From 75a9ae41ae47d678560dec01d70dcda6055c0a43 Mon Sep 17 00:00:00 2001 From: Clair Blacketer Date: Wed, 17 Apr 2024 19:59:32 -0400 Subject: [PATCH] html updates for vocab tables --- docs/cdm53.html | 2576 +---------------------------------------------- docs/cdm54.html | 2566 +--------------------------------------------- 2 files changed, 10 insertions(+), 5132 deletions(-) diff --git a/docs/cdm53.html b/docs/cdm53.html index 88d7de8..b59fa94 100644 --- a/docs/cdm53.html +++ b/docs/cdm53.html @@ -11676,2577 +11676,11 @@ derived from vocabularies, which represent clinical information across a domain (e.g. conditions, drugs, procedures) through the use of codes and associated descriptions. Some Concepts are designated Standard Concepts, meaning these Concepts can be used as normative expressions of a -clinical entity within the OMOP Common Data Model and within -standardized analytics. Each Standard Concept belongs to one domain, -which defines the location where the Concept would be expected to occur -within data tables of the CDM.

-

Concepts can represent broad categories (like ‘Cardiovascular -disease’), detailed clinical elements (‘Myocardial infarction of the -anterolateral wall’) or modifying characteristics and attributes that -define Concepts at various levels of detail (severity of a disease, -associated morphology, etc.).

-

Records in the Standardized Vocabularies tables are derived from -national or international vocabularies such as SNOMED-CT, RxNorm, and -LOINC, or custom Concepts defined to cover various aspects of -observational data analysis.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-concept_id - -A unique identifier for each Concept across all domains. - - -integer - -Yes - -Yes - -No - - -
-concept_name - -An unambiguous, meaningful and descriptive name for the Concept. - - -varchar(255) - -Yes - -No - -No - - -
-domain_id - -A foreign key to the DOMAIN -table the Concept belongs to. - - -varchar(20) - -Yes - -No - -Yes - -DOMAIN - -
-vocabulary_id - -A foreign key to the VOCABULARY -table indicating from which source the Concept has been adapted. - - -varchar(20) - -Yes - -No - -Yes - -VOCABULARY - -
-concept_class_id - -The attribute or concept class of the Concept. Examples are ‘Clinical -Drug’, ‘Ingredient’, ‘Clinical Finding’ etc. - - -varchar(20) - -Yes - -No - -Yes - -CONCEPT_CLASS - -
-standard_concept - -This flag determines where a Concept is a Standard Concept, i.e. is used -in the data, a Classification Concept, or a non-standard Source Concept. -The allowable values are ‘S’ (Standard Concept) and ‘C’ (Classification -Concept), otherwise the content is NULL. - - -varchar(1) - -No - -No - -No - - -
-concept_code - -The concept code represents the identifier of the Concept in the source -vocabulary, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that -concept codes are not unique across vocabularies. - - -varchar(50) - -Yes - -No - -No - - -
-valid_start_date - -The date when the Concept was first recorded. The default value is -1-Jan-1970, meaning, the Concept has no (known) date of inception. - - -date - -Yes - -No - -No - - -
-valid_end_date - -The date when the Concept became invalid because it was deleted or -superseded (updated) by a new concept. The default value is 31-Dec-2099, -meaning, the Concept is valid until it becomes deprecated. - - -date - -Yes - -No - -No - - -
-invalid_reason - -Reason the Concept was invalidated. Possible values are D (deleted), U -(replaced with an update) or NULL when valid_end_date has the default -value. - - -varchar(1) - -No - -No - -No - - -
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vocabulary

-

Table Description

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The VOCABULARY table includes a list of the Vocabularies collected -from various sources or created de novo by the OMOP community. This -reference table is populated with a single record for each Vocabulary -source and includes a descriptive name and other associated attributes -for the Vocabulary.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-vocabulary_id - -A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. - - -varchar(20) - -Yes - -Yes - -No - - -
-vocabulary_name - -The name describing the vocabulary, for example, International -Classification of Diseases, Ninth Revision, Clinical Modification, -Volume 1 and 2 (NCHS) etc. - - -varchar(255) - -Yes - -No - -No - - -
-vocabulary_reference - -External reference to documentation or available download of the about -the vocabulary. - - -varchar(255) - -Yes - -No - -No - - -
-vocabulary_version - -Version of the Vocabulary as indicated in the source. - - -varchar(255) - -No - -No - -No - - -
-vocabulary_concept_id - -A Concept that represents the Vocabulary the VOCABULARY record belongs -to. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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domain

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Table Description

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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 allowable Concepts for the standardized fields in the CDM tables. For -example, the “Condition” Domain contains Concepts that describe a -condition of a patient, and these Concepts can only be stored in the -condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA -tables. This reference table is populated with a single record for each -Domain and includes a descriptive name for the Domain.

-

User Guide

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NA

-

ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-domain_id - -A unique key for each domain. - - -varchar(20) - -Yes - -Yes - -No - - -
-domain_name - -The name describing the Domain, e.g. Condition, Procedure, Measurement -etc. - - -varchar(255) - -Yes - -No - -No - - -
-domain_concept_id - -A Concept representing the Domain Concept the DOMAIN record belongs to. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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concept_class

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Table Description

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The CONCEPT_CLASS table is a reference table, which includes a list -of the classifications used to differentiate Concepts within a given -Vocabulary. This reference table is populated with a single record for -each Concept Class.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-concept_class_id - -A unique key for each class. - - -varchar(20) - -Yes - -Yes - -No - - -
-concept_class_name - -The name describing the Concept Class, e.g. Clinical Finding, -Ingredient, etc. - - -varchar(255) - -Yes - -No - -No - - -
-concept_class_concept_id - -A Concept that represents the Concept Class. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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concept_relationship

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Table Description

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The CONCEPT_RELATIONSHIP table contains records that define direct -relationships between any two Concepts and the nature or type of the -relationship. Each type of a relationship is defined in the RELATIONSHIP -table.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-concept_id_1 - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-concept_id_2 - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-relationship_id - -The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see the -Vocabulary -Conventions. for more information. - - -varchar(20) - -Yes - -No - -Yes - -RELATIONSHIP - -
-valid_start_date - -The date when the relationship is first recorded. - - -date - -Yes - -No - -No - - -
-valid_end_date - -The date when the relationship is invalidated. - - -date - -Yes - -No - -No - - -
-invalid_reason - -Reason the relationship was invalidated. Possible values are ‘D’ -(deleted), ‘U’ (updated) or NULL. - - -varchar(1) - -No - -No - -No - - -
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relationship

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Table Description

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The RELATIONSHIP table provides a reference list of all types of -relationships that can be used to associate any two concepts in the -CONCEPT_RELATIONSHP table.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-relationship_id - -The type of relationship captured by the relationship record. - - -varchar(20) - -Yes - -Yes - -No - - -
-relationship_name - - - -varchar(255) - -Yes - -No - -No - - -
-is_hierarchical - -Defines whether a relationship defines concepts into classes or -hierarchies. Values are 1 for hierarchical relationship or 0 if not. - - -varchar(1) - -Yes - -No - -No - - -
-defines_ancestry - -Defines whether a hierarchical relationship contributes to the -concept_ancestor table. These are subsets of the hierarchical -relationships. Valid values are 1 or 0. - - -varchar(1) - -Yes - -No - -No - - -
-reverse_relationship_id - -The identifier for the relationship used to define the reverse -relationship between two concepts. - - -varchar(20) - -Yes - -No - -No - - -
-relationship_concept_id - -A foreign key that refers to an identifier in the CONCEPT -table for the unique relationship concept. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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concept_synonym

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Table Description

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The CONCEPT_SYNONYM table is used to store alternate names and -descriptions for Concepts.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-concept_synonym_name - - - -varchar(1000) - -Yes - -No - -No - - -
-language_concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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concept_ancestor

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Table Description

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The CONCEPT_ANCESTOR table is designed to simplify observational -analysis by providing the complete hierarchical relationships between -Concepts. Only direct parent-child relationships between Concepts are -stored in the CONCEPT_RELATIONSHIP table. To determine higher level -ancestry connections, all individual direct relationships would have to -be navigated at analysis time. The CONCEPT_ANCESTOR table includes -records for all parent-child relationships, as well as -grandparent-grandchild relationships and those of any other level of -lineage. Using the CONCEPT_ANCESTOR table allows for querying for all -descendants of a hierarchical concept. For example, drug ingredients and -drug products are all descendants of a drug class ancestor.

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This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP -and RELATIONSHIP tables.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-ancestor_concept_id - -The Concept Id for the higher-level concept that forms the ancestor in -the relationship. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-descendant_concept_id - -The Concept Id for the lower-level concept that forms the descendant in -the relationship. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-min_levels_of_separation - -The minimum separation in number of levels of hierarchy between ancestor -and descendant concepts. This is an attribute that is used to simplify -hierarchic analysis. - - -integer - -Yes - -No - -No - - -
-max_levels_of_separation - -The maximum separation in number of levels of hierarchy between ancestor -and descendant concepts. This is an attribute that is used to simplify -hierarchic analysis. - - -integer - -Yes - -No - -No - - -
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source_to_concept_map

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Table Description

-

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 -local source codes which are not available as Concepts in the -Standardized Vocabularies, and to establish mappings for each source -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 -is no longer populated with content within the Standardized Vocabularies -published to the OMOP community.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-source_code - -The source code being translated into a Standard Concept. - - -varchar(50) - -Yes - -No - -No - - -
-source_concept_id - -A foreign key to the Source Concept that is being translated into a -Standard Concept. - -This is either 0 or should be a number above 2 billion, which are the -Concepts reserved for site-specific codes and mappings. - -integer - -Yes - -No - -Yes - -CONCEPT - -
-source_vocabulary_id - -A foreign key to the VOCABULARY table defining the vocabulary of the -source code that is being translated to a Standard Concept. - - -varchar(20) - -Yes - -No - -No - - -
-source_code_description - -An optional description for the source code. This is included as a -convenience to compare the description of the source code to the name of -the concept. - - -varchar(255) - -No - -No - -No - - -
-target_concept_id - -The target Concept to which the source code is being mapped. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-target_vocabulary_id - -The Vocabulary of the target Concept. - - -varchar(20) - -Yes - -No - -Yes - -VOCABULARY - -
-valid_start_date - -The date when the mapping instance was first recorded. - - -date - -Yes - -No - -No - - -
-valid_end_date - -The date when the mapping instance became invalid because it was deleted -or superseded (updated) by a new relationship. Default value is -31-Dec-2099. - - -date - -Yes - -No - -No - - -
-invalid_reason - -Reason the mapping instance was invalidated. Possible values are D -(deleted), U (replaced with an update) or NULL when valid_end_date has -the default value. - - -varchar(1) - -No - -No - -No - - -
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drug_strength

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Table Description

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The DRUG_STRENGTH table contains structured content about the amount -or concentration and associated units of a specific ingredient contained -within a particular drug product. This table is supplemental information -to support standardized analysis of drug utilization.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-drug_concept_id - -The Concept representing the Branded Drug or Clinical Drug Product. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-ingredient_concept_id - -The Concept representing the active ingredient contained within the drug -product. - -Combination Drugs will have more than one record in this table, one for -each active Ingredient. - -integer - -Yes - -No - -Yes - -CONCEPT - -
-amount_value - -The numeric value or the amount of active ingredient contained within -the drug product. - - -float - -No - -No - -No - - -
-amount_unit_concept_id - -The Concept representing the Unit of measure for the amount of active -ingredient contained within the drug product. - - -integer - -No - -No - -Yes - -CONCEPT - -
-numerator_value - -The concentration of the active ingredient contained within the drug -product. - - -float - -No - -No - -No - - -
-numerator_unit_concept_id - -The Concept representing the Unit of measure for the concentration of -active ingredient. - - -integer - -No - -No - -Yes - -CONCEPT - -
-denominator_value - -The amount of total liquid (or other divisible product, such as -ointment, gel, spray, etc.). - - -float - -No - -No - -No - - -
-denominator_unit_concept_id - -The Concept representing the denominator unit for the concentration of -active ingredient. - - -integer - -No - -No - -Yes - -CONCEPT - -
-box_size - -The number of units of Clinical Branded Drug or Quantified Clinical or -Branded Drug contained in a box as dispensed to the patient. - - -integer - -No - -No - -No - - -
-valid_start_date - -The date when the Concept was first recorded. The default value is -1-Jan-1970. - - -date - -Yes - -No - -No - - -
-valid_end_date - -The date when then Concept became invalid. - - -date - -Yes - -No - -No - - -
-invalid_reason - -Reason the concept was invalidated. Possible values are D (deleted), U -(replaced with an update) or NULL when valid_end_date has the default -value. - - -varchar(1) - -No - -No - -No - - -
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cohort_definition

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Table Description

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The COHORT_DEFINITION table contains records defining a Cohort -derived from the data through the associated description and syntax and -upon instantiation (execution of the algorithm) placed into the COHORT -table. Cohorts are a set of subjects that satisfy a given combination of -inclusion criteria for a duration of time. The COHORT_DEFINITION table -provides a standardized structure for maintaining the rules governing -the inclusion of a subject into a cohort, and can store operational -programming code to instantiate the cohort within the OMOP Common Data -Model.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-cohort_definition_id - -This is the identifier given to the cohort, usually by the ATLAS -application - - -integer - -Yes - -No - -No - - -
-cohort_definition_name - -A short description of the cohort - - -varchar(255) - -Yes - -No - -No - - -
-cohort_definition_description - -A complete description of the cohort. - - -varchar(MAX) - -No - -No - -No - - -
-definition_type_concept_id - -Type defining what kind of Cohort Definition the record represents and -how the syntax may be executed. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-cohort_definition_syntax - -Syntax or code to operationalize the Cohort Definition. - - -varchar(MAX) - -No - -No - -No - - -
-subject_concept_id - -This field contains a Concept that represents the domain of the subjects -that are members of the cohort (e.g., Person, Provider, Visit). - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-cohort_initiation_date - -A date to indicate when the Cohort was initiated in the COHORT table. - - -date - -No - -No - -No - - -
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attribute_definition

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Table Description

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The ATTRIBUTE_DEFINITION table contains records to define each -attribute through an associated description and syntax. Attributes are -derived elements that can be selected or calculated for a subject within -a cohort. The ATTRIBUTE_DEFINITION table provides a standardized -structure for maintaining the rules governing the calculation of -covariates for a subject in a cohort, and can store operational -programming code to instantiate the attributes for a given cohort within -the OMOP Common Data Model.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-attribute_definition_id - - - -integer - -Yes - -No - -No - - -
-attribute_name - - - -varchar(255) - -Yes - -No - -No - - -
-attribute_description - - - -varchar(MAX) - -No - -No - -No - - -
-attribute_type_concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-attribute_syntax - - - -varchar(MAX) - -No - -No - -No - - -
+clinical entity within the OMOP Common Data Model and standardized +analytics. Each Standard Concept belongs to one Domain, which defines +the location where the Concept would be expected to occur within the +data tables of the CDM. Concepts can represent broad categories +(like

diff --git a/docs/cdm54.html b/docs/cdm54.html index 32e23c0..7266369 100644 --- a/docs/cdm54.html +++ b/docs/cdm54.html @@ -13057,2567 +13057,11 @@ derived from vocabularies, which represent clinical information across a domain (e.g. conditions, drugs, procedures) through the use of codes and associated descriptions. Some Concepts are designated Standard Concepts, meaning these Concepts can be used as normative expressions of a -clinical entity within the OMOP Common Data Model and within -standardized analytics. Each Standard Concept belongs to one domain, -which defines the location where the Concept would be expected to occur -within data tables of the CDM.

-

Concepts can represent broad categories (like ‘Cardiovascular -disease’), detailed clinical elements (‘Myocardial infarction of the -anterolateral wall’) or modifying characteristics and attributes that -define Concepts at various levels of detail (severity of a disease, -associated morphology, etc.).

-

Records in the Standardized Vocabularies tables are derived from -national or international vocabularies such as SNOMED-CT, RxNorm, and -LOINC, or custom Concepts defined to cover various aspects of -observational data analysis.

-

User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-concept_id - -A unique identifier for each Concept across all domains. - - -integer - -Yes - -Yes - -No - - -
-concept_name - -An unambiguous, meaningful and descriptive name for the Concept. - - -varchar(255) - -Yes - -No - -No - - -
-domain_id - -A foreign key to the DOMAIN -table the Concept belongs to. - - -varchar(20) - -Yes - -No - -Yes - -DOMAIN - -
-vocabulary_id - -A foreign key to the VOCABULARY -table indicating from which source the Concept has been adapted. - - -varchar(20) - -Yes - -No - -Yes - -VOCABULARY - -
-concept_class_id - -The attribute or concept class of the Concept. Examples are ‘Clinical -Drug’, ‘Ingredient’, ‘Clinical Finding’ etc. - - -varchar(20) - -Yes - -No - -Yes - -CONCEPT_CLASS - -
-standard_concept - -This flag determines where a Concept is a Standard Concept, i.e. is used -in the data, a Classification Concept, or a non-standard Source Concept. -The allowable values are ‘S’ (Standard Concept) and ‘C’ (Classification -Concept), otherwise the content is NULL. - - -varchar(1) - -No - -No - -No - - -
-concept_code - -The concept code represents the identifier of the Concept in the source -vocabulary, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that -concept codes are not unique across vocabularies. - - -varchar(50) - -Yes - -No - -No - - -
-valid_start_date - -The date when the Concept was first recorded. The default value is -1-Jan-1970, meaning, the Concept has no (known) date of inception. - - -date - -Yes - -No - -No - - -
-valid_end_date - -The date when the Concept became invalid because it was deleted or -superseded (updated) by a new concept. The default value is 31-Dec-2099, -meaning, the Concept is valid until it becomes deprecated. - - -date - -Yes - -No - -No - - -
-invalid_reason - -Reason the Concept was invalidated. Possible values are D (deleted), U -(replaced with an update) or NULL when valid_end_date has the default -value. - - -varchar(1) - -No - -No - -No - - -
- -
-

vocabulary

-

Table Description

-

The VOCABULARY table includes a list of the Vocabularies collected -from various sources or created de novo by the OMOP community. This -reference table is populated with a single record for each Vocabulary -source and includes a descriptive name and other associated attributes -for the Vocabulary.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-vocabulary_id - -A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. - - -varchar(20) - -Yes - -Yes - -No - - -
-vocabulary_name - -The name describing the vocabulary, for example, International -Classification of Diseases, Ninth Revision, Clinical Modification, -Volume 1 and 2 (NCHS) etc. - - -varchar(255) - -Yes - -No - -No - - -
-vocabulary_reference - -External reference to documentation or available download of the about -the vocabulary. - - -varchar(255) - -No - -No - -No - - -
-vocabulary_version - -Version of the Vocabulary as indicated in the source. - - -varchar(255) - -No - -No - -No - - -
-vocabulary_concept_id - -A Concept that represents the Vocabulary the VOCABULARY record belongs -to. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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domain

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Table Description

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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 allowable Concepts for the standardized fields in the CDM tables. For -example, the “Condition” Domain contains Concepts that describe a -condition of a patient, and these Concepts can only be stored in the -condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA -tables. This reference table is populated with a single record for each -Domain and includes a descriptive name for the Domain.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-domain_id - -A unique key for each domain. - - -varchar(20) - -Yes - -Yes - -No - - -
-domain_name - -The name describing the Domain, e.g. Condition, Procedure, Measurement -etc. - - -varchar(255) - -Yes - -No - -No - - -
-domain_concept_id - -A Concept representing the Domain Concept the DOMAIN record belongs to. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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concept_class

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Table Description

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The CONCEPT_CLASS table is a reference table, which includes a list -of the classifications used to differentiate Concepts within a given -Vocabulary. This reference table is populated with a single record for -each Concept Class.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-concept_class_id - -A unique key for each class. - - -varchar(20) - -Yes - -Yes - -No - - -
-concept_class_name - -The name describing the Concept Class, e.g. Clinical Finding, -Ingredient, etc. - - -varchar(255) - -Yes - -No - -No - - -
-concept_class_concept_id - -A Concept that represents the Concept Class. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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concept_relationship

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Table Description

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The CONCEPT_RELATIONSHIP table contains records that define direct -relationships between any two Concepts and the nature or type of the -relationship. Each type of a relationship is defined in the RELATIONSHIP -table.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-concept_id_1 - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-concept_id_2 - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-relationship_id - -The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see the -Vocabulary -Conventions. for more information. - - -varchar(20) - -Yes - -No - -Yes - -RELATIONSHIP - -
-valid_start_date - -The date when the relationship is first recorded. - - -date - -Yes - -No - -No - - -
-valid_end_date - -The date when the relationship is invalidated. - - -date - -Yes - -No - -No - - -
-invalid_reason - -Reason the relationship was invalidated. Possible values are ‘D’ -(deleted), ‘U’ (updated) or NULL. - - -varchar(1) - -No - -No - -No - - -
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relationship

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Table Description

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The RELATIONSHIP table provides a reference list of all types of -relationships that can be used to associate any two concepts in the -CONCEPT_RELATIONSHP table.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-relationship_id - -The type of relationship captured by the relationship record. - - -varchar(20) - -Yes - -Yes - -No - - -
-relationship_name - - - -varchar(255) - -Yes - -No - -No - - -
-is_hierarchical - -Defines whether a relationship defines concepts into classes or -hierarchies. Values are 1 for hierarchical relationship or 0 if not. - - -varchar(1) - -Yes - -No - -No - - -
-defines_ancestry - -Defines whether a hierarchical relationship contributes to the -concept_ancestor table. These are subsets of the hierarchical -relationships. Valid values are 1 or 0. - - -varchar(1) - -Yes - -No - -No - - -
-reverse_relationship_id - -The identifier for the relationship used to define the reverse -relationship between two concepts. - - -varchar(20) - -Yes - -No - -No - - -
-relationship_concept_id - -A foreign key that refers to an identifier in the CONCEPT -table for the unique relationship concept. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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concept_synonym

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Table Description

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The CONCEPT_SYNONYM table is used to store alternate names and -descriptions for Concepts.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-concept_synonym_name - - - -varchar(1000) - -Yes - -No - -No - - -
-language_concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
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concept_ancestor

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Table Description

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The CONCEPT_ANCESTOR table is designed to simplify observational -analysis by providing the complete hierarchical relationships between -Concepts. Only direct parent-child relationships between Concepts are -stored in the CONCEPT_RELATIONSHIP table. To determine higher level -ancestry connections, all individual direct relationships would have to -be navigated at analysis time. The CONCEPT_ANCESTOR table includes -records for all parent-child relationships, as well as -grandparent-grandchild relationships and those of any other level of -lineage. Using the CONCEPT_ANCESTOR table allows for querying for all -descendants of a hierarchical concept. For example, drug ingredients and -drug products are all descendants of a drug class ancestor.

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This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP -and RELATIONSHIP tables.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-ancestor_concept_id - -The Concept Id for the higher-level concept that forms the ancestor in -the relationship. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-descendant_concept_id - -The Concept Id for the lower-level concept that forms the descendant in -the relationship. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-min_levels_of_separation - -The minimum separation in number of levels of hierarchy between ancestor -and descendant concepts. This is an attribute that is used to simplify -hierarchic analysis. - - -integer - -Yes - -No - -No - - -
-max_levels_of_separation - -The maximum separation in number of levels of hierarchy between ancestor -and descendant concepts. This is an attribute that is used to simplify -hierarchic analysis. - - -integer - -Yes - -No - -No - - -
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source_to_concept_map

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Table Description

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The source to concept map table is recommended for use in ETL -processes to maintain local source codes which are not available as -Concepts in the Standardized Vocabularies, and to establish mappings for -each source 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 is no longer populated with content within -the Standardized Vocabularies published to the OMOP community. -There are OHDSI tools to help you populate this table; Usagi and Perseus. You can read more -about OMOP vocabulary mapping in The -Book of OHDSI Chapter 6.3.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-source_code - -The source code being translated into a Standard Concept. - - -varchar(50) - -Yes - -No - -No - - -
-source_concept_id - -A foreign key to the Source Concept that is being translated into a -Standard Concept. - -This is either 0 or should be a number above 2 billion, which are the -Concepts reserved for site-specific codes and mappings. - -integer - -Yes - -No - -Yes - -CONCEPT - -
-source_vocabulary_id - -A foreign key to the VOCABULARY table defining the vocabulary of the -source code that is being translated to a Standard Concept. - - -varchar(20) - -Yes - -No - -No - - -
-source_code_description - -An optional description for the source code. This is included as a -convenience to compare the description of the source code to the name of -the concept. - - -varchar(255) - -No - -No - -No - - -
-target_concept_id - -The target Concept to which the source code is being mapped. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-target_vocabulary_id - -The Vocabulary of the target Concept. - - -varchar(20) - -Yes - -No - -Yes - -VOCABULARY - -
-valid_start_date - -The date when the mapping instance was first recorded. - - -date - -Yes - -No - -No - - -
-valid_end_date - -The date when the mapping instance became invalid because it was deleted -or superseded (updated) by a new relationship. Default value is -31-Dec-2099. - - -date - -Yes - -No - -No - - -
-invalid_reason - -Reason the mapping instance was invalidated. Possible values are D -(deleted), U (replaced with an update) or NULL when valid_end_date has -the default value. - - -varchar(1) - -No - -No - -No - - -
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drug_strength

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Table Description

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The DRUG_STRENGTH table contains structured content about the amount -or concentration and associated units of a specific ingredient contained -within a particular drug product. This table is supplemental information -to support standardized analysis of drug utilization.

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User Guide

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NA

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ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-drug_concept_id - -The Concept representing the Branded Drug or Clinical Drug Product. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-ingredient_concept_id - -The Concept representing the active ingredient contained within the drug -product. - -Combination Drugs will have more than one record in this table, one for -each active Ingredient. - -integer - -Yes - -No - -Yes - -CONCEPT - -
-amount_value - -The numeric value or the amount of active ingredient contained within -the drug product. - - -float - -No - -No - -No - - -
-amount_unit_concept_id - -The Concept representing the Unit of measure for the amount of active -ingredient contained within the drug product. - - -integer - -No - -No - -Yes - -CONCEPT - -
-numerator_value - -The concentration of the active ingredient contained within the drug -product. - - -float - -No - -No - -No - - -
-numerator_unit_concept_id - -The Concept representing the Unit of measure for the concentration of -active ingredient. - - -integer - -No - -No - -Yes - -CONCEPT - -
-denominator_value - -The amount of total liquid (or other divisible product, such as -ointment, gel, spray, etc.). - - -float - -No - -No - -No - - -
-denominator_unit_concept_id - -The Concept representing the denominator unit for the concentration of -active ingredient. - - -integer - -No - -No - -Yes - -CONCEPT - -
-box_size - -The number of units of Clinical Branded Drug or Quantified Clinical or -Branded Drug contained in a box as dispensed to the patient. - - -integer - -No - -No - -No - - -
-valid_start_date - -The date when the Concept was first recorded. The default value is -1-Jan-1970. - - -date - -Yes - -No - -No - - -
-valid_end_date - -The date when then Concept became invalid. - - -date - -Yes - -No - -No - - -
-invalid_reason - -Reason the concept was invalidated. Possible values are D (deleted), U -(replaced with an update) or NULL when valid_end_date has the default -value. - - -varchar(1) - -No - -No - -No - - -
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cohort

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Table Description

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The subject of a cohort can have multiple, discrete records in the -cohort table per cohort_definition_id, subject_id, and non-overlapping -time periods. The definition of the cohort is contained within the -COHORT_DEFINITION table. It is listed as part of the RESULTS schema -because it is a table that users of the database as 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 and COHORT_DEFINTION -tables are kept in a separate schema to alleviate confusion.

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User Guide

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NA

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ETL Conventions

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Cohorts typically include patients diagnosed with a specific -condition, patients exposed to a particular drug, but can also be -Providers who have performed a specific Procedure. Cohort records must -have a Start Date and an End Date, but the End Date may be set to Start -Date or could have an applied censor date using the Observation Period -Start Date. Cohort records must contain a Subject Id, which can refer to -the Person, Provider, Visit record or Care Site though they are most -often Person Ids. The Cohort Definition will define the type of subject -through the subject concept id. A subject can belong (or not belong) to -a cohort at any moment in time. A subject can only have one record in -the cohort table for any moment of time, i.e. it is not possible for a -person to contain multiple records indicating cohort membership that are -overlapping in time

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-cohort_definition_id - - - -integer - -Yes - -No - -No - - -
-subject_id - - - -integer - -Yes - -No - -No - - -
-cohort_start_date - - - -date - -Yes - -No - -No - - -
-cohort_end_date - - - -date - -Yes - -No - -No - - -
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cohort_definition

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Table Description

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The COHORT_DEFINITION table contains records defining a Cohort -derived from the data through the associated description and syntax and -upon instantiation (execution of the algorithm) placed into the COHORT -table. Cohorts are a set of subjects that satisfy a given combination of -inclusion criteria for a duration of time. The COHORT_DEFINITION table -provides a standardized structure for maintaining the rules governing -the inclusion of a subject into a cohort, and can store operational -programming code to instantiate the cohort within the OMOP Common Data -Model.

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User Guide

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NA

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ETL Conventions

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NA

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-CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-cohort_definition_id - -This is the identifier given to the cohort, usually by the ATLAS -application - - -integer - -Yes - -No - -No - - -
-cohort_definition_name - -A short description of the cohort - - -varchar(255) - -Yes - -No - -No - - -
-cohort_definition_description - -A complete description of the cohort. - - -varchar(MAX) - -No - -No - -No - - -
-definition_type_concept_id - -Type defining what kind of Cohort Definition the record represents and -how the syntax may be executed. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-cohort_definition_syntax - -Syntax or code to operationalize the Cohort Definition. - - -varchar(MAX) - -No - -No - -No - - -
-subject_concept_id - -This field contains a Concept that represents the domain of the subjects -that are members of the cohort (e.g., Person, Provider, Visit). - - -integer - -Yes - -No - -Yes - -CONCEPT - -
-cohort_initiation_date - -A date to indicate when the Cohort was initiated in the COHORT table. - - -date - -No - -No - -No - - -
+clinical entity within the OMOP Common Data Model and standardized +analytics. Each Standard Concept belongs to one Domain, which defines +the location where the Concept would be expected to occur within the +data tables of the CDM. Concepts can represent broad categories +(like