_synonym">CONCEPT_SYNONYM</a>
table.</li>
<li>Each Concept is assigned to a Domain. For Standard Concepts, there
is always a single Domain. Source Concepts can be composite or
Expand Down Expand Up @@ -631,7 +631,7 @@ <h3>Concepts</h3>
used to identify Descendants that may appear in the data. See
CONCEPT_ANCESTOR table. Non-standard Concepts can only appear in
*_source_concept_id fields and are not used in <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor">CONCEPT_ANCESTOR</a>
table. Please refer to the Standardized Vocabularies specifications for
details of the Standard Concept designation.</li>
<li>The lifespan of a Concept is recorded through its valid_start_date,
Expand Down Expand Up @@ -760,12 +760,12 @@ <h3>Concept Relationships</h3>
<li>Concept Relationships define direct relationships between Concepts.
Indirect relationships through 3rd Concepts are not captured in this
table. However, the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor">CONCEPT_ANCESTOR</a>
table does this for hierarchical relationships over several
“generations” of direct relationships.</li>
<li>In previous versions of the CDM, the relationship_id used to be a
numerical identifier. See the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#relationship">RELATIONSHIP</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#relationship">RELATIONSHIP</a>
table.</li>
</ul>
</div>
Expand All @@ -790,7 +790,7 @@ <h3>Relationship Table</h3>
the OMOP CDM are covered by unique Concepts.</li>
<li>Hierarchical Relationships are used to build a hierarchical tree out
of the Concepts, which is recorded in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor">CONCEPT_ANCESTOR</a>
table. For example, “has_ingredient” is a Relationship between Concept
of the Concept Class ‘Clinical Drug’ and those of ‘Ingredient’, and all
Ingredients can be classified as the “parental” hierarchical Concepts
Expand All @@ -806,16 +806,16 @@ <h3>Concept Synonyms</h3>
<li>The concept_synonym_name field contains a valid Synonym of a
concept, including the description in the concept_name itself. I.e. each
Concept has at least one Synonym in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym">CONCEPT_SYNONYM</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_synonym">CONCEPT_SYNONYM</a>
table. As an example, for a SNOMED-CT Concept, if the fully specified
name is stored as the concept_name of the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept">CONCEPT</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept">CONCEPT</a>
table, then the Preferred Term and Synonyms associated with the Concept
are stored in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym">CONCEPT_SYNONYM</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_synonym">CONCEPT_SYNONYM</a>
table.</li>
<li>Only Synonyms that are active and current are stored in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym">CONCEPT_SYNONYM</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_synonym">CONCEPT_SYNONYM</a>
table. Tracking synonym/description history and mapping of obsolete
synonyms to current Concepts/Synonyms is out of scope for the Standard
Vocabularies.</li>
Expand All @@ -827,12 +827,12 @@ <h3>Concept Ancestor</h3>
<ul>
<li>Each concept is also recorded as an ancestor of itself.</li>
<li>Only valid and Standard Concepts participate in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor">CONCEPT_ANCESTOR</a>
table. It is not possible to find ancestors or descendants of deprecated
or Source Concepts.</li>
<li>Usually, only Concepts of the same Domain are connected through
records of the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor">CONCEPT_ANCESTOR</a>
table, but there might be exceptions.</li>
</ul>
</div>
Expand Down
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