mz-health/OMOP
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OMOP
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Made changes to adhere to the new CDM changes for version 5.1

This commit is contained in:
Karthik Natarajan 2017-01-02 19:08:27 -05:00
parent a8d6557a56
commit aef6a3a550
1 changed files with 337 additions and 328 deletions
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119
Sql Server/OMOP CDM ddl - SQL Server.sql
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@ -195,7 +195,7 @@ Standardized meta-data
CREATE TABLE cdm_source CREATE TABLE cdm_source
( (
cdm_source_name VARCHAR(255) NOT NULL, cdm_source_name VARCHAR(255) NOT NULL,
cdm_source_abbreviation VARCHAR(25) NULL, cdm_source_abbreviation VARCHAR(25) NULL,
cdm_holder VARCHAR(255) NULL, cdm_holder VARCHAR(255) NULL,
@ -206,7 +206,7 @@ CREATE TABLE cdm_source
cdm_release_date DATE NULL, cdm_release_date DATE NULL,
cdm_version VARCHAR(10) NULL, cdm_version VARCHAR(10) NULL,
vocabulary_version VARCHAR(20) NULL vocabulary_version VARCHAR(20) NULL
) )
; ;
@ -223,13 +223,13 @@ Standardized clinical data
CREATE TABLE person CREATE TABLE person
( (
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
gender_concept_id INTEGER NOT NULL , gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL , year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL, month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL, day_of_birth INTEGER NULL,
time_of_birth VARCHAR(10) NULL, datetime_of_birth DATETIME2 NULL,
race_concept_id INTEGER NOT NULL, race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL, ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL, location_id INTEGER NULL,
@ -242,7 +242,7 @@ CREATE TABLE person
race_source_concept_id INTEGER NULL, race_source_concept_id INTEGER NULL,
ethnicity_source_value VARCHAR(50) NULL, ethnicity_source_value VARCHAR(50) NULL,
ethnicity_source_concept_id INTEGER NULL ethnicity_source_concept_id INTEGER NULL
) )
; ;
@ -250,25 +250,27 @@ CREATE TABLE person
CREATE TABLE observation_period CREATE TABLE observation_period
( (
observation_period_id INTEGER NOT NULL , observation_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
observation_period_start_date DATE NOT NULL , observation_period_start_date DATE NOT NULL ,
observation_period_start_datetime DATETIME2 NOT NULL ,
observation_period_end_date DATE NOT NULL , observation_period_end_date DATE NOT NULL ,
observation_period_end_datetime DATETIME2 NOT NULL ,
period_type_concept_id INTEGER NOT NULL period_type_concept_id INTEGER NOT NULL
) )
; ;
CREATE TABLE specimen CREATE TABLE specimen
( (
specimen_id INTEGER NOT NULL , specimen_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
specimen_concept_id INTEGER NOT NULL , specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL , specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NOT NULL , specimen_date DATE NOT NULL ,
specimen_time VARCHAR(10) NULL , specimen_datetime DATETIME2 NULL ,
quantity FLOAT NULL , quantity FLOAT NULL ,
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL , anatomic_site_concept_id INTEGER NULL ,
@ -278,49 +280,50 @@ CREATE TABLE specimen
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
anatomic_site_source_value VARCHAR(50) NULL , anatomic_site_source_value VARCHAR(50) NULL ,
disease_status_source_value VARCHAR(50) NULL disease_status_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE death CREATE TABLE death
( (
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
death_date DATE NOT NULL , death_date DATE NOT NULL ,
death_type_concept_id INTEGER NOT NULL , death_type_concept_id INTEGER NOT NULL ,
cause_concept_id INTEGER NULL , cause_concept_id INTEGER NULL ,
cause_source_value VARCHAR(50) NULL, cause_source_value VARCHAR(50) NULL,
cause_source_concept_id INTEGER NULL cause_source_concept_id INTEGER NULL
) )
; ;
CREATE TABLE visit_occurrence CREATE TABLE visit_occurrence
( (
visit_occurrence_id INTEGER NOT NULL , visit_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
visit_concept_id INTEGER NOT NULL , visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NOT NULL , visit_start_date DATE NOT NULL ,
visit_start_time VARCHAR(10) NULL , visit_start_datetime DATETIME2 NULL ,
visit_end_date DATE NOT NULL , visit_end_date DATE NOT NULL ,
visit_end_time VARCHAR(10) NULL , visit_end_datetime DATETIME2 NULL ,
visit_type_concept_id INTEGER NOT NULL , visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL, provider_id INTEGER NULL,
care_site_id INTEGER NULL, care_site_id INTEGER NULL,
visit_source_value VARCHAR(50) NULL, visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL visit_source_concept_id INTEGER NULL
) )
; ;
CREATE TABLE procedure_occurrence CREATE TABLE procedure_occurrence
( (
procedure_occurrence_id INTEGER NOT NULL , procedure_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
procedure_concept_id INTEGER NOT NULL , procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NOT NULL , procedure_date DATE NOT NULL ,
procedure_datetime DATETIME2 NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL , procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL , modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
@ -329,18 +332,20 @@ CREATE TABLE procedure_occurrence
procedure_source_value VARCHAR(50) NULL , procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER NULL , procedure_source_concept_id INTEGER NULL ,
qualifier_source_value VARCHAR(50) NULL qualifier_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE drug_exposure CREATE TABLE drug_exposure
( (
drug_exposure_id INTEGER NOT NULL , drug_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL , drug_exposure_start_date DATE NOT NULL ,
drug_exposure_start_datetime DATETIME2 NOT NULL ,
drug_exposure_end_date DATE NULL , drug_exposure_end_date DATE NULL ,
drug_exposure_end_datetime DATETIME2 NULL ,
drug_type_concept_id INTEGER NOT NULL , drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL , refills INTEGER NULL ,
@ -357,17 +362,19 @@ CREATE TABLE drug_exposure
drug_source_concept_id INTEGER NULL , drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL , route_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL dose_unit_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE device_exposure CREATE TABLE device_exposure
( (
device_exposure_id INTEGER NOT NULL , device_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
device_concept_id INTEGER NOT NULL , device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NOT NULL , device_exposure_start_date DATE NOT NULL ,
device_exposure_start_datetime DATETIME2 NOT NULL ,
device_exposure_end_date DATE NULL , device_exposure_end_date DATE NULL ,
device_exposure_end_datetime DATETIME2 NULL ,
device_type_concept_id INTEGER NOT NULL , device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL , unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
@ -375,35 +382,37 @@ CREATE TABLE device_exposure
visit_occurrence_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
device_source_value VARCHAR(100) NULL , device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL device_source_concept_id INTEGER NULL
) )
; ;
CREATE TABLE condition_occurrence CREATE TABLE condition_occurrence
( (
condition_occurrence_id INTEGER NOT NULL , condition_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL , condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NOT NULL , condition_start_date DATE NOT NULL ,
condition_start_datetime DATETIME2 NOT NULL ,
condition_end_date DATE NULL , condition_end_date DATE NULL ,
condition_end_datetime DATETIME2 NULL ,
condition_type_concept_id INTEGER NOT NULL , condition_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
condition_source_value VARCHAR(50) NULL , condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL condition_source_concept_id INTEGER NULL
) )
; ;
CREATE TABLE measurement CREATE TABLE measurement
( (
measurement_id INTEGER NOT NULL , measurement_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
measurement_concept_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NOT NULL , measurement_date DATE NOT NULL ,
measurement_time VARCHAR(10) NULL , measurement_datetime DATETIME2 NULL ,
measurement_type_concept_id INTEGER NOT NULL , measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL , operator_concept_id INTEGER NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
@ -417,34 +426,34 @@ CREATE TABLE measurement
measurement_source_concept_id INTEGER NULL , measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
value_source_value VARCHAR(50) NULL value_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE note CREATE TABLE note
( (
note_id INTEGER NOT NULL , note_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
note_date DATE NOT NULL , note_date DATE NOT NULL ,
note_time VARCHAR(10) NULL , note_datetime DATETIME2 NULL ,
note_type_concept_id INTEGER NOT NULL , note_type_concept_id INTEGER NOT NULL ,
note_text VARCHAR(MAX) NOT NULL , note_text VARCHAR(MAX) NOT NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
note_source_value VARCHAR(50) NULL note_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE observation CREATE TABLE observation
( (
observation_id INTEGER NOT NULL , observation_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
observation_concept_id INTEGER NOT NULL , observation_concept_id INTEGER NOT NULL ,
observation_date DATE NOT NULL , observation_date DATE NOT NULL ,
observation_time VARCHAR(10) NULL , observation_datetime DATETIME2 NULL ,
observation_type_concept_id INTEGER NOT NULL , observation_type_concept_id INTEGER NOT NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
value_as_string VARCHAR(60) NULL , value_as_string VARCHAR(60) NULL ,
@ -457,19 +466,19 @@ CREATE TABLE observation
observation_source_concept_id INTEGER NULL , observation_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL qualifier_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE fact_relationship CREATE TABLE fact_relationship
( (
domain_concept_id_1 INTEGER NOT NULL , domain_concept_id_1 INTEGER NOT NULL ,
fact_id_1 INTEGER NOT NULL , fact_id_1 INTEGER NOT NULL ,
domain_concept_id_2 INTEGER NOT NULL , domain_concept_id_2 INTEGER NOT NULL ,
fact_id_2 INTEGER NOT NULL , fact_id_2 INTEGER NOT NULL ,
relationship_concept_id INTEGER NOT NULL relationship_concept_id INTEGER NOT NULL
) )
; ;
@ -484,7 +493,7 @@ Standardized health system data
CREATE TABLE location CREATE TABLE location
( (
location_id INTEGER NOT NULL , location_id INTEGER NOT NULL ,
address_1 VARCHAR(50) NULL , address_1 VARCHAR(50) NULL ,
address_2 VARCHAR(50) NULL , address_2 VARCHAR(50) NULL ,
@ -493,26 +502,26 @@ CREATE TABLE location
zip VARCHAR(9) NULL , zip VARCHAR(9) NULL ,
county VARCHAR(20) NULL , county VARCHAR(20) NULL ,
location_source_value VARCHAR(50) NULL location_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE care_site CREATE TABLE care_site
( (
care_site_id INTEGER NOT NULL , care_site_id INTEGER NOT NULL ,
care_site_name VARCHAR(255) NULL , care_site_name VARCHAR(255) NULL ,
place_of_service_concept_id INTEGER NULL , place_of_service_concept_id INTEGER NULL ,
location_id INTEGER NULL , location_id INTEGER NULL ,
care_site_source_value VARCHAR(50) NULL , care_site_source_value VARCHAR(50) NULL ,
place_of_service_source_value VARCHAR(50) NULL place_of_service_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE provider CREATE TABLE provider
( (
provider_id INTEGER NOT NULL , provider_id INTEGER NOT NULL ,
provider_name VARCHAR(255) NULL , provider_name VARCHAR(255) NULL ,
NPI VARCHAR(20) NULL , NPI VARCHAR(20) NULL ,
@ -526,7 +535,7 @@ CREATE TABLE provider
specialty_source_concept_id INTEGER NULL , specialty_source_concept_id INTEGER NULL ,
gender_source_value VARCHAR(50) NULL , gender_source_value VARCHAR(50) NULL ,
gender_source_concept_id INTEGER NULL gender_source_concept_id INTEGER NULL
) )
; ;
@ -540,7 +549,7 @@ Standardized health economics
CREATE TABLE payer_plan_period CREATE TABLE payer_plan_period
( (
payer_plan_period_id INTEGER NOT NULL , payer_plan_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
payer_plan_period_start_date DATE NOT NULL , payer_plan_period_start_date DATE NOT NULL ,
@ -548,7 +557,7 @@ CREATE TABLE payer_plan_period
payer_source_value VARCHAR (50) NULL , payer_source_value VARCHAR (50) NULL ,
plan_source_value VARCHAR (50) NULL , plan_source_value VARCHAR (50) NULL ,
family_source_value VARCHAR (50) NULL family_source_value VARCHAR (50) NULL
) )
; ;
@ -632,7 +641,7 @@ CREATE TABLE device_cost
CREATE TABLE cost CREATE TABLE cost
( (
cost_id INTEGER NOT NULL , cost_id INTEGER NOT NULL ,
cost_event_id INTEGER NOT NULL , cost_event_id INTEGER NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL , cost_domain_id VARCHAR(20) NOT NULL ,
@ -653,7 +662,7 @@ CREATE TABLE cost
amount_allowed FLOAT NULL , amount_allowed FLOAT NULL ,
revenue_code_concept_id INTEGER NULL , revenue_code_concept_id INTEGER NULL ,
reveue_code_source_value VARCHAR(50) NULL reveue_code_source_value VARCHAR(50) NULL
) )
; ;
@ -667,17 +676,17 @@ Standardized derived elements
************************/ ************************/
CREATE TABLE cohort CREATE TABLE cohort
( (
cohort_definition_id INTEGER NOT NULL , cohort_definition_id INTEGER NOT NULL ,
subject_id INTEGER NOT NULL , subject_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL , cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL cohort_end_date DATE NOT NULL
) )
; ;
CREATE TABLE cohort_attribute CREATE TABLE cohort_attribute
( (
cohort_definition_id INTEGER NOT NULL , cohort_definition_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL , cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL , cohort_end_date DATE NOT NULL ,
@ -685,14 +694,14 @@ CREATE TABLE cohort_attribute
attribute_definition_id INTEGER NOT NULL , attribute_definition_id INTEGER NOT NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL value_as_concept_id INTEGER NULL
) )
; ;
CREATE TABLE drug_era CREATE TABLE drug_era
( (
drug_era_id INTEGER NOT NULL , drug_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
@ -700,12 +709,12 @@ CREATE TABLE drug_era
drug_era_end_date DATE NOT NULL , drug_era_end_date DATE NOT NULL ,
drug_exposure_count INTEGER NULL , drug_exposure_count INTEGER NULL ,
gap_days INTEGER NULL gap_days INTEGER NULL
) )
; ;
CREATE TABLE dose_era CREATE TABLE dose_era
( (
dose_era_id INTEGER NOT NULL , dose_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
@ -713,21 +722,21 @@ CREATE TABLE dose_era
dose_value FLOAT NOT NULL , dose_value FLOAT NOT NULL ,
dose_era_start_date DATE NOT NULL , dose_era_start_date DATE NOT NULL ,
dose_era_end_date DATE NOT NULL dose_era_end_date DATE NOT NULL
) )
; ;
CREATE TABLE condition_era CREATE TABLE condition_era
( (
condition_era_id INTEGER NOT NULL , condition_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL , condition_concept_id INTEGER NOT NULL ,
condition_era_start_date DATE NOT NULL , condition_era_start_date DATE NOT NULL ,
condition_era_end_date DATE NOT NULL , condition_era_end_date DATE NOT NULL ,
condition_occurrence_count INTEGER NULL condition_occurrence_count INTEGER NULL
) )
; ;