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OMOP
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Closes cdm proposal #71 and updates headers for CDM v5.2

This commit is contained in:
clairblacketer 2017-07-14 10:28:17 -04:00
parent f5903ad2cc
commit 4786616305
14 changed files with 645 additions and 269 deletions
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19
Impala/OMOP_CDM_ddl_Impala.sql
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@ -17,16 +17,16 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ###
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####### # # ####### # ##### ###### # # ## ##### ### ##### ### ###
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# # # # # # # ###### # # # # # # # # ###### #####
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# # # # # # # # # # # # # # # # # ### #
####### # # ####### # ##### ###### # # ## ##### ### #######
script to create OMOP common data model, version 5.1.0 for Hadoop (Hive/Impala) database
script to create OMOP common data model, version 5.2 for Hadoop (Hive/Impala) database
Based on the PostgreSQL version, with the following changes:
* NULL/NOT NULL is not used.
@ -248,7 +248,7 @@ CREATE TABLE person (
year_of_birth INTEGER,
month_of_birth INTEGER,
day_of_birth INTEGER,
time_of_birth VARCHAR(10),
birth_datetime VARCHAR(10),
race_concept_id INTEGER,
ethnicity_concept_id INTEGER,
location_id INTEGER,
@ -364,6 +364,7 @@ CREATE TABLE drug_exposure (
drug_concept_id INTEGER,
drug_exposure_start_date VARCHAR(8), -- DATE
drug_exposure_end_date VARCHAR(8), -- DATE
verbatim_end_date VARCHAR(8), --DATE
drug_type_concept_id INTEGER,
stop_reason VARCHAR(20),
refills INTEGER,

2
Impala/OMOP_Parquet.sql
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@ -220,7 +220,7 @@ SELECT
person_id,
drug_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_exposure_start_date AS STRING), 1, 4), SUBSTR(CAST(drug_exposure_start_date AS STRING), 5, 2), SUBSTR(CAST(drug_exposure_start_date AS STRING), 7, 2)), 'UTC') AS drug_exposure_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_exposure_end_date AS STRING), 1, 4), SUBSTR(CAST(drug_exposure_end_date AS STRING), 5, 2), SUBSTR(CAST(drug_exposure_end_date AS STRING), 7, 2)), 'UTC') AS drug_exposure_end_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_exposure_end_date AS STRING), 1, 4), SUBSTR(CAST(drug_exposure_end_date AS STRING), 5, 2), SUBSTR(CAST(drug_exposure_end_date AS STRING), 7, 2)), 'UTC') AS drug_exposure_end_date, TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(verbatim_end_date AS STRING), 1, 4), SUBSTR(CAST(verbatim_end_date AS STRING), 5, 2), SUBSTR(CAST(verbatim_end_date AS STRING), 7, 2)), 'UTC') AS verbatim_end_date,
drug_type_concept_id,
stop_reason,
refills,

491
Impala/OMOP_Parquet_v5.2.sql Normal file
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@ -0,0 +1,491 @@
-- Use the search/replace regex in an editor to fix DATE columns:
-- ([^ ]+) VARCHAR\(8\), \-\- DATE
-- TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST($1 AS STRING), 1, 4), SUBSTR(CAST($1 AS STRING), 5, 2), SUBSTR(CAST($1 AS STRING), 7, 2)), 'UTC') AS $1,
CREATE TABLE omop_cdm_parquet.concept
STORED AS PARQUET
AS
SELECT
concept_id,
concept_name,
domain_id,
vocabulary_id,
concept_class_id,
standard_concept,
concept_code,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.concept;
CREATE TABLE omop_cdm_parquet.vocabulary
STORED AS PARQUET
AS
SELECT * from omop_cdm.vocabulary;
CREATE TABLE omop_cdm_parquet.domain
STORED AS PARQUET
AS
SELECT * from omop_cdm.domain;
CREATE TABLE omop_cdm_parquet.concept_class
STORED AS PARQUET
AS
SELECT * from omop_cdm.concept_class;
CREATE TABLE omop_cdm_parquet.concept_relationship
STORED AS PARQUET
AS
SELECT
concept_id_1,
concept_id_2,
relationship_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.concept_relationship;
CREATE TABLE omop_cdm_parquet.relationship
STORED AS PARQUET
AS
SELECT * from omop_cdm.relationship;
CREATE TABLE omop_cdm_parquet.concept_synonym
STORED AS PARQUET
AS
SELECT * from omop_cdm.concept_synonym;
CREATE TABLE omop_cdm_parquet.concept_ancestor
STORED AS PARQUET
AS
SELECT * from omop_cdm.concept_ancestor;
CREATE TABLE omop_cdm_parquet.source_to_concept_map
STORED AS PARQUET
AS
SELECT
source_code,
source_concept_id,
source_vocabulary_id,
source_code_description,
target_concept_id,
target_vocabulary_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.source_to_concept_map;
CREATE TABLE omop_cdm_parquet.drug_strength
STORED AS PARQUET
AS
SELECT
drug_concept_id,
ingredient_concept_id,
amount_value, -- NUMERIC
amount_unit_concept_id,
numerator_value, -- NUMERIC
numerator_unit_concept_id,
denominator_value, -- NUMERIC
denominator_unit_concept_id,
box_size,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_start_date AS STRING), 1, 4), SUBSTR(CAST(valid_start_date AS STRING), 5, 2), SUBSTR(CAST(valid_start_date AS STRING), 7, 2)), 'UTC') AS valid_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(valid_end_date AS STRING), 1, 4), SUBSTR(CAST(valid_end_date AS STRING), 5, 2), SUBSTR(CAST(valid_end_date AS STRING), 7, 2)), 'UTC') AS valid_end_date,
nullif(invalid_reason, '') AS invalid_reason
FROM omop_cdm.drug_strength;
CREATE TABLE omop_cdm_parquet.cohort_definition
STORED AS PARQUET
AS
SELECT
cohort_definition_id,
cohort_definition_name,
cohort_definition_description, -- TEXT
definition_type_concept_id,
cohort_definition_syntax, -- TEXT
subject_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(cohort_initiation_date AS STRING), 1, 4), SUBSTR(CAST(cohort_initiation_date AS STRING), 5, 2), SUBSTR(CAST(cohort_initiation_date AS STRING), 7, 2)), 'UTC') AS cohort_initiation_date
FROM omop_cdm.cohort_definition;
CREATE TABLE omop_cdm_parquet.attribute_definition
STORED AS PARQUET
AS
SELECT * from omop_cdm.attribute_definition;
CREATE TABLE omop_cdm_parquet.cdm_source
STORED AS PARQUET
AS
SELECT
cdm_source_name,
cdm_source_abbreviation,
cdm_holder,
source_description, -- TEXT
source_documentation_reference,
cdm_etl_reference,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(source_release_date AS STRING), 1, 4), SUBSTR(CAST(source_release_date AS STRING), 5, 2), SUBSTR(CAST(source_release_date AS STRING), 7, 2)), 'UTC') AS source_release_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(cdm_release_date AS STRING), 1, 4), SUBSTR(CAST(cdm_release_date AS STRING), 5, 2), SUBSTR(CAST(cdm_release_date AS STRING), 7, 2)), 'UTC') AS cdm_release_date,
cdm_version,
vocabulary_version
FROM omop_cdm.cdm_source;
CREATE TABLE omop_cdm_parquet.person
STORED AS PARQUET
AS
SELECT
person_id,
gender_concept_id,
year_of_birth,
month_of_birth,
day_of_birth,
TO_UTC_TIMESTAMP(CONCAT_WS('-', CAST(year_of_birth AS STRING), SUBSTR(CONCAT('0', CAST(month_of_birth AS STRING)), -2), SUBSTR(CONCAT('0', CAST(day_of_birth AS STRING)), -2)), 'UTC') AS birth_datetime,
race_concept_id,
ethnicity_concept_id,
location_id,
provider_id,
care_site_id,
person_source_value,
gender_source_value,
gender_source_concept_id,
race_source_value,
race_source_concept_id,
ethnicity_source_value,
ethnicity_source_concept_id
FROM omop_cdm.person;
CREATE TABLE omop_cdm_parquet.observation_period
STORED AS PARQUET
AS
SELECT
observation_period_id,
person_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(observation_period_start_date AS STRING), 1, 4), SUBSTR(CAST(observation_period_start_date AS STRING), 5, 2), SUBSTR(CAST(observation_period_start_date AS STRING), 7, 2)), 'UTC') AS observation_period_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(observation_period_start_date AS STRING), 1, 4), SUBSTR(CAST(observation_period_start_date AS STRING), 5, 2), SUBSTR(CAST(observation_period_start_date AS STRING), 7, 2)), 'UTC') AS observation_period_start_datetime,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(observation_period_end_date AS STRING), 1, 4), SUBSTR(CAST(observation_period_end_date AS STRING), 5, 2), SUBSTR(CAST(observation_period_end_date AS STRING), 7, 2)), 'UTC') AS observation_period_end_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(observation_period_end_date AS STRING), 1, 4), SUBSTR(CAST(observation_period_end_date AS STRING), 5, 2), SUBSTR(CAST(observation_period_end_date AS STRING), 7, 2)), 'UTC') AS observation_period_end_datetime,
period_type_concept_id
FROM omop_cdm.observation_period;
CREATE TABLE omop_cdm_parquet.specimen
STORED AS PARQUET
AS
SELECT
specimen_id,
person_id,
specimen_concept_id,
specimen_type_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(specimen_date AS STRING), 1, 4), SUBSTR(CAST(specimen_date AS STRING), 5, 2), SUBSTR(CAST(specimen_date AS STRING), 7, 2)), 'UTC') AS specimen_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(specimen_date AS STRING), 1, 4), SUBSTR(CAST(specimen_date AS STRING), 5, 2), SUBSTR(CAST(specimen_date AS STRING), 7, 2)), 'UTC') AS specimen_datetime,
quantity, -- NUMERIC
unit_concept_id,
anatomic_site_concept_id,
disease_status_concept_id,
specimen_source_id,
specimen_source_value,
unit_source_value,
anatomic_site_source_value,
disease_status_source_value
FROM omop_cdm.specimen;
CREATE TABLE omop_cdm_parquet.death
STORED AS PARQUET
AS
SELECT
person_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(death_date AS STRING), 1, 4), SUBSTR(CAST(death_date AS STRING), 5, 2), SUBSTR(CAST(death_date AS STRING), 7, 2)), 'UTC') AS death_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(death_date AS STRING), 1, 4), SUBSTR(CAST(death_date AS STRING), 5, 2), SUBSTR(CAST(death_date AS STRING), 7, 2)), 'UTC') AS death_datetime,
death_type_concept_id,
cause_concept_id,
cause_source_value,
cause_source_concept_id
FROM omop_cdm.death;
CREATE TABLE omop_cdm_parquet.visit_occurrence
STORED AS PARQUET
AS
SELECT
visit_occurrence_id,
person_id,
visit_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(visit_start_date AS STRING), 1, 4), SUBSTR(CAST(visit_start_date AS STRING), 5, 2), SUBSTR(CAST(visit_start_date AS STRING), 7, 2)), 'UTC') AS visit_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(visit_start_date AS STRING), 1, 4), SUBSTR(CAST(visit_start_date AS STRING), 5, 2), SUBSTR(CAST(visit_start_date AS STRING), 7, 2)), 'UTC') AS visit_start_datetime,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(visit_end_date AS STRING), 1, 4), SUBSTR(CAST(visit_end_date AS STRING), 5, 2), SUBSTR(CAST(visit_end_date AS STRING), 7, 2)), 'UTC') AS visit_end_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(visit_end_date AS STRING), 1, 4), SUBSTR(CAST(visit_end_date AS STRING), 5, 2), SUBSTR(CAST(visit_end_date AS STRING), 7, 2)), 'UTC') AS visit_end_datetime,
visit_type_concept_id,
provider_id,
care_site_id,
visit_source_value,
visit_source_concept_id
FROM omop_cdm.visit_occurrence;
CREATE TABLE omop_cdm_parquet.procedure_occurrence
STORED AS PARQUET
AS
SELECT
procedure_occurrence_id,
person_id,
procedure_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(procedure_date AS STRING), 1, 4), SUBSTR(CAST(procedure_date AS STRING), 5, 2), SUBSTR(CAST(procedure_date AS STRING), 7, 2)), 'UTC') AS procedure_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(procedure_date AS STRING), 1, 4), SUBSTR(CAST(procedure_date AS STRING), 5, 2), SUBSTR(CAST(procedure_date AS STRING), 7, 2)), 'UTC') AS procedure_datetime,
procedure_type_concept_id,
modifier_concept_id,
quantity,
provider_id,
visit_occurrence_id,
procedure_source_value,
procedure_source_concept_id,
qualifier_source_value
FROM omop_cdm.procedure_occurrence;
CREATE TABLE omop_cdm_parquet.drug_exposure
STORED AS PARQUET
AS
SELECT
drug_exposure_id,
person_id,
drug_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_exposure_start_date AS STRING), 1, 4), SUBSTR(CAST(drug_exposure_start_date AS STRING), 5, 2), SUBSTR(CAST(drug_exposure_start_date AS STRING), 7, 2)), 'UTC') AS drug_exposure_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_exposure_start_date AS STRING), 1, 4), SUBSTR(CAST(drug_exposure_start_date AS STRING), 5, 2), SUBSTR(CAST(drug_exposure_start_date AS STRING), 7, 2)), 'UTC') AS drug_exposure_start_datetime,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_exposure_end_date AS STRING), 1, 4), SUBSTR(CAST(drug_exposure_end_date AS STRING), 5, 2), SUBSTR(CAST(drug_exposure_end_date AS STRING), 7, 2)), 'UTC') AS drug_exposure_end_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_exposure_end_date AS STRING), 1, 4), SUBSTR(CAST(drug_exposure_end_date AS STRING), 5, 2), SUBSTR(CAST(drug_exposure_end_date AS STRING), 7, 2)), 'UTC') AS drug_exposure_end_datetime,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(verbatim_end_date AS STRING), 1, 4), SUBSTR(CAST(verbatim_end_date AS STRING), 5, 2), SUBSTR(CAST(verbatim_end_date AS STRING), 7, 2)), 'UTC') AS verbatim_end_date,
drug_type_concept_id,
stop_reason,
refills,
quantity, -- NUMERIC
days_supply,
sig, -- TEXT
route_concept_id,
effective_drug_dose, -- NUMERIC
dose_unit_concept_id,
lot_number,
provider_id,
visit_occurrence_id,
drug_source_value,
drug_source_concept_id,
route_source_value,
dose_unit_source_value
FROM omop_cdm.drug_exposure;
CREATE TABLE omop_cdm_parquet.device_exposure
STORED AS PARQUET
AS
SELECT
device_exposure_id,
person_id,
device_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(device_exposure_start_date AS STRING), 1, 4), SUBSTR(CAST(device_exposure_start_date AS STRING), 5, 2), SUBSTR(CAST(device_exposure_start_date AS STRING), 7, 2)), 'UTC') AS device_exposure_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(device_exposure_start_date AS STRING), 1, 4), SUBSTR(CAST(device_exposure_start_date AS STRING), 5, 2), SUBSTR(CAST(device_exposure_start_date AS STRING), 7, 2)), 'UTC') AS device_exposure_start_datetime,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(device_exposure_end_date AS STRING), 1, 4), SUBSTR(CAST(device_exposure_end_date AS STRING), 5, 2), SUBSTR(CAST(device_exposure_end_date AS STRING), 7, 2)), 'UTC') AS device_exposure_end_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(device_exposure_end_date AS STRING), 1, 4), SUBSTR(CAST(device_exposure_end_date AS STRING), 5, 2), SUBSTR(CAST(device_exposure_end_date AS STRING), 7, 2)), 'UTC') AS device_exposure_end_datetime,
device_type_concept_id,
unique_device_id,
quantity,
provider_id,
visit_occurrence_id,
device_source_value,
device_source_concept_id
FROM omop_cdm.device_exposure;
CREATE TABLE omop_cdm_parquet.condition_occurrence
STORED AS PARQUET
AS
SELECT
condition_occurrence_id,
person_id,
condition_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(condition_start_date AS STRING), 1, 4), SUBSTR(CAST(condition_start_date AS STRING), 5, 2), SUBSTR(CAST(condition_start_date AS STRING), 7, 2)), 'UTC') AS condition_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(condition_start_date AS STRING), 1, 4), SUBSTR(CAST(condition_start_date AS STRING), 5, 2), SUBSTR(CAST(condition_start_date AS STRING), 7, 2)), 'UTC') AS condition_start_datetime,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(condition_end_date AS STRING), 1, 4), SUBSTR(CAST(condition_end_date AS STRING), 5, 2), SUBSTR(CAST(condition_end_date AS STRING), 7, 2)), 'UTC') AS condition_end_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(condition_end_date AS STRING), 1, 4), SUBSTR(CAST(condition_end_date AS STRING), 5, 2), SUBSTR(CAST(condition_end_date AS STRING), 7, 2)), 'UTC') AS condition_end_datetime,
condition_type_concept_id,
stop_reason,
provider_id,
visit_occurrence_id,
condition_source_value,
condition_source_concept_id
FROM omop_cdm.condition_occurrence;
CREATE TABLE omop_cdm_parquet.measurement
STORED AS PARQUET
AS
SELECT
measurement_id,
person_id,
measurement_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(measurement_date AS STRING), 1, 4), SUBSTR(CAST(measurement_date AS STRING), 5, 2), SUBSTR(CAST(measurement_date AS STRING), 7, 2)), 'UTC') AS measurement_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(measurement_date AS STRING), 1, 4), SUBSTR(CAST(measurement_date AS STRING), 5, 2), SUBSTR(CAST(measurement_date AS STRING), 7, 2)), 'UTC') AS measurement_datetime,
measurement_type_concept_id,
operator_concept_id,
value_as_number, -- NUMERIC
value_as_concept_id,
unit_concept_id,
range_low, -- NUMERIC
range_high, -- NUMERIC
provider_id,
visit_occurrence_id,
measurement_source_value,
measurement_source_concept_id,
unit_source_value,
value_source_value
FROM omop_cdm.measurement;
CREATE TABLE omop_cdm_parquet.note
STORED AS PARQUET
AS
SELECT
note_id,
person_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(note_date AS STRING), 1, 4), SUBSTR(CAST(note_date AS STRING), 5, 2), SUBSTR(CAST(note_date AS STRING), 7, 2)), 'UTC') AS note_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(note_date AS STRING), 1, 4), SUBSTR(CAST(note_date AS STRING), 5, 2), SUBSTR(CAST(note_date AS STRING), 7, 2)), 'UTC') AS note_datetime,
note_type_concept_id,
note_text, -- TEXT
provider_id,
visit_occurrence_id,
note_source_value
FROM omop_cdm.note;
CREATE TABLE omop_cdm_parquet.observation
STORED AS PARQUET
AS
SELECT
observation_id,
person_id,
observation_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(observation_date AS STRING), 1, 4), SUBSTR(CAST(observation_date AS STRING), 5, 2), SUBSTR(CAST(observation_date AS STRING), 7, 2)), 'UTC') AS observation_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(observation_date AS STRING), 1, 4), SUBSTR(CAST(observation_date AS STRING), 5, 2), SUBSTR(CAST(observation_date AS STRING), 7, 2)), 'UTC') AS observation_datetime,
observation_type_concept_id,
value_as_number, -- NUMERIC
value_as_string,
value_as_concept_id,
qualifier_concept_id,
unit_concept_id,
provider_id,
visit_occurrence_id,
observation_source_value,
observation_source_concept_id ,
unit_source_value,
qualifier_source_value
FROM omop_cdm.observation;
CREATE TABLE omop_cdm_parquet.fact_relationship
STORED AS PARQUET
AS
SELECT * from omop_cdm.fact_relationship;
CREATE TABLE omop_cdm_parquet.`location`
STORED AS PARQUET
AS
SELECT * from omop_cdm.`location`;
CREATE TABLE omop_cdm_parquet.care_site
STORED AS PARQUET
AS
SELECT * from omop_cdm.care_site;
CREATE TABLE omop_cdm_parquet.provider
STORED AS PARQUET
AS
SELECT * from omop_cdm.provider;
CREATE TABLE omop_cdm_parquet.payer_plan_period
STORED AS PARQUET
AS
SELECT
payer_plan_period_id,
person_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(payer_plan_period_start_date AS STRING), 1, 4), SUBSTR(CAST(payer_plan_period_start_date AS STRING), 5, 2), SUBSTR(CAST(payer_plan_period_start_date AS STRING), 7, 2)), 'UTC') AS payer_plan_period_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(payer_plan_period_end_date AS STRING), 1, 4), SUBSTR(CAST(payer_plan_period_end_date AS STRING), 5, 2), SUBSTR(CAST(payer_plan_period_end_date AS STRING), 7, 2)), 'UTC') AS payer_plan_period_end_date,
payer_source_value,
plan_source_value,
family_source_value
FROM omop_cdm.payer_plan_period;
/* The individual cost tables are being phased out and will disappear soon
CREATE TABLE omop_cdm_parquet.visit_cost
STORED AS PARQUET
AS
SELECT * from omop_cdm.visit_cost;
CREATE TABLE omop_cdm_parquet.procedure_cost
STORED AS PARQUET
AS
SELECT * from omop_cdm.procedure_cost;
CREATE TABLE omop_cdm_parquet.drug_cost
STORED AS PARQUET
AS
SELECT * from omop_cdm.drug_cost;
CREATE TABLE omop_cdm_parquet.device_cost
STORED AS PARQUET
AS
SELECT * from omop_cdm.device_cost;
*/
CREATE TABLE omop_cdm_parquet.cost
STORED AS PARQUET
AS
SELECT * from omop_cdm.cost;
CREATE TABLE omop_cdm_parquet.cohort
STORED AS PARQUET
AS
SELECT
cohort_definition_id,
subject_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(cohort_start_date AS STRING), 1, 4), SUBSTR(CAST(cohort_start_date AS STRING), 5, 2), SUBSTR(CAST(cohort_start_date AS STRING), 7, 2)), 'UTC') AS cohort_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(cohort_end_date AS STRING), 1, 4), SUBSTR(CAST(cohort_end_date AS STRING), 5, 2), SUBSTR(CAST(cohort_end_date AS STRING), 7, 2)), 'UTC') AS cohort_end_date
FROM omop_cdm.cohort;
CREATE TABLE omop_cdm_parquet.cohort_attribute
STORED AS PARQUET
AS
SELECT
cohort_definition_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(cohort_start_date AS STRING), 1, 4), SUBSTR(CAST(cohort_start_date AS STRING), 5, 2), SUBSTR(CAST(cohort_start_date AS STRING), 7, 2)), 'UTC') AS cohort_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(cohort_end_date AS STRING), 1, 4), SUBSTR(CAST(cohort_end_date AS STRING), 5, 2), SUBSTR(CAST(cohort_end_date AS STRING), 7, 2)), 'UTC') AS cohort_end_date,
subject_id,
attribute_definition_id,
value_as_number, -- NUMERIC
value_as_concept_id
FROM omop_cdm.cohort_attribute;
CREATE TABLE omop_cdm_parquet.drug_era
STORED AS PARQUET
AS
SELECT
drug_era_id,
person_id,
drug_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_era_start_date AS STRING), 1, 4), SUBSTR(CAST(drug_era_start_date AS STRING), 5, 2), SUBSTR(CAST(drug_era_start_date AS STRING), 7, 2)), 'UTC') AS drug_era_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(drug_era_end_date AS STRING), 1, 4), SUBSTR(CAST(drug_era_end_date AS STRING), 5, 2), SUBSTR(CAST(drug_era_end_date AS STRING), 7, 2)), 'UTC') AS drug_era_end_date,
drug_exposure_count,
gap_days
FROM omop_cdm.drug_era;
CREATE TABLE omop_cdm_parquet.dose_era
STORED AS PARQUET
AS
SELECT
dose_era_id,
person_id,
drug_concept_id,
unit_concept_id,
dose_value, -- NUMERIC
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(dose_era_start_date AS STRING), 1, 4), SUBSTR(CAST(dose_era_start_date AS STRING), 5, 2), SUBSTR(CAST(dose_era_start_date AS STRING), 7, 2)), 'UTC') AS dose_era_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(dose_era_end_date AS STRING), 1, 4), SUBSTR(CAST(dose_era_end_date AS STRING), 5, 2), SUBSTR(CAST(dose_era_end_date AS STRING), 7, 2)), 'UTC') AS dose_era_end_date
FROM omop_cdm.dose_era;
CREATE TABLE omop_cdm_parquet.condition_era
STORED AS PARQUET
AS
SELECT
condition_era_id,
person_id,
condition_concept_id,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(condition_era_start_date AS STRING), 1, 4), SUBSTR(CAST(condition_era_start_date AS STRING), 5, 2), SUBSTR(CAST(condition_era_start_date AS STRING), 7, 2)), 'UTC') AS condition_era_start_date,
TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(condition_era_end_date AS STRING), 1, 4), SUBSTR(CAST(condition_era_end_date AS STRING), 5, 2), SUBSTR(CAST(condition_era_end_date AS STRING), 7, 2)), 'UTC') AS condition_era_end_date,
condition_occurrence_count
FROM omop_cdm.condition_era;

18
Oracle/OMOP CDM constraints - Oracle.sql
View File

@ -17,19 +17,19 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ### #####
# # ## ## # # # # # # # # ## ## # # # ## # # # # #### # # #### ##### ##### ## # # # ##### ####
# # # # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
# # # # # # # ###### # # # # # # # # ###### # # # # # # # # # #### # # # # # # # # # # ####
# # # # # # # # # # # # # # # ### # ### # # # # # # # # # # ##### ###### # # # # # #
# # # # # # # # # # # # # # # # # ### # ### # # # # # # # ## # # # # # # # # # ## # # #
####### # # ####### # ##### ###### # # ## ##### ### ##### ### ### ##### #### # # #### # # # # # # # # # ####
####### # # ####### ###### ##### ###### # # ####### ##### #####
# # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### ####
# # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
# # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # ####
# # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # #
# # # # # # # # # # # # # # # # # ### # # # # # # ## # # # # # # # # # ## # # #
####### # # ####### # ##### ###### # # ## ##### ### ####### ##### #### # # #### # # # # # # # # # ####
script to create constraints within OMOP common data model, version 5.1.0 for Oracle database
script to create constraints within OMOP common data model, version 5.2 for Oracle database
last revised: 12 Oct 2014
last revised: 14 July 2017
author: Patrick Ryan

27
Oracle/OMOP CDM ddl - Oracle.sql
View File

@ -17,18 +17,18 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ###
# # ## ## # # # # # # # # ## ## # # # ## # #
# # # # # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # # #
# # # # # # # # # # # # # # # ### # ### # #
# # # # # # # # # # # # # # # # # ### # ### # #
####### # # ####### # ##### ###### # # ## ##### ### ##### ### ###
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# # ## ## # # # # # # # # ## ## # # # # #
# # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### #####
# # # # # # # # # # # # # # # ### #
# # # # # # # # # # # # # # # # # ### #
####### # # ####### # ##### ###### # # ## ##### ### #######
script to create OMOP common data model, version 5.1.0 for Oracle database
script to create OMOP common data model, version 5.2 for Oracle database
last revised: 1-May-2016
last revised: 14 July 2017
Authors: Patrick Ryan, Christian Reich
@ -344,10 +344,11 @@ CREATE TABLE drug_exposure
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL ,
drug_exposure_start_datetime TIMESTAMP WITH TIME ZONE NOT NULL ,
drug_exposure_end_date DATE NULL ,
drug_exposure_end_datetime TIMESTAMP WITH TIME ZONE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
drug_exposure_start_datetime TIMESTAMP WITH TIME ZONE NOT NULL ,
drug_exposure_end_date DATE NOT NULL ,
drug_exposure_end_datetime TIMESTAMP WITH TIME ZONE NULL ,
verbatim_end_date DATE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL ,
quantity FLOAT NULL ,

18
Oracle/OMOP CDM indexes required - Oracle - With constraints.sql
View File

@ -17,18 +17,18 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ### ###
# # ## ## # # # # # # # # ## ## # # # ## # # # # # ##### ###### # # ###### ####
# # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
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# # # # # # # # # # # # # # # ### # # # # # # # # ## # #
# # # # # # # # # # # # # # # # # ### # # # ## # # # # # # # #
####### # # ####### # ##### ###### # # ## ##### ### ####### ### # # ##### ###### # # ###### ####
script to create the required indexes within OMOP common data model, version 5.1.0 for Oracle database
script to create the required indexes within OMOP common data model, version 5.2 for Oracle database
last revised: 12 Oct 2014
last revised: 17 July 2017
author: Patrick Ryan

18
Oracle/OMOP CDM indexes required - Oracle - Without constraints.sql
View File

@ -17,18 +17,18 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ### ###
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####### # # ####### # ##### ###### # # ## ##### ### ####### ### # # ##### ###### # # ###### ####
script to create the required indexes within OMOP common data model, version 5.1.0 for Oracle database
script to create the required indexes within OMOP common data model, version 5.2 for Oracle database
last revised: 12 Oct 2014
last revised: 14 July 2017
author: Patrick Ryan

18
PostgreSQL/OMOP CDM constraints - PostgreSQL.sql
View File

@ -17,18 +17,18 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ### #####
# # ## ## # # # # # # # # ## ## # # # ## # # # # #### # # #### ##### ##### ## # # # ##### ####
# # # # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
# # # # # # # ###### # # # # # # # # ###### # # # # # # # # # #### # # # # # # # # # # ####
# # # # # # # # # # # # # # # ### # ### # # # # # # # # # # ##### ###### # # # # # #
# # # # # # # # # # # # # # # # # ### # ### # # # # # # # ## # # # # # # # # # ## # # #
####### # # ####### # ##### ###### # # ## ##### ### ##### ### ### ##### #### # # #### # # # # # # # # # ####
####### # # ####### ###### ##### ###### # # ####### ##### #####
# # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### ####
# # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
# # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # ####
# # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # #
# # # # # # # # # # # # # # # # # ### # # # # # # ## # # # # # # # # # ## # # #
####### # # ####### # ##### ###### # # ## ##### ### ####### ##### #### # # #### # # # # # # # # # ####
script to create constraints within OMOP common data model, version 5.1.0 for PostgreSQL database
script to create constraints within OMOP common data model, version 5.2 for PostgreSQL database
last revised: 12 Oct 2014
last revised: 14 July 2017
author: Patrick Ryan

27
PostgreSQL/OMOP CDM ddl - PostgreSQL.sql
View File

@ -17,18 +17,18 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ###
# # ## ## # # # # # # # # ## ## # # # ## # #
# # # # # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # # #
# # # # # # # # # # # # # # # ### # ### # #
# # # # # # # # # # # # # # # # # ### # ### # #
####### # # ####### # ##### ###### # # ## ##### ### ##### ### ###
####### # # ####### ###### ##### ###### # # ####### #####
# # ## ## # # # # # # # # ## ## # # # # #
# # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### #####
# # # # # # # # # # # # # # # ### #
# # # # # # # # # # # # # # # # # ### #
####### # # ####### # ##### ###### # # ## ##### ### #######
script to create OMOP common data model, version 5.1.0 for PostgreSQL database
script to create OMOP common data model, version 5.2 for PostgreSQL database
last revised: 1-May-2016
last revised: 14 July 2017
Authors: Patrick Ryan, Christian Reich
@ -344,10 +344,11 @@ CREATE TABLE drug_exposure
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL ,
drug_exposure_start_datetime TIMESTAMP NOT NULL ,
drug_exposure_end_date DATE NULL ,
drug_exposure_end_datetime TIMESTAMP NULL ,
drug_type_concept_id INTEGER NOT NULL ,
drug_exposure_start_datetime TIMESTAMP NOT NULL ,
drug_exposure_end_date DATE NOT NULL ,
drug_exposure_end_datetime TIMESTAMP NULL ,
verbatim_end_date DATE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL ,
quantity NUMERIC NULL ,

18
PostgreSQL/OMOP CDM indexes required - PostgreSQL.sql
View File

@ -17,18 +17,18 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ### ###
# # ## ## # # # # # # # # ## ## # # # ## # # # # # ##### ###### # # ###### ####
# # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # # # # # # # # # ##### ## ##### ####
# # # # # # # # # # # # # # # ### # ### # # # # # # # # # ## # #
# # # # # # # # # # # # # # # # # ### # ### # # # # ## # # # # # # # #
####### # # ####### # ##### ###### # # ## ##### ### ##### ### ### ### # # ##### ###### # # ###### ####
####### # # ####### ###### ##### ###### # # ####### ##### ###
# # ## ## # # # # # # # # ## ## # # # # # # # # ##### ###### # # ###### ####
# # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### ##### # # # # # # ##### ## ##### ####
# # # # # # # # # # # # # # # ### # # # # # # # # ## # #
# # # # # # # # # # # # # # # # # ### # # # ## # # # # # # # #
####### # # ####### # ##### ###### # # ## ##### ### ####### ### # # ##### ###### # # ###### ####
script to create the required indexes within OMOP common data model, version 5.1.0 for PostgreSQL database
script to create the required indexes within OMOP common data model, version 5.2 for PostgreSQL database
last revised: 12 Oct 2014
last revised: 14 July 2017
author: Patrick Ryan

56
README.md
View File

@ -1,57 +1,17 @@
Common Data Model v5.1.1
Common Data Model v5.2
=================
See full CDM specification file on our github [wiki](https://github.com/OHDSI/CommonDataModel/wiki) or in the [CDM V5.1.1 PDF](https://github.com/OHDSI/CommonDataModel/blob/master/OMOP_CDM_v5_1_1.pdf)
See full CDM specification file on our github [wiki](https://github.com/OHDSI/CommonDataModel/wiki) or in the [CDM V5.2 PDF](**link needed**)
Release Notes for v5.1.1
Release Notes for v5.2.0
=============
This version has a small bug-fix for impala to make it compatible with ATLAS cohort generation.
This version is based on the CDM working group proposals:
* [#71](https://github.com/OHDSI/CommonDataModel/issues/71)
* Adds the field VERBATIM_END_DATE to DRUG_EXPOSURE and makes DRUG_EXPOSURE_END_DATE a required field
Release Notes for v5.1.0
=============
This version is based on the CDM working group proposal [#60](https://github.com/OHDSI/CommonDataModel/issues/60) and [#59](https://github.com/OHDSI/CommonDataModel/issues/59) and is **backwards compatibile with v5.0.1**. The proposed and accepted changes include adding a datetime field to every table that had a date column and adding field DENOMINATOR_VALUE to the DRUG_STRENGTH table. These were the new columns added:
and is **backwards compatibile with v5.0.1**. The proposed and accepted changes include adding a datetime field to every table that had a date column and adding field DENOMINATOR_VALUE to the DRUG_STRENGTH table. These were the new columns added:
**PERSON**
* birth_datetime, not required
**SPECIMEN**
* specimen_datetime, not required
**DEATH**
* death_datetime, not required
**VISIT_OCCURRENCE**
* visit_start_datetime, not required
* visit_end_datetime, not required
**PROCEDURE_OCCURRENCE**
* procedure_datetime, not required
**DRUG_EXPOSURE**
* drug_exposure_start_datetime, not required
* drug_exposure_end_datetime, not required
**DRUG_STRENGTH**
* DENOMINATOR_VALUE, not required
**DEVICE_EXPOSURE**
* device_exposure_start_datetime, not required
* device_exposure_end_datetime, not required
**CONDITION_OCCURRENCE**
* condition_start_datetime, not required
* condition_end_datetime, not required
**MEASUREMENT**
* measurement_datetime as time, not required
**OBSERVATION**
* observation_datetime, not required
**NOTE**
* note_datetime, not required
There are additional changes listed on the [OHDSI wiki](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:next_cdm) that have been accepted but are not listed in this version because after being accepted they were never added to the DDL. Version 5.1.0 as it is now is being used by members of the community and any changes would cause problems so the additional accepted proposals will be added in subsequent versions.
---------

14
Sql Server/OMOP CDM constraints - SQL Server.sql
View File

@ -17,13 +17,13 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ### #####
# # ## ## # # # # # # # # ## ## # # # ## # # # # #### # # #### ##### ##### ## # # # ##### ####
# # # # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
# # # # # # # ###### # # # # # # # # ###### # # # # # # # # # #### # # # # # # # # # # ####
# # # # # # # # # # # # # # # ### # ### # # # # # # # # # # ##### ###### # # # # # #
# # # # # # # # # # # # # # # # # ### # ### # # # # # # # ## # # # # # # # # # ## # # #
####### # # ####### # ##### ###### # # ## ##### ### ##### ### ### ##### #### # # #### # # # # # # # # # ####
####### # # ####### ###### ##### ###### # # ####### ##### #####
# # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### ####
# # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
# # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # ####
# # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # #
# # # # # # # # # # # # # # # # # ### # # # # # # ## # # # # # # # # # ## # # #
####### # # ####### # ##### ###### # # ## ##### ### ####### ##### #### # # #### # # # # # # # # # ####
script to create constraints within OMOP common data model, version 5.1.0 for SQL Server database

170
Sql Server/OMOP CDM ddl - SQL Server.sql
View File

@ -17,18 +17,18 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ###
# # ## ## # # # # # # # # ## ## # # # ## # #
# # # # # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # # #
# # # # # # # # # # # # # # # ### # ### # #
# # # # # # # # # # # # # # # # # ### # ### # #
####### # # ####### # ##### ###### # # ## ##### ### ##### ### ###
####### # # ####### ###### ##### ###### # # ####### #####
# # ## ## # # # # # # # # ## ## # # # # #
# # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### #####
# # # # # # # # # # # # # # # ### #
# # # # # # # # # # # # # # # # # ### #
####### # # ####### # ##### ###### # # ## ##### ### #######
script to create OMOP common data model, version 5.1.0 for SQL Server database
script to create OMOP common data model, version 5.2 for SQL Server database
last revised: 1-May-2016
last revised: 14-July-2017
Authors: Patrick Ryan, Christian Reich
@ -227,9 +227,9 @@ CREATE TABLE person
person_id INTEGER NOT NULL ,
gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL,
month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL,
birth_datetime DATETIME2 NULL,
birth_datetime DATETIME2 NULL,
race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL,
@ -239,8 +239,8 @@ CREATE TABLE person
gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL,
race_source_value VARCHAR(50) NULL,
race_source_concept_id INTEGER NULL,
ethnicity_source_value VARCHAR(50) NULL,
race_source_concept_id INTEGER NULL,
ethnicity_source_value VARCHAR(50) NULL,
ethnicity_source_concept_id INTEGER NULL
)
;
@ -254,10 +254,10 @@ CREATE TABLE observation_period
observation_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
observation_period_start_date DATE NOT NULL ,
observation_period_start_datetime DATETIME2 NOT NULL ,
observation_period_start_datetime DATETIME2 NOT NULL ,
observation_period_end_date DATE NOT NULL ,
observation_period_end_datetime DATETIME2 NOT NULL ,
period_type_concept_id INTEGER NOT NULL
observation_period_end_datetime DATETIME2 NOT NULL ,
period_type_concept_id INTEGER NOT NULL
)
;
@ -270,15 +270,15 @@ CREATE TABLE specimen
specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NOT NULL ,
specimen_datetime DATETIME2 NULL ,
specimen_datetime DATETIME2 NULL ,
quantity FLOAT NULL ,
unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL ,
disease_status_concept_id INTEGER NULL ,
specimen_source_id VARCHAR(50) NULL ,
specimen_source_id VARCHAR(50) NULL ,
specimen_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
)
;
@ -323,16 +323,16 @@ CREATE TABLE procedure_occurrence
procedure_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NOT NULL ,
procedure_datetime DATETIME2 NOT NULL ,
procedure_date DATE NOT NULL ,
procedure_datetime DATETIME2 NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
procedure_source_value VARCHAR(50) NULL ,
procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER NULL ,
qualifier_source_value VARCHAR(50) NULL
qualifier_source_value VARCHAR(50) NULL
)
;
@ -344,9 +344,10 @@ CREATE TABLE drug_exposure
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER 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_datetime DATETIME2 NULL ,
drug_exposure_start_datetime DATETIME2 NOT NULL ,
drug_exposure_end_date DATE NOT NULL ,
drug_exposure_end_datetime DATETIME2 NULL ,
verbatim_end_date DATE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL ,
@ -356,27 +357,27 @@ CREATE TABLE drug_exposure
route_concept_id INTEGER NULL ,
effective_drug_dose FLOAT NULL ,
dose_unit_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL ,
lot_number VARCHAR(50) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
drug_source_value VARCHAR(50) NULL ,
drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL
drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL
)
;
CREATE TABLE device_exposure
(
device_exposure_id INTEGER NOT NULL ,
device_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NOT NULL ,
device_exposure_start_datetime DATETIME2 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_datetime DATETIME2 NULL ,
device_type_concept_id INTEGER NOT NULL ,
device_exposure_end_datetime DATETIME2 NULL ,
device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
@ -393,14 +394,14 @@ CREATE TABLE condition_occurrence
person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NOT NULL ,
condition_start_datetime DATETIME2 NOT NULL ,
condition_end_date DATE NULL ,
condition_end_datetime DATETIME2 NULL ,
condition_start_datetime DATETIME2 NOT NULL ,
condition_end_date DATE NULL ,
condition_end_datetime DATETIME2 NULL ,
condition_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
provider_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
)
;
@ -409,24 +410,24 @@ CREATE TABLE condition_occurrence
CREATE TABLE measurement
(
measurement_id INTEGER NOT NULL ,
measurement_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_datetime DATETIME2 NULL ,
measurement_datetime DATETIME2 NULL ,
measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL ,
value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
range_low FLOAT NULL ,
range_high FLOAT NULL ,
range_high FLOAT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
value_source_value VARCHAR(50) NULL
value_source_value VARCHAR(50) NULL
)
;
@ -437,7 +438,7 @@ CREATE TABLE note
note_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
note_date DATE NOT NULL ,
note_datetime DATETIME2 NULL ,
note_datetime DATETIME2 NULL ,
note_type_concept_id INTEGER NOT NULL ,
note_text VARCHAR(MAX) NOT NULL ,
provider_id INTEGER NULL ,
@ -562,85 +563,6 @@ CREATE TABLE payer_plan_period
;
/* The individual cost tables are being phased out and will disappear
CREATE TABLE visit_cost
(
visit_cost_id INTEGER NOT NULL ,
visit_occurrence_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
CREATE TABLE procedure_cost
(
procedure_cost_id INTEGER NOT NULL ,
procedure_occurrence_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
revenue_code_concept_id INTEGER NULL ,
payer_plan_period_id INTEGER NULL ,
revenue_code_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_cost
(
drug_cost_id INTEGER NOT NULL ,
drug_exposure_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
ingredient_cost FLOAT NULL ,
dispensing_fee FLOAT NULL ,
average_wholesale_price FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
CREATE TABLE device_cost
(
device_cost_id INTEGER NOT NULL ,
device_exposure_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
*/
CREATE TABLE cost
(
cost_id INTEGER NOT NULL ,

18
Sql Server/OMOP CDM indexes required - SQL Server.sql
View File

@ -17,18 +17,18 @@
/************************
####### # # ####### ###### ##### ###### # # ####### # ### ###
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# # # # # # # ###### # # # # # # # # ###### ##### # # # # # # ##### ## ##### ####
# # # # # # # # # # # # # # # ### # # # # # # # # ## # #
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script to create the required indexes within OMOP common data model, version 5.1.0 for SQL Server database
script to create the required indexes within OMOP common data model, version 5.2 for SQL Server database
last revised: 12 Oct 2014
last revised: 14-July-2017
author: Patrick Ryan