From 9bfa59a43ef8b5de469f0e6f2ad8ed856b6fd3e0 Mon Sep 17 00:00:00 2001 From: Clair Blacketer Date: Wed, 7 Feb 2018 15:25:57 -0500 Subject: [PATCH] closes #140, #144, #135 --- BigQuery/OMOP CDM bigquery ddl.txt | 8 ++-- .../COHORT_DEFINITION.md | 2 +- .../CONCEPT_SYNONYM.md | 2 +- Impala/OMOP CDM impala ddl.txt | 6 ++- Netezza/OMOP CDM netezza ddl.txt | 11 +++-- Oracle/OMOP CDM oracle ddl.txt | 8 ++-- ParallelDataWarehouse/OMOP CDM pdw ddl.txt | 46 +++++++++---------- PostgreSQL/OMOP CDM postgresql ddl.txt | 8 ++-- Redshift/OMOP CDM redshift ddl.txt | 46 +++++++++---------- Sql Server/OMOP CDM sql server ddl.txt | 8 ++-- 10 files changed, 74 insertions(+), 71 deletions(-) diff --git a/BigQuery/OMOP CDM bigquery ddl.txt b/BigQuery/OMOP CDM bigquery ddl.txt index 385c177..84c2656 100644 --- a/BigQuery/OMOP CDM bigquery ddl.txt +++ b/BigQuery/OMOP CDM bigquery ddl.txt @@ -17,7 +17,7 @@ create table vocabulary ( vocabulary_id varchar(20) not null, vocabulary_name varchar(255) not null, vocabulary_reference varchar(255) not null, - vocabulary_version varchar(255) not null, + vocabulary_version varchar(255) null, vocabulary_concept_id integer not null ) ; @@ -390,8 +390,8 @@ create table measurement person_id integer not null , measurement_concept_id integer not null , measurement_date date not null , + measurement_datetime datetime null , measurement_time varchar(10) null , - measurement_datetime datetime null , measurement_type_concept_id integer not null , operator_concept_id integer null , value_as_number float null , @@ -551,7 +551,7 @@ create table payer_plan_period sponsor_source_concept_id integer null , family_source_value varchar(50) null , stop_reason_concept_id integer null , - stop_reason_source_value integer null , + stop_reason_source_value varchar(50) null , stop_reason_source_concept_id integer null ) ; @@ -578,7 +578,7 @@ create table cost payer_plan_period_id integer null , amount_allowed float null , revenue_code_concept_id integer null , - reveue_code_source_value varchar(50) null, + revenue_code_source_value varchar(50) null, drg_concept_id integer null, drg_source_value varchar(3) null ) diff --git a/Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md b/Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md index 0f5db69..de0fd37 100644 --- a/Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md +++ b/Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md @@ -8,7 +8,7 @@ Field|Required|Type|Description |definition_type_concept_id|Yes|integer|Type defining what kind of Cohort Definition the record represents and how the syntax may be executed| |cohort_definition_syntax|No|varchar(MAX)|Syntax or code to operationalize the Cohort definition| |subject_concept_id|Yes|integer|A foreign key to the Concept to which defines the domain of subjects that are members of the cohort (e.g., Person, Provider, Visit).| -|cohort_instantiation_date|No|Date|A date to indicate when the Cohort was instantiated in the COHORT table| +|cohort_initiation_date|No|Date|A date to indicate when the Cohort was instantiated in the COHORT table| ### Conventions * The cohort_definition_syntax does not prescribe any specific syntax or programming language. Typically, it would be any flavor SQL, a cohort definition language, or a free-text description of the algorithm. diff --git a/Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md b/Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md index 38abb18..dc7916d 100644 --- a/Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md +++ b/Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md @@ -8,6 +8,6 @@ The CONCEPT_SYNONYM table is used to store alternate names and descriptions for ### Conventions - * The concept_name field contains a valid Synonym of a concept, including the description in the concept_name itself. I.e. each Concept has at least one Synonym in the CONCEPT_SYNONYM table. As an example, for a SNOMED-CT Concept, if the fully specified name is stored as the concept_name of the CONCEPT table, then the Preferred Term and Synonyms associated with the Concept are stored in the CONCEPT_SYNONYM table. + * The concept_synonym_name field contains a valid Synonym of a concept, including the description in the concept_name itself. I.e. each Concept has at least one Synonym in the CONCEPT_SYNONYM table. As an example, for a SNOMED-CT Concept, if the fully specified name is stored as the concept_name of the CONCEPT table, then the Preferred Term and Synonyms associated with the Concept are stored in the CONCEPT_SYNONYM table. * Only Synonyms that are active and current are stored in the CONCEPT_SYNONYM table. Tracking synonym/description history and mapping of obsolete synonyms to current Concepts/Synonyms is out of scope for the Standard Vocabularies. * Currently, only English Synonyms are included. diff --git a/Impala/OMOP CDM impala ddl.txt b/Impala/OMOP CDM impala ddl.txt index 3be1202..58f691a 100644 --- a/Impala/OMOP CDM impala ddl.txt +++ b/Impala/OMOP CDM impala ddl.txt @@ -818,6 +818,8 @@ CREATE TABLE measurement measurement_datetime TIMESTAMP, + measurement_time VARCHAR(10), + measurement_type_concept_id INTEGER, operator_concept_id INTEGER, @@ -1134,7 +1136,7 @@ CREATE TABLE payer_plan_period stop_reason_concept_id INTEGER, - stop_reason_source_value INTEGER, + stop_reason_source_value VARCHAR(50), stop_reason_source_concept_id INTEGER ) @@ -1185,7 +1187,7 @@ CREATE TABLE cost revenue_code_concept_id INTEGER, - reveue_code_source_value VARCHAR(50), + revenue_code_source_value VARCHAR(50), drg_concept_id INTEGER, diff --git a/Netezza/OMOP CDM netezza ddl.txt b/Netezza/OMOP CDM netezza ddl.txt index d140cca..a9d4ad7 100644 --- a/Netezza/OMOP CDM netezza ddl.txt +++ b/Netezza/OMOP CDM netezza ddl.txt @@ -28,7 +28,7 @@ netezza script to create OMOP common data model version 5.3 -last revised: 6-Nov-2017 +last revised: 8-Jan-2018 Authors: Patrick Ryan, Christian Reich, Clair Blacketer @@ -64,7 +64,7 @@ CREATE TABLE vocabulary ( vocabulary_id VARCHAR(20) NOT NULL, vocabulary_name VARCHAR(255) NOT NULL, vocabulary_reference VARCHAR(255) NOT NULL, - vocabulary_version VARCHAR(255) NOT NULL, + vocabulary_version VARCHAR(255) NULL, vocabulary_concept_id INTEGER NOT NULL ) DISTRIBUTE ON RANDOM @@ -479,7 +479,8 @@ CREATE TABLE measurement person_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL , measurement_date DATE NOT NULL , - measurement_datetime DATETIME NULL , + measurement_datetime DATETIME NULL , + measurement_time VARCHAR(10) NULL , measurement_type_concept_id INTEGER NOT NULL , operator_concept_id INTEGER NULL , value_as_number REAL NULL , @@ -665,7 +666,7 @@ CREATE TABLE payer_plan_period sponsor_source_concept_id INTEGER NULL , family_source_value VARCHAR(50) NULL , stop_reason_concept_id INTEGER NULL , - stop_reason_source_value INTEGER NULL , + stop_reason_source_value VARCHAR(50) NULL , stop_reason_source_concept_id INTEGER NULL ) DISTRIBUTE ON (person_id) @@ -694,7 +695,7 @@ CREATE TABLE cost payer_plan_period_id INTEGER NULL , amount_allowed REAL NULL , revenue_code_concept_id INTEGER NULL , - reveue_code_source_value VARCHAR(50) NULL, + revenue_code_source_value VARCHAR(50) NULL, drg_concept_id INTEGER NULL, drg_source_value VARCHAR(3) NULL ) diff --git a/Oracle/OMOP CDM oracle ddl.txt b/Oracle/OMOP CDM oracle ddl.txt index d61bdc2..3960b59 100644 --- a/Oracle/OMOP CDM oracle ddl.txt +++ b/Oracle/OMOP CDM oracle ddl.txt @@ -62,7 +62,7 @@ CREATE TABLE vocabulary ( vocabulary_id VARCHAR(20) NOT NULL, vocabulary_name VARCHAR(255) NOT NULL, vocabulary_reference VARCHAR(255) NOT NULL, - vocabulary_version VARCHAR(255) NOT NULL, + vocabulary_version VARCHAR(255) NULL, vocabulary_concept_id INTEGER NOT NULL ) ; @@ -447,8 +447,8 @@ CREATE TABLE measurement person_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL , measurement_date DATE NOT NULL , + measurement_datetime TIMESTAMP NULL , measurement_time VARCHAR(10) NULL , - measurement_datetime TIMESTAMP NULL , measurement_type_concept_id INTEGER NOT NULL , operator_concept_id INTEGER NULL , value_as_number FLOAT NULL , @@ -623,7 +623,7 @@ CREATE TABLE payer_plan_period sponsor_source_concept_id INTEGER NULL , family_source_value VARCHAR(50) NULL , stop_reason_concept_id INTEGER NULL , - stop_reason_source_value INTEGER NULL , + stop_reason_source_value VARCHAR(50) NULL , stop_reason_source_concept_id INTEGER NULL ) ; @@ -650,7 +650,7 @@ CREATE TABLE cost payer_plan_period_id INTEGER NULL , amount_allowed FLOAT NULL , revenue_code_concept_id INTEGER NULL , - reveue_code_source_value VARCHAR(50) NULL, + revenue_code_source_value VARCHAR(50) NULL, drg_concept_id INTEGER NULL, drg_source_value VARCHAR(3) NULL ) diff --git a/ParallelDataWarehouse/OMOP CDM pdw ddl.txt b/ParallelDataWarehouse/OMOP CDM pdw ddl.txt index 1c71fac..c8a5c76 100644 --- a/ParallelDataWarehouse/OMOP CDM pdw ddl.txt +++ b/ParallelDataWarehouse/OMOP CDM pdw ddl.txt @@ -60,7 +60,7 @@ WITH (DISTRIBUTION = REPLICATE); IF XACT_STATE() = 1 COMMIT; CREATE TABLE vocabulary (vocabulary_id VARCHAR(20) NOT NULL, vocabulary_name VARCHAR(255) NOT NULL, vocabulary_reference VARCHAR(255) NOT NULL, - vocabulary_version VARCHAR(255) NOT NULL, + vocabulary_version VARCHAR(255) NULL, vocabulary_concept_id INTEGER NOT NULL ) WITH (DISTRIBUTION = REPLICATE); @@ -207,7 +207,7 @@ Standardized clinical data ************************/ ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE person (person_id INTEGER NOT NULL , gender_concept_id INTEGER NOT NULL , @@ -231,7 +231,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE person WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE observation_period (observation_period_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -242,7 +242,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE observation_period WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE specimen (specimen_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -263,7 +263,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE specimen WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE death (person_id INTEGER NOT NULL , death_date DATE NOT NULL , @@ -276,7 +276,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE death WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE visit_occurrence (visit_occurrence_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -299,7 +299,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE visit_occurrence WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE visit_detail (visit_detail_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -324,7 +324,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE visit_detail WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE procedure_occurrence (procedure_occurrence_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -344,7 +344,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE procedure_occurrence WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE drug_exposure (drug_exposure_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -373,7 +373,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE drug_exposure WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE device_exposure (device_exposure_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -394,7 +394,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE device_exposure WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE condition_occurrence (condition_occurrence_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -416,14 +416,14 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE condition_occurrence WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE measurement (measurement_id INTEGER NOT NULL , person_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL , measurement_date DATE NOT NULL , + measurement_datetime DATETIME NULL , measurement_time VARCHAR(10) NULL , - measurement_datetime DATETIME NULL , measurement_type_concept_id INTEGER NOT NULL , operator_concept_id INTEGER NULL , value_as_number FLOAT NULL , @@ -442,7 +442,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE measurement WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE note (note_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -482,7 +482,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE note_nlp WITH (DISTRIBUTION = REPLICATE); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE observation (observation_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -573,7 +573,7 @@ Standardized health economics ************************/ ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE payer_plan_period (payer_plan_period_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -590,7 +590,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE payer_plan_period sponsor_source_concept_id INTEGER NULL , family_source_value VARCHAR(50) NULL , stop_reason_concept_id INTEGER NULL , - stop_reason_source_value INTEGER NULL , + stop_reason_source_value VARCHAR(50) NULL , stop_reason_source_concept_id INTEGER NULL ) WITH (DISTRIBUTION = HASH(person_id)); @@ -616,7 +616,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE cost payer_plan_period_id INTEGER NULL , amount_allowed FLOAT NULL , revenue_code_concept_id INTEGER NULL , - reveue_code_source_value VARCHAR(50) NULL, + revenue_code_source_value VARCHAR(50) NULL, drg_concept_id INTEGER NULL, drg_source_value VARCHAR(3) NULL ) @@ -630,7 +630,7 @@ Standardized derived elements ************************/ ---HINT DISTRIBUTE_ON_KEY(subject_id) +--HINT DISTRIBUTE_ON_KEY(subject_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE cohort (cohort_definition_id INTEGER NOT NULL , subject_id INTEGER NOT NULL , @@ -640,7 +640,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE cohort WITH (DISTRIBUTION = HASH(subject_id)); ---HINT DISTRIBUTE_ON_KEY(subject_id) +--HINT DISTRIBUTE_ON_KEY(subject_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE cohort_attribute (cohort_definition_id INTEGER NOT NULL , subject_id INTEGER NOT NULL , @@ -653,7 +653,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE cohort_attribute WITH (DISTRIBUTION = HASH(subject_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE drug_era (drug_era_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -666,7 +666,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE drug_era WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE dose_era (dose_era_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -679,7 +679,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE dose_era WITH (DISTRIBUTION = HASH(person_id)); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) IF XACT_STATE() = 1 COMMIT; CREATE TABLE condition_era (condition_era_id INTEGER NOT NULL , person_id INTEGER NOT NULL , diff --git a/PostgreSQL/OMOP CDM postgresql ddl.txt b/PostgreSQL/OMOP CDM postgresql ddl.txt index 4c0b3ed..91aad55 100644 --- a/PostgreSQL/OMOP CDM postgresql ddl.txt +++ b/PostgreSQL/OMOP CDM postgresql ddl.txt @@ -62,7 +62,7 @@ CREATE TABLE vocabulary ( vocabulary_id VARCHAR(20) NOT NULL, vocabulary_name VARCHAR(255) NOT NULL, vocabulary_reference VARCHAR(255) NOT NULL, - vocabulary_version VARCHAR(255) NOT NULL, + vocabulary_version VARCHAR(255) NULL, vocabulary_concept_id INTEGER NOT NULL ) ; @@ -447,8 +447,8 @@ CREATE TABLE measurement person_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL , measurement_date DATE NOT NULL , + measurement_datetime TIMESTAMP NULL , measurement_time VARCHAR(10) NULL , - measurement_datetime TIMESTAMP NULL , measurement_type_concept_id INTEGER NOT NULL , operator_concept_id INTEGER NULL , value_as_number NUMERIC NULL , @@ -623,7 +623,7 @@ CREATE TABLE payer_plan_period sponsor_source_concept_id INTEGER NULL , family_source_value VARCHAR(50) NULL , stop_reason_concept_id INTEGER NULL , - stop_reason_source_value INTEGER NULL , + stop_reason_source_value VARCHAR(50) NULL , stop_reason_source_concept_id INTEGER NULL ) ; @@ -650,7 +650,7 @@ CREATE TABLE cost payer_plan_period_id INTEGER NULL , amount_allowed NUMERIC NULL , revenue_code_concept_id INTEGER NULL , - reveue_code_source_value VARCHAR(50) NULL, + revenue_code_source_value VARCHAR(50) NULL, drg_concept_id INTEGER NULL, drg_source_value VARCHAR(3) NULL ) diff --git a/Redshift/OMOP CDM redshift ddl.txt b/Redshift/OMOP CDM redshift ddl.txt index de4d591..54ed060 100644 --- a/Redshift/OMOP CDM redshift ddl.txt +++ b/Redshift/OMOP CDM redshift ddl.txt @@ -60,7 +60,7 @@ DISTSTYLE ALL; CREATE TABLE vocabulary (vocabulary_id VARCHAR(20) NOT NULL, vocabulary_name VARCHAR(255) NOT NULL, vocabulary_reference VARCHAR(255) NOT NULL, - vocabulary_version VARCHAR(255) NOT NULL, + vocabulary_version VARCHAR(255) NULL, vocabulary_concept_id INTEGER NOT NULL ) DISTSTYLE ALL; @@ -207,7 +207,7 @@ Standardized clinical data ************************/ ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE person (person_id INTEGER NOT NULL , gender_concept_id INTEGER NOT NULL , @@ -231,7 +231,7 @@ CREATE TABLE person DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE observation_period (observation_period_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -242,7 +242,7 @@ CREATE TABLE observation_period DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE specimen (specimen_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -263,7 +263,7 @@ CREATE TABLE specimen DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE death (person_id INTEGER NOT NULL , death_date DATE NOT NULL , @@ -276,7 +276,7 @@ CREATE TABLE death DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE visit_occurrence (visit_occurrence_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -299,7 +299,7 @@ CREATE TABLE visit_occurrence DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE visit_detail (visit_detail_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -324,7 +324,7 @@ CREATE TABLE visit_detail DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE procedure_occurrence (procedure_occurrence_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -344,7 +344,7 @@ CREATE TABLE procedure_occurrence DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE drug_exposure (drug_exposure_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -373,7 +373,7 @@ CREATE TABLE drug_exposure DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE device_exposure (device_exposure_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -394,7 +394,7 @@ CREATE TABLE device_exposure DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE condition_occurrence (condition_occurrence_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -416,14 +416,14 @@ CREATE TABLE condition_occurrence DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE measurement (measurement_id INTEGER NOT NULL , person_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL , measurement_date DATE NOT NULL , + measurement_datetime TIMESTAMP NULL , measurement_time VARCHAR(10) NULL , - measurement_datetime TIMESTAMP NULL , measurement_type_concept_id INTEGER NOT NULL , operator_concept_id INTEGER NULL , value_as_number FLOAT NULL , @@ -442,7 +442,7 @@ CREATE TABLE measurement DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE note (note_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -482,7 +482,7 @@ CREATE TABLE note_nlp DISTSTYLE ALL; ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE observation (observation_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -573,7 +573,7 @@ Standardized health economics ************************/ ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE payer_plan_period (payer_plan_period_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -590,7 +590,7 @@ CREATE TABLE payer_plan_period sponsor_source_concept_id INTEGER NULL , family_source_value VARCHAR(50) NULL , stop_reason_concept_id INTEGER NULL , - stop_reason_source_value INTEGER NULL , + stop_reason_source_value VARCHAR(50) NULL , stop_reason_source_concept_id INTEGER NULL ) DISTKEY(person_id); @@ -616,7 +616,7 @@ CREATE TABLE cost payer_plan_period_id INTEGER NULL , amount_allowed FLOAT NULL , revenue_code_concept_id INTEGER NULL , - reveue_code_source_value VARCHAR(50) NULL, + revenue_code_source_value VARCHAR(50) NULL, drg_concept_id INTEGER NULL, drg_source_value VARCHAR(3) NULL ) @@ -630,7 +630,7 @@ Standardized derived elements ************************/ ---HINT DISTRIBUTE_ON_KEY(subject_id) +--HINT DISTRIBUTE_ON_KEY(subject_id) CREATE TABLE cohort (cohort_definition_id INTEGER NOT NULL , subject_id INTEGER NOT NULL , @@ -640,7 +640,7 @@ CREATE TABLE cohort DISTKEY(subject_id); ---HINT DISTRIBUTE_ON_KEY(subject_id) +--HINT DISTRIBUTE_ON_KEY(subject_id) CREATE TABLE cohort_attribute (cohort_definition_id INTEGER NOT NULL , subject_id INTEGER NOT NULL , @@ -653,7 +653,7 @@ CREATE TABLE cohort_attribute DISTKEY(subject_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE drug_era (drug_era_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -666,7 +666,7 @@ CREATE TABLE drug_era DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE dose_era (dose_era_id INTEGER NOT NULL , person_id INTEGER NOT NULL , @@ -679,7 +679,7 @@ CREATE TABLE dose_era DISTKEY(person_id); ---HINT DISTRIBUTE_ON_KEY(person_id) +--HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE condition_era (condition_era_id INTEGER NOT NULL , person_id INTEGER NOT NULL , diff --git a/Sql Server/OMOP CDM sql server ddl.txt b/Sql Server/OMOP CDM sql server ddl.txt index 9d635f2..05d173a 100644 --- a/Sql Server/OMOP CDM sql server ddl.txt +++ b/Sql Server/OMOP CDM sql server ddl.txt @@ -62,7 +62,7 @@ CREATE TABLE vocabulary ( vocabulary_id VARCHAR(20) NOT NULL, vocabulary_name VARCHAR(255) NOT NULL, vocabulary_reference VARCHAR(255) NOT NULL, - vocabulary_version VARCHAR(255) NOT NULL, + vocabulary_version VARCHAR(255) NULL, vocabulary_concept_id INTEGER NOT NULL ) ; @@ -447,8 +447,8 @@ CREATE TABLE measurement person_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL , measurement_date DATE NOT NULL , + measurement_datetime DATETIME NULL , measurement_time VARCHAR(10) NULL , - measurement_datetime DATETIME NULL , measurement_type_concept_id INTEGER NOT NULL , operator_concept_id INTEGER NULL , value_as_number FLOAT NULL , @@ -623,7 +623,7 @@ CREATE TABLE payer_plan_period sponsor_source_concept_id INTEGER NULL , family_source_value VARCHAR(50) NULL , stop_reason_concept_id INTEGER NULL , - stop_reason_source_value INTEGER NULL , + stop_reason_source_value VARCHAR(50) NULL , stop_reason_source_concept_id INTEGER NULL ) ; @@ -650,7 +650,7 @@ CREATE TABLE cost payer_plan_period_id INTEGER NULL , amount_allowed FLOAT NULL , revenue_code_concept_id INTEGER NULL , - reveue_code_source_value VARCHAR(50) NULL, + revenue_code_source_value VARCHAR(50) NULL, drg_concept_id INTEGER NULL, drg_source_value VARCHAR(3) NULL )