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
-NA
-ETL Conventions
-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 - | -- | -- | -
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.
-User Guide
-NA
-ETL Conventions
-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) - | --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 - | -- | -
Table Description
-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
-NA
-ETL Conventions
-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 - | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-NA
-| -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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-NA
-| -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 - | -- | -
Table Description
-The CONCEPT_SYNONYM table is used to store alternate names and -descriptions for Concepts.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -
Table Description
-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.
-This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP -and RELATIONSHIP tables.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -- | -
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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-NA
-| -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 - | -- | -- | -
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
-NA
-ETL Conventions
-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 - | -- | -- | -
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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -
Table Description
-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
-NA
-ETL Conventions
-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 - | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-NA
-| -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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-NA
-| -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 - | -- | -
Table Description
-The CONCEPT_SYNONYM table is used to store alternate names and -descriptions for Concepts.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -
Table Description
-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.
-This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP -and RELATIONSHIP tables.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-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
-| -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 - | -- | -- | -
Table Description
-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.
-User Guide
-NA
-ETL Conventions
-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 - | -- | -- | -