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fix: data model conventions dead links

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Lawrence Adams 2024-10-02 08:14:53 +01:00
parent 080816f659
commit 720b5480e9
2 changed files with 21 additions and 21 deletions
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docs/dataModelConventions.html
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@ -603,7 +603,7 @@ the same Concept between releases of the Standardized Vocabularies.</li>
<li>A descriptive name for each Concept is stored as the Concept Name as <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 part of the CONCEPT table. Additional names and descriptions for the
Concept are stored as Synonyms in the <a 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> table.</li>
<li>Each Concept is assigned to a Domain. For Standard Concepts, there <li>Each Concept is assigned to a Domain. For Standard Concepts, there
is always a single Domain. Source Concepts can be composite or is always a single Domain. Source Concepts can be composite or
@ -631,7 +631,7 @@ participate in the construction of the CONCEPT_ANCESTOR table and can be
used to identify Descendants that may appear in the data. See used to identify Descendants that may appear in the data. See
CONCEPT_ANCESTOR table. Non-standard Concepts can only appear in CONCEPT_ANCESTOR table. Non-standard Concepts can only appear in
*_source_concept_id fields and are not used in <a *_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 table. Please refer to the Standardized Vocabularies specifications for
details of the Standard Concept designation.</li> details of the Standard Concept designation.</li>
<li>The lifespan of a Concept is recorded through its valid_start_date, <li>The lifespan of a Concept is recorded through its valid_start_date,
@ -760,12 +760,12 @@ concept_id_1 and concept_id_2 fields.</li>
<li>Concept Relationships define direct relationships between Concepts. <li>Concept Relationships define direct relationships between Concepts.
Indirect relationships through 3rd Concepts are not captured in this Indirect relationships through 3rd Concepts are not captured in this
table. However, the <a 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 table does this for hierarchical relationships over several
“generations” of direct relationships.</li> “generations” of direct relationships.</li>
<li>In previous versions of the CDM, the relationship_id used to be a <li>In previous versions of the CDM, the relationship_id used to be a
numerical identifier. See the <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> table.</li>
</ul> </ul>
</div> </div>
@ -790,7 +790,7 @@ purposes of creating a closed Information Model, where all entities in
the OMOP CDM are covered by unique Concepts.</li> the OMOP CDM are covered by unique Concepts.</li>
<li>Hierarchical Relationships are used to build a hierarchical tree out <li>Hierarchical Relationships are used to build a hierarchical tree out
of the Concepts, which is recorded in the <a 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 table. For example, “has_ingredient” is a Relationship between Concept
of the Concept Class ‘Clinical Drug’ and those of ‘Ingredient’, and all of the Concept Class ‘Clinical Drug’ and those of ‘Ingredient’, and all
Ingredients can be classified as the “parental” hierarchical Concepts Ingredients can be classified as the “parental” hierarchical Concepts
@ -806,16 +806,16 @@ same Vocabulary or those adopted from different Vocabulary sources.</li>
<li>The concept_synonym_name field contains a valid Synonym of a <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, including the description in the concept_name itself. I.e. each
Concept has at least one Synonym in the <a 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 table. As an example, for a SNOMED-CT Concept, if the fully specified
name is stored as the concept_name of the <a 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 table, then the Preferred Term and Synonyms associated with the Concept
are stored in the <a 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> table.</li>
<li>Only Synonyms that are active and current are stored in the <a <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 table. Tracking synonym/description history and mapping of obsolete
synonyms to current Concepts/Synonyms is out of scope for the Standard synonyms to current Concepts/Synonyms is out of scope for the Standard
Vocabularies.</li> Vocabularies.</li>
@ -827,12 +827,12 @@ Vocabularies.</li>
<ul> <ul>
<li>Each concept is also recorded as an ancestor of itself.</li> <li>Each concept is also recorded as an ancestor of itself.</li>
<li>Only valid and Standard Concepts participate in the <a <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 table. It is not possible to find ancestors or descendants of deprecated
or Source Concepts.</li> or Source Concepts.</li>
<li>Usually, only Concepts of the same Domain are connected through <li>Usually, only Concepts of the same Domain are connected through
records of the <a 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> table, but there might be exceptions.</li>
</ul> </ul>
</div> </div>

20
rmd/dataModelConventions.Rmd
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@ -42,7 +42,7 @@ corresponding Concept reference data.
- The concept_id of a Concept is persistent, i.e. stays the same for the same Concept between releases of - The concept_id of a Concept is persistent, i.e. stays the same for the same Concept between releases of
the Standardized Vocabularies. the Standardized Vocabularies.
- A descriptive name for each Concept is stored as the Concept Name as part of the CONCEPT table. Additional - 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 [CONCEPT_SYNONYM](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym) names and descriptions for the Concept are stored as Synonyms in the [CONCEPT_SYNONYM](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_synonym)
table. table.
- Each Concept is assigned to a Domain. For Standard Concepts, there is always a single Domain. Source - Each Concept is assigned to a Domain. For Standard Concepts, there is always a single Domain. Source
Concepts can be composite or coordinated entities, and therefore can belong to more than one Domain. Concepts can be composite or coordinated entities, and therefore can belong to more than one Domain.
@ -61,7 +61,7 @@ field and can be used to reference the source vocabulary.
in all *_concept_id fields, whereas Classification Concepts (‘C’) should not appear in the CDM in all *_concept_id fields, whereas Classification Concepts (‘C’) should not appear in the CDM
data, but participate in the construction of the CONCEPT_ANCESTOR table and can be used to data, but participate in the construction of the CONCEPT_ANCESTOR table and can be used to
identify Descendants that may appear in the data. See CONCEPT_ANCESTOR table. Non-standard 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 [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor) Concepts can only appear in *_source_concept_id fields and are not used in [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor)
table. Please refer to the Standardized Vocabularies specifications for details of the Standard Concept table. Please refer to the Standardized Vocabularies specifications for details of the Standard Concept
designation. designation.
- The lifespan of a Concept is recorded through its valid_start_date, valid_end_date and the invalid_ - The lifespan of a Concept is recorded through its valid_start_date, valid_end_date and the invalid_
@ -144,10 +144,10 @@ and the relationship_id replaced by the reverse_relationship_id from the RELATIO
not necessary to query for the existence of a relationship both in the concept_id_1 and concept_id_2 not necessary to query for the existence of a relationship both in the concept_id_1 and concept_id_2
fields. fields.
- Concept Relationships define direct relationships between Concepts. Indirect relationships through 3rd - Concept Relationships define direct relationships between Concepts. Indirect relationships through 3rd
Concepts are not captured in this table. However, the [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor) table does this for Concepts are not captured in this table. However, the [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor) table does this for
hierarchical relationships over several “generations” of direct relationships. hierarchical relationships over several “generations” of direct relationships.
- In previous versions of the CDM, the relationship_id used to be a numerical identifier. See the - In previous versions of the CDM, the relationship_id used to be a numerical identifier. See the
[RELATIONSHIP](https://ohdsi.github.io/CommonDataModel/cdm531.html#relationship) table. [RELATIONSHIP](https://ohdsi.github.io/CommonDataModel/cdm54.html#relationship) table.
### Relationship Table ### Relationship Table
- There is one record for each Relationship. - There is one record for each Relationship.
@ -163,7 +163,7 @@ Relationship is provided in the reverse_relationship_id field.
concept_id field. This is for purposes of creating a closed Information Model, where all entities in concept_id field. This is for purposes of creating a closed Information Model, where all entities in
the OMOP CDM are covered by unique Concepts. the OMOP CDM are covered by unique Concepts.
- Hierarchical Relationships are used to build a hierarchical tree out of the Concepts, which is recorded in - Hierarchical Relationships are used to build a hierarchical tree out of the Concepts, which is recorded in
the [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor) table. For example, “has_ingredient” is a Relationship between Concept the [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor) 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 of the Concept Class ‘Clinical Drug’ and those of ‘Ingredient’, and all Ingredients can be classified as
the “parental” hierarchical Concepts for the drug products they are part of. All ‘Is a’ Relationships are the “parental” hierarchical Concepts for the drug products they are part of. All ‘Is a’ Relationships are
hierarchical. hierarchical.
@ -172,19 +172,19 @@ from different Vocabulary sources.
### Concept Synonyms ### Concept Synonyms
- The concept_synonym_name field contains a valid Synonym of a concept, including the description in - 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 [CONCEPT_SYNONYM](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym) the concept_name itself. I.e. each Concept has at least one Synonym in the [CONCEPT_SYNONYM](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_synonym)
table. As an example, for a SNOMED-CT Concept, if the fully specified name is stored as the table. As an example, for a SNOMED-CT Concept, if the fully specified name is stored as the
concept_name of the [CONCEPT](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept) table, then the Preferred Term and Synonyms associated with the Concept are stored in the [CONCEPT_SYNONYM](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym) table. concept_name of the [CONCEPT](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept) table, then the Preferred Term and Synonyms associated with the Concept are stored in the [CONCEPT_SYNONYM](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_synonym) table.
- Only Synonyms that are active and current are stored in the [CONCEPT_SYNONYM](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym) table. Tracking - Only Synonyms that are active and current are stored in the [CONCEPT_SYNONYM](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_synonym) table. Tracking
synonym/description history and mapping of obsolete synonyms to current Concepts/Synonyms is out synonym/description history and mapping of obsolete synonyms to current Concepts/Synonyms is out
of scope for the Standard Vocabularies. of scope for the Standard Vocabularies.
- Currently, only English Synonyms are included. - Currently, only English Synonyms are included.
### Concept Ancestor ### Concept Ancestor
- Each concept is also recorded as an ancestor of itself. - Each concept is also recorded as an ancestor of itself.
- Only valid and Standard Concepts participate in the [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor) table. It is not possible - Only valid and Standard Concepts participate in the [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor) table. It is not possible
to find ancestors or descendants of deprecated or Source Concepts. to find ancestors or descendants of deprecated or Source Concepts.
- Usually, only Concepts of the same Domain are connected through records of the [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor) table, but there might be exceptions. - Usually, only Concepts of the same Domain are connected through records of the [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm54.html#concept_ancestor) table, but there might be exceptions.
### Source to Concept Map ### Source to Concept Map
- This table is no longer used to distribute mapping information between source codes and Standard - This table is no longer used to distribute mapping information between source codes and Standard