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Merge branch 'main' of https://github.com/OHDSI/CommonDataModel

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Clair Blacketer 2025-03-06 09:21:41 -05:00
parent 766171a6a3 d2dddc5318
commit b4d867c5f1
14 changed files with 2131 additions and 4 deletions
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README
------
v5.3 to v5.4 CDM conversion
NOTES
-----
The *_v53_to_v54_migration.sql scripts are SQL scripts that migrate a v5.3 CDM to a v5.4 CDM.
The changes implemented are found here: http://ohdsi.github.io/CommonDataModel/cdm54Changes.html.
Please replace @cdmDatabaseSchema with your schema name.
Links to database documentation are included in each script to facilitate debugging.

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
-- BigQuery SQL references:
-- https://cloud.google.com/bigquery/docs/reference/standard-sql/data-definition-language#creating_a_new_table_from_an_existing_table
-- https://cloud.google.com/bigquery/docs/manually-changing-schemas
-- https://cloud.google.com/bigquery/docs/reference/standard-sql/data-definition-language#alter_column_set_data_type_statement
-- https://cloud.google.com/bigquery/docs/managing-tables#renaming-table
--
-- VISIT_OCCURRENCE
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
alter table @cdmDatabaseSchema.visit_occurrence rename to visit_occurrence_old;
create table @cdmDatabaseSchema.visit_occurrence
as
select * EXCEPT(admitting_source_concept_id,admitting_source_value,discharge_to_concept_id,discharge_to_source_value),
admitting_source_concept_id as admitted_from_concept_id,
admitting_source_value as admitted_from_source_value,
discharge_to_concept_id as discharged_to_concept_id,
discharge_to_source_value as discharged_to_source_value
from visit_occurrence_old;
--
-- VISIT_DETAIL
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
-- visit_detail_parent_id -> parent_visit_detail_id
alter table @cdmDatabaseSchema.visit_detail rename to visit_detail_old;
create table @cdmDatabaseSchema.visit_occurrence
as
select * EXCEPT(admitting_source_concept_id,admitting_source_value,discharge_to_concept_id,discharge_to_source_value,visit_detail_parent_id),
admitting_source_concept_id as admitted_from_concept_id,
admitting_source_value as admitted_from_source_value,
discharge_to_concept_id as discharged_to_concept_id,
discharge_to_source_value as discharged_to_source_value,
visit_detail_parent_id as parent_visit_detail_id
from visit_detail_old;
-- PROCEDURE_OCCURRENCE
-- + Procedure_end_date
-- + Procedure_end_datetime
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date date;
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime datetime;
-- DEVICE_EXPOSURE
-- Unique_device_id -> Changed to varchar(255) (already a STRING on bigquery)
-- + Production_id
-- + Unit_concept_id
-- + Unit_source_value
-- + Unit_source_concept_id
alter table @cdmDatabaseSchema.device_exposure add column production_id int64;
alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id int64;
alter table @cdmDatabaseSchema.device_exposure add column unit_source_value string;
alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id int64;
-- MEASUREMENT
-- + Unit_source_concept_id
-- + Measurement_event_id
-- + Meas_event_field_concept_id
alter table @cdmDatabaseSchema.measurement add column unit_source_concept_id int64;
alter table @cdmDatabaseSchema.measurement add column measurement_event_id int64;
alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id int64;
-- OBSERVATION
-- + Value_source_value
-- + Observation_event_id
-- + Obs_event_field_concept_id
alter table @cdmDatabaseSchema.observation add column value_source_value string;
alter table @cdmDatabaseSchema.observation add column observation_event_id int64;
alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id int64;
-- NOTE
-- + Note_event_id
-- + Note_event_field_concept_id
alter table @cdmDatabaseSchema.note add column note_event_id int64;
alter table @cdmDatabaseSchema.note add column note_event_field_concept_id int64;
-- LOCATION
-- + Country_concept_id
-- + Country_source_value
-- + Latitude
-- + Longitude
alter table @cdmDatabaseSchema.location add column country_concept_id int64;
alter table @cdmDatabaseSchema.location add column country_source_value string;
alter table @cdmDatabaseSchema.location add column latitude float64;
alter table @cdmDatabaseSchema.location add column longitude float64;
-- EPISODE
create table @cdmDatabaseSchema.episode (
episode_id INT64 not null,
person_id INT64 not null,
episode_concept_id INT64 not null,
episode_start_date date not null,
episode_start_datetime datetime null,
episode_end_date date null,
episode_end_datetime datetime null,
episode_parent_id INT64,
episode_number INT64,
episode_object_concept_id INT64 not null,
episode_type_concept_id INT64 not null,
episode_source_value STRING,
episode_source_concept_id INT64 );
-- EPISODE_EVENT
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id int64 NOT NULL,
event_id int64 NOT NULL,
episode_event_field_concept_id int64 NOT NULL );
-- METADATA
-- + Metadata_id
-- + Value_as_number
alter table @cdmDatabaseSchema.metadata add column metadata_id int64;
alter table @cdmDatabaseSchema.metadata add column value_as_number float64;
-- CDM_SOURCE
-- Cdm_source_name -> Mandatory field
-- Cdm_source_abbreviation -> Mandatory field
-- Cdm_holder -> Mandatory field
-- Source_release_date -> Mandatory field
-- Cdm_release_date -> Mandatory field
-- + Cdm_version_concept_id
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
CREATE TABLE @cdmDatabaseSchema.cdm_source (
cdm_source_name string NOT NULL,
cdm_source_abbreviation string NOT NULL,
cdm_holder string NOT NULL,
source_description string NULL,
source_documentation_reference string NULL,
cdm_etl_reference string NULL,
source_release_date datetime NOT NULL,
cdm_release_date datetime NOT NULL,
cdm_version string NULL,
cdm_version_concept_id int64 NOT NULL,
vocabulary_version string NOT NULL );
insert into @cdmDatabaseSchema.cdm_source
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
source_description,source_documentation_reference,cdm_etl_reference,
source_release_date,cdm_release_date,'5.4',
756265,vocabulary_version
from @cdmDatabaseSchema.cdm_source_v53;
-- VOCABULARY
-- Vocabulary_reference -> Non-mandatory field
-- Vocabulary_version -> Non-mandatory field
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
CREATE TABLE @cdmDatabaseSchema.vocabulary (
vocabulary_id string NOT NULL,
vocabulary_name string NOT NULL,
vocabulary_reference string NULL,
vocabulary_version string NULL,
vocabulary_concept_id int64 NOT NULL );
insert into @cdmDatabaseSchema.vocabulary
select vocabulary_id,vocabulary_name,vocabulary_reference,
vocabulary_version, vocabulary_concept_id
from @cdmDatabaseSchema.vocabulary_v53;
-- ATTRIBUTE_DEFINITION
drop table @cdmDatabaseSchema.attribute_definition;
-- COHORT
CREATE TABLE @cdmDatabaseSchema.cohort (
cohort_definition_id int64 NOT NULL,
subject_id int64 NOT NULL,
cohort_start_date datetime NOT NULL,
cohort_end_date datetime NOT NULL );

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
-- Impala SQL references:
-- https://docs.cloudera.com/documentation/enterprise/6/6.3/topics/impala_alter_table.html
--
-- VISIT_OCCURRENCE
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
alter table @cdmDatabaseSchema.visit_occurrence change admitting_source_concept_id admitted_from_concept_id int;
alter table @cdmDatabaseSchema.visit_occurrence change admitting_source_value admitted_from_source_value int;
alter table @cdmDatabaseSchema.visit_occurrence change discharge_to_concept_id discharged_to_concept_id int;
alter table @cdmDatabaseSchema.visit_occurrence change discharge_to_source_value discharged_to_source_value int;
--
-- VISIT_DETAIL
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
-- visit_detail_parent_id -> parent_visit_detail_id
alter table @cdmDatabaseSchema.visit_detail change admitting_source_concept_id admitted_from_concept_id int;
alter table @cdmDatabaseSchema.visit_detail change admitting_source_value admitted_from_source_value int;
alter table @cdmDatabaseSchema.visit_detail change discharge_to_concept_id discharged_to_concept_id int;
alter table @cdmDatabaseSchema.visit_detail change discharge_to_source_value discharged_to_source_value int;
alter table @cdmDatabaseSchema.visit_detail change visit_detail_parent_id parent_visit_detail_id int;
-- PROCEDURE_OCCURRENCE
-- + Procedure_end_date
-- + Procedure_end_datetime
alter table @cdmDatabaseSchema.procedure_occurrence add columns (procedure_end_date timestamp);
alter table @cdmDatabaseSchema.procedure_occurrence add columns (procedure_end_datetime timestamp);
-- DEVICE_EXPOSURE
-- Unique_device_id -> Changed to varchar(255)
-- + Production_id
-- + Unit_concept_id
-- + Unit_source_value
-- + Unit_source_concept_id
alter table @cdmDatabaseSchema.device_exposure change unique_device_id unique_device_id varchar(300);
alter table @cdmDatabaseSchema.device_exposure add columns (production_id int);
alter table @cdmDatabaseSchema.device_exposure add columns (unit_concept_id int);
alter table @cdmDatabaseSchema.device_exposure add columns (unit_source_value int);
alter table @cdmDatabaseSchema.device_exposure add columns (unit_source_concept_id int);
-- MEASUREMENT
-- + Unit_source_concept_id
-- + Measurement_event_id
-- + Meas_event_field_concept_id
alter table @cdmDatabaseSchema.measurement add columns (unit_source_concept_id int);
alter table @cdmDatabaseSchema.measurement add columns (measurement_event_id int);
alter table @cdmDatabaseSchema.measurement add columns (meas_event_field_concept_id int);
-- OBSERVATION
-- + Value_source_value
-- + Observation_event_id
-- + Obs_event_field_concept_id
alter table @cdmDatabaseSchema.observation add columns (value_source_value varchar(50));
alter table @cdmDatabaseSchema.observation add columns (observation_event_id int);
alter table @cdmDatabaseSchema.observation add columns (obs_event_field_concept_id int);
-- NOTE
-- + Note_event_id
-- + Note_event_field_concept_id
alter table @cdmDatabaseSchema.note add columns (note_event_id int);
alter table @cdmDatabaseSchema.note add columns (note_event_field_concept_id int);
-- LOCATION
-- + Country_concept_id
-- + Country_source_value
-- + Latitude
-- + Longitude
alter table @cdmDatabaseSchema.location add columns (country_concept_id int);
alter table @cdmDatabaseSchema.location add columns (country_source_value varchar(80));
alter table @cdmDatabaseSchema.location add columns (latitude float);
alter table @cdmDatabaseSchema.location add columns (longitude float);
-- EPISODE
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id int,
person_id int,
episode_concept_id int,
episode_start_date timestamp,
episode_start_datetime TIMESTAMP,
episode_end_date timestamp,
episode_end_datetime timestamp,
episode_parent_id int,
episode_number int,
episode_object_concept_id int,
episode_type_concept_id int,
episode_source_value varchar(50),
episode_source_concept_id int );
-- EPISODE_EVENT
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id int,
event_id int,
episode_event_field_concept_id int );
-- METADATA
-- + Metadata_id
-- + Value_as_number
alter table @cdmDatabaseSchema.metadata add columns (metadata_id int);
alter table @cdmDatabaseSchema.metadata add columns (value_as_number float);
-- CDM_SOURCE
-- Cdm_source_name -> Mandatory field
-- Cdm_source_abbreviation -> Mandatory field
-- Cdm_holder -> Mandatory field
-- Source_release_date -> Mandatory field
-- Cdm_release_date -> Mandatory field
-- + Cdm_version_concept_id
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
CREATE TABLE @cdmDatabaseSchema.cdm_source (
cdm_source_name varchar(255),
cdm_source_abbreviation varchar(25),
cdm_holder varchar(255),
source_description varchar(max),
source_documentation_reference varchar(255),
cdm_etl_reference varchar(255),
source_release_date timestamp,
cdm_release_date timestamp,
cdm_version varchar(10),
cdm_version_concept_id int,
vocabulary_version varchar(20));
insert into @cdmDatabaseSchema.cdm_source
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
source_description,source_documentation_reference,cdm_etl_reference,
source_release_date,cdm_release_date,'5.4',
756265,vocabulary_version
from @cdmDatabaseSchema.cdm_source_v53;
-- VOCABULARY
-- Vocabulary_reference -> Non-mandatory field
-- Vocabulary_version -> Non-mandatory field
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
CREATE TABLE @cdmDatabaseSchema.vocabulary (
vocabulary_id varchar(20),
vocabulary_name varchar(255),
vocabulary_reference varchar(255),
vocabulary_version varchar(255),
vocabulary_concept_id int );
insert into @cdmDatabaseSchema.vocabulary
select vocabulary_id,vocabulary_name,vocabulary_reference,
vocabulary_version, vocabulary_concept_id
from @cdmDatabaseSchema.vocabulary_v53;
-- ATTRIBUTE_DEFINITION
drop table @cdmDatabaseSchema.attribute_definition;
-- COHORT
CREATE TABLE @cdmDatabaseSchema.cohort (
cohort_definition_id int,
subject_id int,
cohort_start_date timestamp,
cohort_end_date timestamp );

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
-- Netezza SQL references:
-- https://www.ibm.com/docs/en/psfa/7.2.1?topic=reference-alter-table
-- https://www.ibm.com/docs/en/psfa/7.2.1?topic=tables-add-drop-column
--
-- VISIT_OCCURRENCE
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_concept_id to admitted_from_concept_id;
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_value to admitted_from_source_value;
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
--
-- VISIT_DETAIL
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
-- visit_detail_parent_id -> parent_visit_detail_id
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_concept_id to admitted_from_concept_id;
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_value to admitted_from_source_value;
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_source_value to discharged_to_source_value;
alter table @cdmDatabaseSchema.visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
-- PROCEDURE_OCCURRENCE
-- + Procedure_end_date
-- + Procedure_end_datetime
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date timestamp null;
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime timestamp null;
-- DEVICE_EXPOSURE
-- Unique_device_id -> Changed to varchar(255)
-- + Production_id
-- + Unit_concept_id
-- + Unit_source_value
-- + Unit_source_concept_id
alter table @cdmDatabaseSchema.device_exposure modify column (unique_device_id varchar(300);
alter table @cdmDatabaseSchema.device_exposure add column production_id integer null;
alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id integer null;
alter table @cdmDatabaseSchema.device_exposure add column unit_source_value varchar(50) null;
alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id integer null;
-- MEASUREMENT
-- + Unit_source_concept_id
-- + Measurement_event_id
-- + Meas_event_field_concept_id
alter table @cdmDatabaseSchema.measurement add column unit_source_concept_id integer default null;
alter table @cdmDatabaseSchema.measurement add column measurement_event_id bigint null;
alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id integer null;
-- OBSERVATION
-- + Value_source_value
-- + Observation_event_id
-- + Obs_event_field_concept_id
alter table @cdmDatabaseSchema.observation add column value_source_value varchar(50) null;
alter table @cdmDatabaseSchema.observation add column observation_event_id bigint null;
alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id integer null;
-- NOTE
-- + Note_event_id
-- + Note_event_field_concept_id
alter table @cdmDatabaseSchema.note add column note_event_id bigint null;
alter table @cdmDatabaseSchema.note add column note_event_field_concept_id integer null;
-- LOCATION
-- + Country_concept_id
-- + Country_source_value
-- + Latitude
-- + Longitude
alter table @cdmDatabaseSchema.location add column country_concept_id integer null;
alter table @cdmDatabaseSchema.location add column country_source_value varchar(80) null;
alter table @cdmDatabaseSchema.location add column latitude float null;
alter table @cdmDatabaseSchema.location add column longitude float null;
-- EPISODE
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date timestamp NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date timestamp NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id bigint NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
episode_source_value varchar(50) NULL,
episode_source_concept_id integer NULL );
-- EPISODE_EVENT
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_event_field_concept_id integer NOT NULL );
-- METADATA
-- + Metadata_id
-- + Value_as_number
alter table @cdmDatabaseSchema.metadata add column metadata_id integer null;
alter table @cdmDatabaseSchema.metadata add column value_as_number float null;
-- CDM_SOURCE
-- Cdm_source_name -> Mandatory field
-- Cdm_source_abbreviation -> Mandatory field
-- Cdm_holder -> Mandatory field
-- Source_release_date -> Mandatory field
-- Cdm_release_date -> Mandatory field
-- + Cdm_version_concept_id
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
CREATE TABLE @cdmDatabaseSchema.cdm_source (
cdm_source_name varchar(255) NOT NULL,
cdm_source_abbreviation varchar(25) NOT NULL,
cdm_holder varchar(255) NOT NULL,
source_description varchar(1000) NULL,
source_documentation_reference varchar(255) NULL,
cdm_etl_reference varchar(255) NULL,
source_release_date timestamp NOT NULL,
cdm_release_date timestamp NOT NULL,
cdm_version varchar(10) NULL,
cdm_version_concept_id integer NOT NULL,
vocabulary_version varchar(20) NOT NULL );
insert into @cdmDatabaseSchema.cdm_source
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
source_description,source_documentation_reference,cdm_etl_reference,
source_release_date,cdm_release_date,'5.4',
756265,vocabulary_version
from @cdmDatabaseSchema.cdm_source_v53;
-- VOCABULARY
-- Vocabulary_reference -> Non-mandatory field
-- Vocabulary_version -> Non-mandatory field
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
CREATE TABLE @cdmDatabaseSchema.vocabulary (
vocabulary_id varchar(20) NOT NULL,
vocabulary_name varchar(255) NOT NULL,
vocabulary_reference varchar(255) NULL,
vocabulary_version varchar(255) NULL,
vocabulary_concept_id integer NOT NULL );
insert into @cdmDatabaseSchema.vocabulary
select vocabulary_id,vocabulary_name,vocabulary_reference,
vocabulary_version, vocabulary_concept_id
from @cdmDatabaseSchema.vocabulary_v53;
-- ATTRIBUTE_DEFINITION
drop table @cdmDatabaseSchema.attribute_definition;
-- COHORT
CREATE TABLE @cdmDatabaseSchema.cohort (
cohort_definition_id integer NOT NULL,
subject_id integer NOT NULL,
cohort_start_date timestamp NOT NULL,
cohort_end_date timestamp NOT NULL );

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
-- Oracle SQL references:
-- https://docs.oracle.com/en/database/oracle/oracle-database/19/sqlrf/ALTER-TABLE.html#GUID-552E7373-BF93-477D-9DA3-B2C9386F2877
-- https://docs.oracle.com/en/database/oracle/oracle-database/19/sqlrf/Data-Types.html#GUID-0DC7FFAA-F03F-4448-8487-F2592496A510
-- https://docs.oracle.com/en/database/oracle/oracle-database/19/sqlrf/RENAME.html#GUID-573347CE-3EB8-42E5-B4D5-EF71CA06FAFC
--
-- VISIT_OCCURRENCE
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_concept_id to admitted_from_concept_id;
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_value to admitted_from_source_value;
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
--
-- VISIT_DETAIL
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
-- visit_detail_parent_id -> parent_visit_detail_id
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_concept_id to admitted_from_concept_id;
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_value to admitted_from_source_value;
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_source_value to discharged_to_source_value;
alter table @cdmDatabaseSchema.visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
-- PROCEDURE_OCCURRENCE
-- + Procedure_end_date
-- + Procedure_end_datetime
alter table @cdmDatabaseSchema.procedure_occurrence add (procedure_end_date date default null);
alter table @cdmDatabaseSchema.procedure_occurrence add (procedure_end_datetime timestamp default null);
-- DEVICE_EXPOSURE
-- Unique_device_id -> Changed to varchar(255)
-- + Production_id
-- + Unit_concept_id
-- + Unit_source_value
-- + Unit_source_concept_id
alter table @cdmDatabaseSchema.device_exposure modify (unique_device_id varchar2(300));
alter table @cdmDatabaseSchema.device_exposure add (production_id number default null);
alter table @cdmDatabaseSchema.device_exposure add (unit_concept_id number default null);
alter table @cdmDatabaseSchema.device_exposure add (unit_source_value varchar2(50) default null);
alter table @cdmDatabaseSchema.device_exposure add (unit_source_concept_id number default null);
-- MEASUREMENT
-- + Unit_source_concept_id
-- + Measurement_event_id
-- + Meas_event_field_concept_id
alter table @cdmDatabaseSchema.measurement add (unit_source_concept_id number default null);
alter table @cdmDatabaseSchema.measurement add (measurement_event_id number default null);
alter table @cdmDatabaseSchema.measurement add (meas_event_field_concept_id number default null);
-- OBSERVATION
-- + Value_source_value
-- + Observation_event_id
-- + Obs_event_field_concept_id
alter table @cdmDatabaseSchema.observation add (value_source_value varchar2(50) default null);
alter table @cdmDatabaseSchema.observation add (observation_event_id number default null);
alter table @cdmDatabaseSchema.observation add (obs_event_field_concept_id number default null);
-- NOTE
-- + Note_event_id
-- + Note_event_field_concept_id
alter table @cdmDatabaseSchema.note add (note_event_id number default null);
alter table @cdmDatabaseSchema.note add (note_event_field_concept_id number default null);
-- LOCATION
-- + Country_concept_id
-- + Country_source_value
-- + Latitude
-- + Longitude
alter table @cdmDatabaseSchema.location add (country_concept_id number default null);
alter table @cdmDatabaseSchema.location add (country_source_value varchar2(80) default null);
alter table @cdmDatabaseSchema.location add (latitude float default null);
alter table @cdmDatabaseSchema.location add (longitude float default null);
-- EPISODE
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id number NOT NULL,
person_id number NOT NULL,
episode_concept_id number NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id number NULL,
episode_number number NULL,
episode_object_concept_id number NOT NULL,
episode_type_concept_id number NOT NULL,
episode_source_value varchar2(50) NULL,
episode_source_concept_id number NULL );
-- EPISODE_EVENT
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id number NOT NULL,
event_id number NOT NULL,
episode_event_field_concept_id number NOT NULL );
-- METADATA
-- + Metadata_id
-- + Value_as_number
alter table @cdmDatabaseSchema.metadata add (metadata_id number default null);
alter table @cdmDatabaseSchema.metadata add (value_as_number float default null);
-- CDM_SOURCE
-- Cdm_source_name -> Mandatory field
-- Cdm_source_abbreviation -> Mandatory field
-- Cdm_holder -> Mandatory field
-- Source_release_date -> Mandatory field
-- Cdm_release_date -> Mandatory field
-- + Cdm_version_concept_id
rename @cdmDatabaseSchema.cdm_source to cdm_source_v53;
CREATE TABLE @cdmDatabaseSchema.cdm_source (
cdm_source_name varchar2(255) NOT NULL,
cdm_source_abbreviation varchar2(25) NOT NULL,
cdm_holder varchar2(255) NOT NULL,
-- 32767 bytes if MAX_STRING_SIZE = EXTENDED
-- 4000 bytes if MAX_STRING_SIZE = STANDARD
source_description varchar2(32767) NULL,
source_documentation_reference varchar2(255) NULL,
cdm_etl_reference varchar2(255) NULL,
source_release_date date NOT NULL,
cdm_release_date date NOT NULL,
cdm_version varchar2(10) NULL,
cdm_version_concept_id number NOT NULL,
vocabulary_version varchar2(20) NOT NULL );
insert into @cdmDatabaseSchema.cdm_source
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
source_description,source_documentation_reference,cdm_etl_reference,
source_release_date,cdm_release_date,'5.4',
756265,vocabulary_version
from @cdmDatabaseSchema.cdm_source_v53;
-- VOCABULARY
-- Vocabulary_reference -> Non-mandatory field
-- Vocabulary_version -> Non-mandatory field
rename @cdmDatabaseSchema.vocabulary to vocabulary_v53;
CREATE TABLE @cdmDatabaseSchema.vocabulary (
vocabulary_id varchar2(20) NOT NULL,
vocabulary_name varchar2(255) NOT NULL,
vocabulary_reference varchar2(255) NULL,
vocabulary_version varchar2(255) NULL,
vocabulary_concept_id number NOT NULL );
insert into @cdmDatabaseSchema.vocabulary
select vocabulary_id,vocabulary_name,vocabulary_reference,
vocabulary_version, vocabulary_concept_id
from @cdmDatabaseSchema.vocabulary_v53;
-- ATTRIBUTE_DEFINITION
drop table @cdmDatabaseSchema.attribute_definition;
-- COHORT
CREATE TABLE @cdmDatabaseSchema.cohort (
cohort_definition_id number NOT NULL,
subject_id number NOT NULL,
cohort_start_date date NOT NULL,
cohort_end_date date NOT NULL );

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
-- PostgreSQL SQL references:
-- https://www.postgresql.org/docs/current/sql-altertable.html
--
-- VISIT_OCCURRENCE
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_concept_id to admitted_from_concept_id;
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_value to admitted_from_source_value;
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
--
-- VISIT_DETAIL
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
-- visit_detail_parent_id -> parent_visit_detail_id
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_concept_id to admitted_from_concept_id;
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_value to admitted_from_source_value;
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_source_value to discharged_to_source_value;
alter table @cdmDatabaseSchema.visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
-- PROCEDURE_OCCURRENCE
-- + Procedure_end_date
-- + Procedure_end_datetime
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date date default null;
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime timestamp default null;
-- DEVICE_EXPOSURE
-- Unique_device_id -> Changed to varchar(255)
-- + Production_id
-- + Unit_concept_id
-- + Unit_source_value
-- + Unit_source_concept_id
alter table @cdmDatabaseSchema.device_exposure alter column unique_device_id type varchar(300);
alter table @cdmDatabaseSchema.device_exposure add column production_id integer default null;
alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id integer default null;
alter table @cdmDatabaseSchema.device_exposure add column unit_source_value varchar(50) default null;
alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id integer default null;
-- MEASUREMENT
-- + Unit_source_concept_id
-- + Measurement_event_id
-- + Meas_event_field_concept_id
alter table @cdmDatabaseSchema.measurement add column unit_source_concept_id integer default null;
alter table @cdmDatabaseSchema.measurement add column measurement_event_id bigint default null;
alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id integer default null;
-- OBSERVATION
-- + Value_source_value
-- + Observation_event_id
-- + Obs_event_field_concept_id
alter table @cdmDatabaseSchema.observation add column value_source_value varchar(50) default null;
alter table @cdmDatabaseSchema.observation add column observation_event_id bigint default null;
alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id integer default null;
-- NOTE
-- + Note_event_id
-- + Note_event_field_concept_id
alter table @cdmDatabaseSchema.note add column note_event_id bigint default null;
alter table @cdmDatabaseSchema.note add column note_event_field_concept_id integer default null;
-- LOCATION
-- + Country_concept_id
-- + Country_source_value
-- + Latitude
-- + Longitude
alter table @cdmDatabaseSchema.location add column country_concept_id integer default null;
alter table @cdmDatabaseSchema.location add column country_source_value varchar(80) default null;
alter table @cdmDatabaseSchema.location add column latitude numeric default null;
alter table @cdmDatabaseSchema.location add column longitude numeric default null;
-- EPISODE
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id bigint NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
episode_source_value varchar(50) NULL,
episode_source_concept_id integer NULL );
-- EPISODE_EVENT
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_event_field_concept_id integer NOT NULL );
-- METADATA
-- + Metadata_id
-- + Value_as_number
alter table @cdmDatabaseSchema.metadata add column metadata_id integer default null;
alter table @cdmDatabaseSchema.metadata add column value_as_number numeric default null;
-- CDM_SOURCE
-- Cdm_source_name -> Mandatory field
-- Cdm_source_abbreviation -> Mandatory field
-- Cdm_holder -> Mandatory field
-- Source_release_date -> Mandatory field
-- Cdm_release_date -> Mandatory field
-- + Cdm_version_concept_id
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
CREATE TABLE @cdmDatabaseSchema.cdm_source (
cdm_source_name varchar(255) NOT NULL,
cdm_source_abbreviation varchar(25) NOT NULL,
cdm_holder varchar(255) NOT NULL,
source_description text NULL,
source_documentation_reference varchar(255) NULL,
cdm_etl_reference varchar(255) NULL,
source_release_date date NOT NULL,
cdm_release_date date NOT NULL,
cdm_version varchar(10) NULL,
cdm_version_concept_id integer NOT NULL,
vocabulary_version varchar(20) NOT NULL );
insert into @cdmDatabaseSchema.cdm_source
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
source_description,source_documentation_reference,cdm_etl_reference,
source_release_date,cdm_release_date,'5.4',
756265,vocabulary_version
from @cdmDatabaseSchema.cdm_source_v53;
-- VOCABULARY
-- Vocabulary_reference -> Non-mandatory field
-- Vocabulary_version -> Non-mandatory field
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
CREATE TABLE @cdmDatabaseSchema.vocabulary (
vocabulary_id varchar(20) NOT NULL,
vocabulary_name varchar(255) NOT NULL,
vocabulary_reference varchar(255) NULL,
vocabulary_version varchar(255) NULL,
vocabulary_concept_id integer NOT NULL );
insert into @cdmDatabaseSchema.vocabulary
select vocabulary_id,vocabulary_name,vocabulary_reference,
vocabulary_version, vocabulary_concept_id
from @cdmDatabaseSchema.vocabulary_v53;
-- ATTRIBUTE_DEFINITION
drop table @cdmDatabaseSchema.attribute_definition;
-- COHORT
CREATE TABLE @cdmDatabaseSchema.cohort (
cohort_definition_id integer NOT NULL,
subject_id integer NOT NULL,
cohort_start_date date NOT NULL,
cohort_end_date date NOT NULL );

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
-- Redshift SQL references:
-- https://docs.aws.amazon.com/redshift/latest/dg/r_ALTER_TABLE_examples_basic.html
-- https://docs.aws.amazon.com/redshift/latest/dg/r_ALTER_TABLE_COL_ex-add-drop.html
--
-- VISIT_OCCURRENCE
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_concept_id to admitted_from_concept_id;
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_value to admitted_from_source_value;
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
--
-- VISIT_DETAIL
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
-- visit_detail_parent_id -> parent_visit_detail_id
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_concept_id to admitted_from_concept_id;
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_value to admitted_from_source_value;
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_source_value to discharged_to_source_value;
alter table @cdmDatabaseSchema.visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
-- PROCEDURE_OCCURRENCE
-- + Procedure_end_date
-- + Procedure_end_datetime
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date date default null;
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime timestamp default null;
-- DEVICE_EXPOSURE
-- Unique_device_id -> Changed to varchar(255)
-- + Production_id
-- + Unit_concept_id
-- + Unit_source_value
-- + Unit_source_concept_id
alter table @cdmDatabaseSchema.device_exposure alter column unique_device_id varchar(300);
alter table @cdmDatabaseSchema.device_exposure add column production_id integer default null;
alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id integer default null;
alter table @cdmDatabaseSchema.device_exposure add column unit_source_value varchar(50) default null;
alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id integer default null;
-- MEASUREMENT
-- + Unit_source_concept_id
-- + Measurement_event_id
-- + Meas_event_field_concept_id
alter table @cdmDatabaseSchema.measurement add column unit_source_concept_id integer default null;
alter table @cdmDatabaseSchema.measurement add column measurement_event_id bigint default null;
alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id integer default null;
-- OBSERVATION
-- + Value_source_value
-- + Observation_event_id
-- + Obs_event_field_concept_id
alter table @cdmDatabaseSchema.observation add column value_source_value varchar(50) default null;
alter table @cdmDatabaseSchema.observation add column observation_event_id bigint default null;
alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id integer default null;
-- NOTE
-- + Note_event_id
-- + Note_event_field_concept_id
alter table @cdmDatabaseSchema.note add column note_event_id bigint default null;
alter table @cdmDatabaseSchema.note add column note_event_field_concept_id integer default null;
-- LOCATION
-- + Country_concept_id
-- + Country_source_value
-- + Latitude
-- + Longitude
alter table @cdmDatabaseSchema.location add column country_concept_id integer default null;
alter table @cdmDatabaseSchema.location add column country_source_value varchar(80) default null;
alter table @cdmDatabaseSchema.location add column latitude float default null;
alter table @cdmDatabaseSchema.location add column longitude float default null;
-- EPISODE
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id bigint NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
episode_source_value varchar(50) NULL,
episode_source_concept_id integer NULL );
-- EPISODE_EVENT
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_event_field_concept_id integer NOT NULL );
-- METADATA
-- + Metadata_id
-- + Value_as_number
alter table @cdmDatabaseSchema.metadata add column metadata_id integer default null;
alter table @cdmDatabaseSchema.metadata add column value_as_number float default null;
-- CDM_SOURCE
-- Cdm_source_name -> Mandatory field
-- Cdm_source_abbreviation -> Mandatory field
-- Cdm_holder -> Mandatory field
-- Source_release_date -> Mandatory field
-- Cdm_release_date -> Mandatory field
-- + Cdm_version_concept_id
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
CREATE TABLE @cdmDatabaseSchema.cdm_source (
cdm_source_name varchar(255) NOT NULL,
cdm_source_abbreviation varchar(25) NOT NULL,
cdm_holder varchar(255) NOT NULL,
source_description varchar(MAX) NULL,
source_documentation_reference varchar(255) NULL,
cdm_etl_reference varchar(255) NULL,
source_release_date date NOT NULL,
cdm_release_date date NOT NULL,
cdm_version varchar(10) NULL,
cdm_version_concept_id integer NOT NULL,
vocabulary_version varchar(20) NOT NULL );
insert into @cdmDatabaseSchema.cdm_source
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
source_description,source_documentation_reference,cdm_etl_reference,
source_release_date,cdm_release_date,'5.4',
756265,vocabulary_version
from @cdmDatabaseSchema.cdm_source_v53;
-- VOCABULARY
-- Vocabulary_reference -> Non-mandatory field
-- Vocabulary_version -> Non-mandatory field
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
CREATE TABLE @cdmDatabaseSchema.vocabulary (
vocabulary_id varchar(20) NOT NULL,
vocabulary_name varchar(255) NOT NULL,
vocabulary_reference varchar(255) NULL,
vocabulary_version varchar(255) NULL,
vocabulary_concept_id integer NOT NULL );
insert into @cdmDatabaseSchema.vocabulary
select vocabulary_id,vocabulary_name,vocabulary_reference,
vocabulary_version, vocabulary_concept_id
from @cdmDatabaseSchema.vocabulary_v53;
-- ATTRIBUTE_DEFINITION
drop table @cdmDatabaseSchema.attribute_definition;
-- COHORT
CREATE TABLE @cdmDatabaseSchema.cohort (
cohort_definition_id integer NOT NULL,
subject_id integer NOT NULL,
cohort_start_date date NOT NULL,
cohort_end_date date NOT NULL );

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
-- SQL SERVER SQL References:
-- https://docs.microsoft.com/en-us/sql/relational-databases/tables/rename-columns-database-engine?view=sql-server-ver15
-- https://docs.microsoft.com/en-us/sql/relational-databases/system-stored-procedures/sp-rename-transact-sql?view=sql-server-ver15
-- https://docs.microsoft.com/en-us/sql/relational-databases/tables/add-columns-to-a-table-database-engine?view=sql-server-ver15
-- https://docs.microsoft.com/en-us/sql/relational-databases/tables/modify-columns-database-engine?view=sql-server-ver15
-- https://docs.microsoft.com/en-us/sql/t-sql/data-types/data-types-transact-sql?view=sql-server-ver15
--
-- VISIT_OCCURRENCE
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
EXEC sp_rename '@cdmDatabaseSchema.visit_occurrence.admitting_source_concept_id', 'admitted_from_concept_id', 'COLUMN';
EXEC sp_rename '@cdmDatabaseSchema.visit_occurrence.admitting_source_value', 'admitted_from_source_value', 'COLUMN';
EXEC sp_rename '@cdmDatabaseSchema.visit_occurrence.discharge_to_concept_id', 'discharged_to_concept_id', 'COLUMN';
EXEC sp_rename '@cdmDatabaseSchema.visit_occurrence.discharge_to_source_value', 'discharged_to_source_value', 'COLUMN';
--
-- VISIT_DETAIL
-- admitting_source_concept_id -> admitted_from_concept_id
-- admitting_source_value -> admitted_from_source_value
-- discharge_to_concept_id -> discharged_to_concept_id
-- discharge_to_source_value -> discharged_to_source_value
-- visit_detail_parent_id -> parent_visit_detail_id
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.admitting_source_concept_id', 'admitted_from_concept_id', 'COLUMN';
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.admitting_source_value', 'admitted_from_source_value', 'COLUMN';
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.discharge_to_concept_id', 'discharged_to_concept_id', 'COLUMN';
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.discharge_to_source_value', 'discharged_to_source_value', 'COLUMN';
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.visit_detail_parent_id', 'parent_visit_detail_id', 'COLUMN';
-- PROCEDURE_OCCURRENCE
-- + Procedure_end_date
-- + Procedure_end_datetime
alter table @cdmDatabaseSchema.procedure_occurrence add procedure_end_date date null;
alter table @cdmDatabaseSchema.procedure_occurrence add procedure_end_datetime datetime null;
-- DEVICE_EXPOSURE
-- Unique_device_id -> Changed to varchar(255)
-- + Production_id
-- + Unit_concept_id
-- + Unit_source_value
-- + Unit_source_concept_id
alter table @cdmDatabaseSchema.device_exposure alter column unique_device_id varchar(300);
alter table @cdmDatabaseSchema.device_exposure add production_id int null;
alter table @cdmDatabaseSchema.device_exposure add unit_concept_id int null;
alter table @cdmDatabaseSchema.device_exposure add unit_source_value varchar(50) null;
alter table @cdmDatabaseSchema.device_exposure add unit_source_concept_id int null;
-- MEASUREMENT
-- + Unit_source_concept_id
-- + Measurement_event_id
-- + Meas_event_field_concept_id
alter table @cdmDatabaseSchema.measurement add unit_source_concept_id int null;
alter table @cdmDatabaseSchema.measurement add measurement_event_id bigint null;
alter table @cdmDatabaseSchema.measurement add meas_event_field_concept_id int null;
-- OBSERVATION
-- + Value_source_value
-- + Observation_event_id
-- + Obs_event_field_concept_id
alter table @cdmDatabaseSchema.observation add value_source_value varchar(50) null;
alter table @cdmDatabaseSchema.observation add observation_event_id bigint null;
alter table @cdmDatabaseSchema.observation add obs_event_field_concept_id int null;
-- NOTE
-- + Note_event_id
-- + Note_event_field_concept_id
alter table @cdmDatabaseSchema.note add note_event_id bigint null;
alter table @cdmDatabaseSchema.note add note_event_field_concept_id int null;
-- LOCATION
-- + Country_concept_id
-- + Country_source_value
-- + Latitude
-- + Longitude
alter table @cdmDatabaseSchema.location add country_concept_id int null;
alter table @cdmDatabaseSchema.location add country_source_value varchar(80) null;
alter table @cdmDatabaseSchema.location add latitude numeric null;
alter table @cdmDatabaseSchema.location add longitude numeric null;
-- EPISODE
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_concept_id int NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime datetime NULL,
episode_end_date date NULL,
episode_end_datetime datetime NULL,
episode_parent_id bigint NULL,
episode_number int NULL,
episode_object_concept_id int NOT NULL,
episode_type_concept_id int NOT NULL,
episode_source_value varchar(50) NULL,
episode_source_concept_id int NULL );
-- EPISODE_EVENT
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_event_field_concept_id int NOT NULL );
-- METADATA
-- + Metadata_id
-- + Value_as_number
alter table @cdmDatabaseSchema.metadata add metadata_id int null;
alter table @cdmDatabaseSchema.metadata add value_as_number numeric null;
-- CDM_SOURCE
-- Cdm_source_name -> Mandatory field
-- Cdm_source_abbreviation -> Mandatory field
-- Cdm_holder -> Mandatory field
-- Source_release_date -> Mandatory field
-- Cdm_release_date -> Mandatory field
-- + Cdm_version_concept_id
EXEC sp_rename '@cdmDatabaseSchema.cdm_source', 'cdm_source_v53';
CREATE TABLE @cdmDatabaseSchema.cdm_source (
cdm_source_name varchar(255) NOT NULL,
cdm_source_abbreviation varchar(25) NOT NULL,
cdm_holder varchar(255) NOT NULL,
source_description varchar(MAX) NULL,
source_documentation_reference varchar(255) NULL,
cdm_etl_reference varchar(255) NULL,
source_release_date date NOT NULL,
cdm_release_date date NOT NULL,
cdm_version varchar(10) NULL,
cdm_version_concept_id int NOT NULL,
vocabulary_version varchar(20) NOT NULL );
insert into @cdmDatabaseSchema.cdm_source
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
source_description,source_documentation_reference,cdm_etl_reference,
source_release_date,cdm_release_date,'5.4',
756265,vocabulary_version
from @cdmDatabaseSchema.cdm_source_v53;
-- VOCABULARY
-- Vocabulary_reference -> Non-mandatory field
-- Vocabulary_version -> Non-mandatory field
EXEC sp_rename '@cdmDatabaseSchema.vocabulary', 'vocabulary_v53';
CREATE TABLE @cdmDatabaseSchema.vocabulary (
vocabulary_id varchar(20) NOT NULL,
vocabulary_name varchar(255) NOT NULL,
vocabulary_reference varchar(255) NULL,
vocabulary_version varchar(255) NULL,
vocabulary_concept_id int NOT NULL );
insert into @cdmDatabaseSchema.vocabulary
select vocabulary_id,vocabulary_name,vocabulary_reference,
vocabulary_version, vocabulary_concept_id
from @cdmDatabaseSchema.vocabulary_v53;
-- ATTRIBUTE_DEFINITION
drop table @cdmDatabaseSchema.attribute_definition;
-- COHORT
CREATE TABLE @cdmDatabaseSchema.cohort (
cohort_definition_id int NOT NULL,
subject_id int NOT NULL,
cohort_start_date date NOT NULL,
cohort_end_date date NOT NULL );

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with cdm_v540 as (
select *
from information_schema.columns
where table_schema = 'cdm_v540' --> ENTER YOUR V5.4 CDM HERE
and table_name not in ('cohort','cohort_attribute','cohort_definition')
), cdm_v601 as (
select *
from information_schema.columns
where table_schema = 'cdm_v601' --> ENTER YOUR V6.0 CDM HERE
and table_name not in ('cohort','cohort_attribute','cohort_definition')
)
select a.table_name,
a.column_name,
a.is_nullable v54_nullable,
b.is_nullable v60_nullable,
a.data_type v54_datatype,
b.data_type v60_datatype
from cdm_v540 a
join cdm_v601 b
on a.table_name = b.table_name
and a.column_name = b.column_name
and (a.is_nullable != b.is_nullable or a.data_type != b.data_type)
order by 1,2;

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--
-- RETRIEVE TABLE AND COLUMN NAMES FOR V5.4 AND V6.0 CDMS.
-- SUPPLY THE NAME OF EACH SCHEMA WHERE INDICATED.
-- THE "STATUS" COLUMN:
-- "IN BOTH": INDICATES COLUMN IS IN BOTH 5.4 AND 6.0
-- "MISSING FROM v6.0.1": INDICATES COLUMN IS IN BOTH 5.4 BUT NOT 6.0 AND NEEDS TO BE ADDED OR RENAMED
-- "MISSING FROM v5.4.0": INDICATES COLUMN IS IN BOTH 6.0 BUT NOT 5.4 AND NEED TO BE DROPPED OR RENAMED
with cdm_v540 as (
select *
from information_schema.columns
where table_schema = 'cdm_v540' --> YOUR V5.4 CDM SCHEMA NAME HERE
and table_name not in ('_version','cohort','cohort_attribute','cohort_definition')
), cdm_v601 as (
select *
from information_schema.columns
where table_schema = 'cdm_v601' --> YOUR V6.0 CDM SCHEMA NAME HERE
and table_name not in ('_version','cohort','cohort_attribute','cohort_definition')
)
select a.table_name,
a.column_name,
'IN BOTH' status
from cdm_v540 a
join cdm_v601 b
on a.table_name = b.table_name
and a.column_name = b.column_name
union all
select a.table_name,
a.column_name,
'MISSING FROM v6.0.1' status
from cdm_v540 a
left join cdm_v601 b
on a.table_name = b.table_name
and a.column_name = b.column_name
where b.column_name is null
union all
select b.table_name,
b.column_name,
'MISSING FROM v5.4.0' status
from cdm_v540 a
right join cdm_v601 b
on a.table_name = b.table_name
and a.column_name = b.column_name
where a.column_name is null
order by 1,3;

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table_name | column_name | v54_nullable | v60_nullable | v54_datatype | v60_datatype
----------------------+--------------------------------+--------------+--------------+-----------------------------+----------------------------
care_site | care_site_id | YES | NO | bigint | bigint
care_site | place_of_service_concept_id | YES | NO | integer | integer
cdm_source | cdm_holder | NO | YES | character varying | character varying
cdm_source | cdm_release_date | NO | YES | date | date
cdm_source | cdm_source_abbreviation | NO | YES | character varying | character varying
cdm_source | source_release_date | NO | YES | date | date
cdm_source | vocabulary_version | NO | YES | character varying | character varying
concept | concept_class_id | YES | NO | character varying | character varying
concept | concept_code | YES | NO | character varying | character varying
concept | concept_id | YES | NO | integer | integer
concept | concept_name | YES | NO | character varying | character varying
concept | domain_id | YES | NO | character varying | character varying
concept | valid_end_date | YES | NO | date | date
concept | valid_start_date | YES | NO | date | date
concept | vocabulary_id | YES | NO | character varying | character varying
concept_ancestor | ancestor_concept_id | YES | NO | integer | integer
concept_ancestor | descendant_concept_id | YES | NO | integer | integer
concept_ancestor | max_levels_of_separation | YES | NO | integer | integer
concept_ancestor | min_levels_of_separation | YES | NO | integer | integer
concept_class | concept_class_concept_id | YES | NO | integer | integer
concept_class | concept_class_id | YES | NO | character varying | character varying
concept_class | concept_class_name | YES | NO | character varying | character varying
concept_relationship | concept_id_1 | YES | NO | integer | integer
concept_relationship | concept_id_2 | YES | NO | integer | integer
concept_relationship | relationship_id | YES | NO | character varying | character varying
concept_relationship | valid_end_date | YES | NO | date | date
concept_relationship | valid_start_date | YES | NO | date | date
concept_synonym | concept_id | YES | NO | integer | integer
concept_synonym | concept_synonym_name | YES | NO | character varying | character varying
concept_synonym | language_concept_id | YES | NO | integer | integer
condition_era | condition_concept_id | YES | NO | integer | integer
condition_era | condition_era_id | YES | NO | bigint | bigint
condition_era | person_id | YES | NO | bigint | bigint
condition_occurrence | condition_concept_id | YES | NO | integer | integer
condition_occurrence | condition_occurrence_id | YES | NO | bigint | bigint
condition_occurrence | condition_source_concept_id | YES | NO | integer | integer
condition_occurrence | condition_start_date | YES | NO | date | date
condition_occurrence | condition_status_concept_id | YES | NO | integer | integer
condition_occurrence | condition_type_concept_id | YES | NO | integer | integer
condition_occurrence | person_id | YES | NO | bigint | bigint
cost | cost_event_id | YES | NO | bigint | bigint
cost | cost_id | YES | NO | bigint | bigint
cost | payer_plan_period_id | YES | YES | integer | bigint
device_exposure | device_concept_id | YES | NO | integer | integer
device_exposure | device_exposure_id | YES | NO | bigint | bigint
device_exposure | device_exposure_start_date | YES | NO | date | date
device_exposure | device_source_concept_id | YES | NO | integer | integer
device_exposure | device_type_concept_id | YES | NO | integer | integer
device_exposure | person_id | YES | NO | bigint | bigint
domain | domain_concept_id | YES | NO | integer | integer
domain | domain_id | YES | NO | character varying | character varying
domain | domain_name | YES | NO | character varying | character varying
dose_era | dose_era_id | YES | NO | bigint | bigint
dose_era | dose_value | YES | NO | double precision | double precision
dose_era | drug_concept_id | YES | NO | integer | integer
dose_era | person_id | YES | NO | bigint | bigint
dose_era | unit_concept_id | YES | NO | integer | integer
drug_era | drug_concept_id | YES | NO | integer | integer
drug_era | drug_era_id | YES | NO | bigint | bigint
drug_era | person_id | YES | NO | bigint | bigint
drug_exposure | drug_concept_id | YES | NO | integer | integer
drug_exposure | drug_exposure_end_date | YES | NO | date | date
drug_exposure | drug_exposure_id | YES | NO | bigint | bigint
drug_exposure | drug_exposure_start_date | YES | NO | date | date
drug_exposure | drug_source_concept_id | YES | NO | integer | integer
drug_exposure | drug_type_concept_id | YES | NO | integer | integer
drug_exposure | person_id | YES | NO | bigint | bigint
drug_strength | drug_concept_id | YES | NO | integer | integer
drug_strength | ingredient_concept_id | YES | NO | integer | integer
drug_strength | valid_end_date | YES | NO | date | date
drug_strength | valid_start_date | YES | NO | date | date
fact_relationship | domain_concept_id_1 | YES | NO | integer | integer
fact_relationship | domain_concept_id_2 | YES | NO | integer | integer
fact_relationship | fact_id_1 | YES | NO | bigint | bigint
fact_relationship | fact_id_2 | YES | NO | bigint | bigint
fact_relationship | relationship_concept_id | YES | NO | integer | integer
location | location_id | YES | NO | bigint | bigint
measurement | measurement_concept_id | YES | NO | integer | integer
measurement | measurement_date | YES | NO | date | date
measurement | measurement_id | YES | NO | bigint | bigint
measurement | measurement_source_concept_id | YES | NO | integer | integer
measurement | measurement_time | YES | YES | timestamp without time zone | character varying
measurement | measurement_type_concept_id | YES | NO | integer | integer
measurement | person_id | YES | NO | bigint | bigint
metadata | metadata_concept_id | YES | NO | integer | integer
metadata | metadata_type_concept_id | YES | NO | integer | integer
metadata | name | YES | NO | character varying | character varying
note | encoding_concept_id | YES | NO | integer | integer
note | language_concept_id | YES | NO | integer | integer
note | note_class_concept_id | YES | NO | integer | integer
note | note_date | YES | NO | date | date
note | note_id | YES | NO | bigint | integer
note | note_text | YES | NO | character varying | character varying
note | note_type_concept_id | YES | NO | integer | integer
note | person_id | YES | NO | bigint | bigint
note | provider_id | YES | YES | integer | bigint
note_nlp | lexical_variant | YES | NO | character varying | character varying
note_nlp | nlp_date | YES | NO | date | date
note_nlp | note_id | YES | NO | bigint | integer
note_nlp | note_nlp_id | YES | NO | bigint | bigint
observation | observation_concept_id | YES | NO | integer | integer
observation | observation_datetime | YES | NO | timestamp without time zone | timestamp without time zone
observation | observation_id | YES | NO | bigint | bigint
observation | observation_source_concept_id | YES | NO | integer | integer
observation | observation_type_concept_id | YES | NO | integer | integer
observation | person_id | YES | NO | bigint | bigint
observation_period | observation_period_end_date | YES | NO | date | date
observation_period | observation_period_id | YES | NO | bigint | bigint
observation_period | observation_period_start_date | YES | NO | date | date
observation_period | period_type_concept_id | YES | NO | integer | integer
observation_period | person_id | YES | NO | bigint | bigint
payer_plan_period | payer_concept_id | YES | NO | integer | integer
payer_plan_period | payer_plan_period_end_date | YES | NO | date | date
payer_plan_period | payer_plan_period_id | YES | NO | integer | bigint
payer_plan_period | payer_plan_period_start_date | YES | NO | date | date
payer_plan_period | payer_source_concept_id | YES | NO | integer | integer
payer_plan_period | person_id | YES | NO | integer | bigint
payer_plan_period | plan_concept_id | YES | NO | integer | integer
payer_plan_period | plan_source_concept_id | YES | NO | integer | integer
payer_plan_period | sponsor_concept_id | YES | NO | integer | integer
person | ethnicity_concept_id | YES | NO | integer | integer
person | ethnicity_source_concept_id | YES | NO | integer | integer
person | gender_concept_id | YES | NO | integer | integer
person | gender_source_concept_id | YES | NO | integer | integer
person | person_id | YES | NO | bigint | bigint
person | race_concept_id | YES | NO | integer | integer
person | race_source_concept_id | YES | NO | integer | integer
person | year_of_birth | YES | NO | integer | integer
procedure_occurrence | person_id | YES | NO | bigint | bigint
procedure_occurrence | procedure_concept_id | YES | NO | integer | integer
procedure_occurrence | procedure_datetime | YES | NO | timestamp without time zone | timestamp without time zone
procedure_occurrence | procedure_occurrence_id | YES | NO | bigint | bigint
procedure_occurrence | procedure_source_concept_id | YES | NO | integer | integer
procedure_occurrence | procedure_type_concept_id | YES | NO | integer | integer
provider | gender_concept_id | YES | NO | integer | integer
provider | gender_source_concept_id | YES | NO | integer | integer
provider | provider_id | YES | NO | bigint | bigint
provider | specialty_concept_id | YES | NO | integer | integer
provider | specialty_source_concept_id | YES | NO | integer | integer
provider | year_of_birth | YES | YES | bigint | integer
relationship | defines_ancestry | YES | NO | character varying | character varying
relationship | is_hierarchical | YES | NO | character varying | character varying
relationship | relationship_concept_id | YES | NO | integer | integer
relationship | relationship_id | YES | NO | character varying | character varying
relationship | relationship_name | YES | NO | character varying | character varying
relationship | reverse_relationship_id | YES | NO | character varying | character varying
source_to_concept_map | source_code | YES | NO | character varying | character varying
source_to_concept_map | source_concept_id | YES | NO | integer | integer
source_to_concept_map | source_vocabulary_id | YES | NO | character varying | character varying
source_to_concept_map | target_concept_id | YES | NO | integer | integer
source_to_concept_map | target_vocabulary_id | YES | NO | character varying | character varying
source_to_concept_map | valid_end_date | YES | NO | date | date
source_to_concept_map | valid_start_date | YES | NO | date | date
specimen | person_id | YES | NO | bigint | bigint
specimen | specimen_concept_id | YES | NO | integer | integer
specimen | specimen_date | YES | NO | date | date
specimen | specimen_id | YES | NO | bigint | bigint
specimen | specimen_type_concept_id | YES | NO | integer | integer
visit_detail | admitted_from_concept_id | YES | YES | integer | character varying
visit_detail | admitted_from_source_value | YES | NO | character varying | integer
visit_detail | care_site_id | YES | YES | integer | bigint
visit_detail | person_id | YES | NO | bigint | bigint
visit_detail | preceding_visit_detail_id | YES | YES | integer | bigint
visit_detail | provider_id | YES | YES | integer | bigint
visit_detail | visit_detail_concept_id | YES | NO | integer | integer
visit_detail | visit_detail_end_date | YES | NO | date | date
visit_detail | visit_detail_id | YES | NO | bigint | bigint
visit_detail | visit_detail_source_concept_id | YES | NO | integer | integer
visit_detail | visit_detail_start_date | YES | NO | date | date
visit_detail | visit_detail_type_concept_id | YES | NO | integer | integer
visit_detail | visit_occurrence_id | YES | NO | bigint | bigint
visit_occurrence | admitted_from_concept_id | YES | NO | integer | integer
visit_occurrence | person_id | YES | NO | bigint | bigint
visit_occurrence | visit_concept_id | YES | NO | integer | integer
visit_occurrence | visit_end_datetime | YES | NO | timestamp without time zone | timestamp without time zone
visit_occurrence | visit_occurrence_id | YES | NO | bigint | bigint
visit_occurrence | visit_source_concept_id | YES | NO | integer | integer
visit_occurrence | visit_start_datetime | YES | NO | timestamp without time zone | timestamp without time zone
visit_occurrence | visit_type_concept_id | YES | NO | integer | integer
vocabulary | vocabulary_reference | YES | NO | character varying | character varying

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table_name | column_name | status
----------------------+--------------------------------+--------------------
care_site | care_site_id | IN BOTH
care_site | place_of_service_concept_id | IN BOTH
care_site | location_id | IN BOTH
care_site | care_site_name | IN BOTH
care_site | care_site_source_value | IN BOTH
care_site | place_of_service_source_value | IN BOTH
cdm_source | cdm_source_name | IN BOTH
cdm_source | cdm_source_abbreviation | IN BOTH
cdm_source | cdm_holder | IN BOTH
cdm_source | source_description | IN BOTH
cdm_source | source_documentation_reference | IN BOTH
cdm_source | cdm_etl_reference | IN BOTH
cdm_source | source_release_date | IN BOTH
cdm_source | cdm_release_date | IN BOTH
cdm_source | cdm_version | IN BOTH
cdm_source | vocabulary_version | IN BOTH
cdm_source | cdm_version_concept_id | MISSING FROM v6.0.1
concept | concept_id | IN BOTH
concept | valid_start_date | IN BOTH
concept | valid_end_date | IN BOTH
concept | concept_name | IN BOTH
concept | domain_id | IN BOTH
concept | vocabulary_id | IN BOTH
concept | concept_class_id | IN BOTH
concept | standard_concept | IN BOTH
concept | concept_code | IN BOTH
concept | invalid_reason | IN BOTH
concept_ancestor | ancestor_concept_id | IN BOTH
concept_ancestor | descendant_concept_id | IN BOTH
concept_ancestor | min_levels_of_separation | IN BOTH
concept_ancestor | max_levels_of_separation | IN BOTH
concept_class | concept_class_concept_id | IN BOTH
concept_class | concept_class_id | IN BOTH
concept_class | concept_class_name | IN BOTH
concept_relationship | concept_id_1 | IN BOTH
concept_relationship | concept_id_2 | IN BOTH
concept_relationship | valid_start_date | IN BOTH
concept_relationship | valid_end_date | IN BOTH
concept_relationship | relationship_id | IN BOTH
concept_relationship | invalid_reason | IN BOTH
concept_synonym | concept_id | IN BOTH
concept_synonym | language_concept_id | IN BOTH
concept_synonym | concept_synonym_name | IN BOTH
condition_era | condition_era_id | IN BOTH
condition_era | person_id | IN BOTH
condition_era | condition_concept_id | IN BOTH
condition_era | condition_occurrence_count | IN BOTH
condition_era | condition_era_start_datetime | MISSING FROM v5.4.0
condition_era | condition_era_end_datetime | MISSING FROM v5.4.0
condition_era | condition_era_start_date | MISSING FROM v6.0.1
condition_era | condition_era_end_date | MISSING FROM v6.0.1
condition_occurrence | condition_occurrence_id | IN BOTH
condition_occurrence | person_id | IN BOTH
condition_occurrence | condition_concept_id | IN BOTH
condition_occurrence | condition_start_date | IN BOTH
condition_occurrence | condition_start_datetime | IN BOTH
condition_occurrence | condition_end_date | IN BOTH
condition_occurrence | condition_end_datetime | IN BOTH
condition_occurrence | condition_type_concept_id | IN BOTH
condition_occurrence | provider_id | IN BOTH
condition_occurrence | visit_occurrence_id | IN BOTH
condition_occurrence | visit_detail_id | IN BOTH
condition_occurrence | condition_source_concept_id | IN BOTH
condition_occurrence | condition_status_concept_id | IN BOTH
condition_occurrence | stop_reason | IN BOTH
condition_occurrence | condition_source_value | IN BOTH
condition_occurrence | condition_status_source_value | IN BOTH
cost | cost_id | IN BOTH
cost | cost_event_id | IN BOTH
cost | cost_type_concept_id | IN BOTH
cost | currency_concept_id | IN BOTH
cost | payer_plan_period_id | IN BOTH
cost | revenue_code_concept_id | IN BOTH
cost | drg_concept_id | IN BOTH
cost | drg_source_value | IN BOTH
cost | person_id | MISSING FROM v5.4.0
cost | cost_event_field_concept_id | MISSING FROM v5.4.0
cost | cost_concept_id | MISSING FROM v5.4.0
cost | cost_source_concept_id | MISSING FROM v5.4.0
cost | cost_source_value | MISSING FROM v5.4.0
cost | cost | MISSING FROM v5.4.0
cost | incurred_date | MISSING FROM v5.4.0
cost | billed_date | MISSING FROM v5.4.0
cost | paid_date | MISSING FROM v5.4.0
cost | revenue_code_source_value | MISSING FROM v5.4.0
cost | total_charge | MISSING FROM v6.0.1
cost | total_cost | MISSING FROM v6.0.1
cost | total_paid | MISSING FROM v6.0.1
cost | paid_by_payer | MISSING FROM v6.0.1
cost | paid_by_patient | MISSING FROM v6.0.1
cost | paid_patient_copay | MISSING FROM v6.0.1
cost | paid_patient_coinsurance | MISSING FROM v6.0.1
cost | paid_patient_deductible | MISSING FROM v6.0.1
cost | paid_by_primary | MISSING FROM v6.0.1
cost | paid_ingredient_cost | MISSING FROM v6.0.1
cost | paid_dispensing_fee | MISSING FROM v6.0.1
cost | amount_allowed | MISSING FROM v6.0.1
cost | cost_domain_id | MISSING FROM v6.0.1
cost | reveue_code_source_value | MISSING FROM v6.0.1
death | person_id | MISSING FROM v6.0.1
death | death_date | MISSING FROM v6.0.1
death | death_datetime | MISSING FROM v6.0.1
death | death_type_concept_id | MISSING FROM v6.0.1
death | cause_concept_id | MISSING FROM v6.0.1
death | cause_source_concept_id | MISSING FROM v6.0.1
death | cause_source_value | MISSING FROM v6.0.1
device_exposure | device_exposure_id | IN BOTH
device_exposure | person_id | IN BOTH
device_exposure | device_concept_id | IN BOTH
device_exposure | device_exposure_start_date | IN BOTH
device_exposure | device_exposure_start_datetime | IN BOTH
device_exposure | device_exposure_end_date | IN BOTH
device_exposure | device_exposure_end_datetime | IN BOTH
device_exposure | device_type_concept_id | IN BOTH
device_exposure | quantity | IN BOTH
device_exposure | provider_id | IN BOTH
device_exposure | visit_occurrence_id | IN BOTH
device_exposure | visit_detail_id | IN BOTH
device_exposure | device_source_concept_id | IN BOTH
device_exposure | device_source_value | IN BOTH
device_exposure | unique_device_id | IN BOTH
device_exposure | production_id | MISSING FROM v6.0.1
device_exposure | unit_concept_id | MISSING FROM v6.0.1
device_exposure | unit_source_value | MISSING FROM v6.0.1
device_exposure | unit_source_concept_id | MISSING FROM v6.0.1
domain | domain_concept_id | IN BOTH
domain | domain_id | IN BOTH
domain | domain_name | IN BOTH
dose_era | dose_era_id | IN BOTH
dose_era | person_id | IN BOTH
dose_era | drug_concept_id | IN BOTH
dose_era | unit_concept_id | IN BOTH
dose_era | dose_value | IN BOTH
dose_era | dose_era_start_datetime | MISSING FROM v5.4.0
dose_era | dose_era_end_datetime | MISSING FROM v5.4.0
dose_era | dose_era_start_date | MISSING FROM v6.0.1
dose_era | dose_era_end_date | MISSING FROM v6.0.1
drug_era | drug_era_id | IN BOTH
drug_era | person_id | IN BOTH
drug_era | drug_concept_id | IN BOTH
drug_era | drug_exposure_count | IN BOTH
drug_era | gap_days | IN BOTH
drug_era | drug_era_start_datetime | MISSING FROM v5.4.0
drug_era | drug_era_end_datetime | MISSING FROM v5.4.0
drug_era | drug_era_start_date | MISSING FROM v6.0.1
drug_era | drug_era_end_date | MISSING FROM v6.0.1
drug_exposure | drug_exposure_id | IN BOTH
drug_exposure | person_id | IN BOTH
drug_exposure | drug_concept_id | IN BOTH
drug_exposure | drug_exposure_start_date | IN BOTH
drug_exposure | drug_exposure_start_datetime | IN BOTH
drug_exposure | drug_exposure_end_date | IN BOTH
drug_exposure | drug_exposure_end_datetime | IN BOTH
drug_exposure | verbatim_end_date | IN BOTH
drug_exposure | drug_type_concept_id | IN BOTH
drug_exposure | refills | IN BOTH
drug_exposure | quantity | IN BOTH
drug_exposure | days_supply | IN BOTH
drug_exposure | route_concept_id | IN BOTH
drug_exposure | provider_id | IN BOTH
drug_exposure | visit_occurrence_id | IN BOTH
drug_exposure | visit_detail_id | IN BOTH
drug_exposure | drug_source_concept_id | IN BOTH
drug_exposure | stop_reason | IN BOTH
drug_exposure | sig | IN BOTH
drug_exposure | lot_number | IN BOTH
drug_exposure | drug_source_value | IN BOTH
drug_exposure | route_source_value | IN BOTH
drug_exposure | dose_unit_source_value | IN BOTH
drug_strength | drug_concept_id | IN BOTH
drug_strength | ingredient_concept_id | IN BOTH
drug_strength | amount_value | IN BOTH
drug_strength | amount_unit_concept_id | IN BOTH
drug_strength | numerator_value | IN BOTH
drug_strength | numerator_unit_concept_id | IN BOTH
drug_strength | denominator_value | IN BOTH
drug_strength | denominator_unit_concept_id | IN BOTH
drug_strength | box_size | IN BOTH
drug_strength | valid_start_date | IN BOTH
drug_strength | valid_end_date | IN BOTH
drug_strength | invalid_reason | IN BOTH
episode | episode_id | MISSING FROM v6.0.1
episode | person_id | MISSING FROM v6.0.1
episode | episode_concept_id | MISSING FROM v6.0.1
episode | episode_start_date | MISSING FROM v6.0.1
episode | episode_start_datetime | MISSING FROM v6.0.1
episode | episode_end_date | MISSING FROM v6.0.1
episode | episode_end_datetime | MISSING FROM v6.0.1
episode | episode_parent_id | MISSING FROM v6.0.1
episode | episode_number | MISSING FROM v6.0.1
episode | episode_object_concept_id | MISSING FROM v6.0.1
episode | episode_type_concept_id | MISSING FROM v6.0.1
episode | episode_source_value | MISSING FROM v6.0.1
episode | episode_source_concept_id | MISSING FROM v6.0.1
episode_event | episode_id | MISSING FROM v6.0.1
episode_event | event_id | MISSING FROM v6.0.1
episode_event | episode_event_field_concept_id | MISSING FROM v6.0.1
fact_relationship | domain_concept_id_1 | IN BOTH
fact_relationship | fact_id_1 | IN BOTH
fact_relationship | domain_concept_id_2 | IN BOTH
fact_relationship | fact_id_2 | IN BOTH
fact_relationship | relationship_concept_id | IN BOTH
location | location_id | IN BOTH
location | address_1 | IN BOTH
location | address_2 | IN BOTH
location | city | IN BOTH
location | state | IN BOTH
location | zip | IN BOTH
location | county | IN BOTH
location | location_source_value | IN BOTH
location | latitude | IN BOTH
location | longitude | IN BOTH
location | country_concept_id | MISSING FROM v6.0.1
location | country_source_value | MISSING FROM v6.0.1
location_history | location_id | MISSING FROM v5.4.0
location_history | relationship_type_concept_id | MISSING FROM v5.4.0
location_history | domain_id | MISSING FROM v5.4.0
location_history | entity_id | MISSING FROM v5.4.0
location_history | start_date | MISSING FROM v5.4.0
location_history | end_date | MISSING FROM v5.4.0
measurement | measurement_id | IN BOTH
measurement | person_id | IN BOTH
measurement | measurement_concept_id | IN BOTH
measurement | measurement_date | IN BOTH
measurement | measurement_datetime | IN BOTH
measurement | measurement_time | IN BOTH
measurement | measurement_type_concept_id | IN BOTH
measurement | operator_concept_id | IN BOTH
measurement | value_as_number | IN BOTH
measurement | value_as_concept_id | IN BOTH
measurement | unit_concept_id | IN BOTH
measurement | range_low | IN BOTH
measurement | range_high | IN BOTH
measurement | provider_id | IN BOTH
measurement | visit_occurrence_id | IN BOTH
measurement | visit_detail_id | IN BOTH
measurement | measurement_source_concept_id | IN BOTH
measurement | measurement_source_value | IN BOTH
measurement | unit_source_value | IN BOTH
measurement | value_source_value | IN BOTH
measurement | unit_source_id | MISSING FROM v6.0.1
measurement | measurement_event_id | MISSING FROM v6.0.1
measurement | meas_event_field_concept_id | MISSING FROM v6.0.1
metadata | metadata_concept_id | IN BOTH
metadata | metadata_type_concept_id | IN BOTH
metadata | value_as_concept_id | IN BOTH
metadata | metadata_date | IN BOTH
metadata | metadata_datetime | IN BOTH
metadata | name | IN BOTH
metadata | value_as_string | IN BOTH
metadata | metadata_id | MISSING FROM v6.0.1
metadata | value_as_number | MISSING FROM v6.0.1
note | note_id | IN BOTH
note | person_id | IN BOTH
note | note_date | IN BOTH
note | note_datetime | IN BOTH
note | note_type_concept_id | IN BOTH
note | note_class_concept_id | IN BOTH
note | encoding_concept_id | IN BOTH
note | language_concept_id | IN BOTH
note | provider_id | IN BOTH
note | visit_occurrence_id | IN BOTH
note | visit_detail_id | IN BOTH
note | note_title | IN BOTH
note | note_text | IN BOTH
note | note_source_value | IN BOTH
note | note_event_id | IN BOTH
note | note_event_field_concept_id | IN BOTH
note_nlp | note_nlp_id | IN BOTH
note_nlp | note_id | IN BOTH
note_nlp | section_concept_id | IN BOTH
note_nlp | note_nlp_concept_id | IN BOTH
note_nlp | note_nlp_source_concept_id | IN BOTH
note_nlp | nlp_date | IN BOTH
note_nlp | nlp_datetime | IN BOTH
note_nlp | snippet | IN BOTH
note_nlp | offset | IN BOTH
note_nlp | lexical_variant | IN BOTH
note_nlp | nlp_system | IN BOTH
note_nlp | term_exists | IN BOTH
note_nlp | term_temporal | IN BOTH
note_nlp | term_modifiers | IN BOTH
observation | observation_id | IN BOTH
observation | person_id | IN BOTH
observation | observation_concept_id | IN BOTH
observation | observation_date | IN BOTH
observation | observation_datetime | IN BOTH
observation | observation_type_concept_id | IN BOTH
observation | value_as_number | IN BOTH
observation | value_as_concept_id | IN BOTH
observation | qualifier_concept_id | IN BOTH
observation | unit_concept_id | IN BOTH
observation | provider_id | IN BOTH
observation | visit_occurrence_id | IN BOTH
observation | visit_detail_id | IN BOTH
observation | observation_source_concept_id | IN BOTH
observation | value_as_string | IN BOTH
observation | observation_source_value | IN BOTH
observation | unit_source_value | IN BOTH
observation | qualifier_source_value | IN BOTH
observation | observation_event_id | IN BOTH
observation | obs_event_field_concept_id | IN BOTH
observation | value_as_datetime | MISSING FROM v5.4.0
observation | value_source_value | MISSING FROM v6.0.1
observation_period | observation_period_id | IN BOTH
observation_period | person_id | IN BOTH
observation_period | observation_period_start_date | IN BOTH
observation_period | observation_period_end_date | IN BOTH
observation_period | period_type_concept_id | IN BOTH
payer_plan_period | payer_plan_period_id | IN BOTH
payer_plan_period | person_id | IN BOTH
payer_plan_period | payer_plan_period_start_date | IN BOTH
payer_plan_period | payer_plan_period_end_date | IN BOTH
payer_plan_period | payer_concept_id | IN BOTH
payer_plan_period | payer_source_concept_id | IN BOTH
payer_plan_period | plan_concept_id | IN BOTH
payer_plan_period | plan_source_concept_id | IN BOTH
payer_plan_period | sponsor_concept_id | IN BOTH
payer_plan_period | sponsor_source_concept_id | IN BOTH
payer_plan_period | stop_reason_concept_id | IN BOTH
payer_plan_period | stop_reason_source_concept_id | IN BOTH
payer_plan_period | payer_source_value | IN BOTH
payer_plan_period | plan_source_value | IN BOTH
payer_plan_period | sponsor_source_value | IN BOTH
payer_plan_period | family_source_value | IN BOTH
payer_plan_period | stop_reason_source_value | IN BOTH
payer_plan_period | contract_person_id | MISSING FROM v5.4.0
payer_plan_period | contract_concept_id | MISSING FROM v5.4.0
payer_plan_period | contract_source_value | MISSING FROM v5.4.0
payer_plan_period | contract_source_concept_id | MISSING FROM v5.4.0
person | person_id | IN BOTH
person | gender_concept_id | IN BOTH
person | year_of_birth | IN BOTH
person | month_of_birth | IN BOTH
person | day_of_birth | IN BOTH
person | birth_datetime | IN BOTH
person | race_concept_id | IN BOTH
person | ethnicity_concept_id | IN BOTH
person | location_id | IN BOTH
person | provider_id | IN BOTH
person | care_site_id | IN BOTH
person | gender_source_concept_id | IN BOTH
person | race_source_concept_id | IN BOTH
person | ethnicity_source_concept_id | IN BOTH
person | person_source_value | IN BOTH
person | gender_source_value | IN BOTH
person | race_source_value | IN BOTH
person | ethnicity_source_value | IN BOTH
person | death_datetime | MISSING FROM v5.4.0
procedure_occurrence | procedure_occurrence_id | IN BOTH
procedure_occurrence | person_id | IN BOTH
procedure_occurrence | procedure_concept_id | IN BOTH
procedure_occurrence | procedure_date | IN BOTH
procedure_occurrence | procedure_datetime | IN BOTH
procedure_occurrence | procedure_type_concept_id | IN BOTH
procedure_occurrence | modifier_concept_id | IN BOTH
procedure_occurrence | quantity | IN BOTH
procedure_occurrence | provider_id | IN BOTH
procedure_occurrence | visit_occurrence_id | IN BOTH
procedure_occurrence | visit_detail_id | IN BOTH
procedure_occurrence | procedure_source_concept_id | IN BOTH
procedure_occurrence | procedure_source_value | IN BOTH
procedure_occurrence | modifier_source_value | IN BOTH
procedure_occurrence | procedure_end_date | MISSING FROM v6.0.1
procedure_occurrence | procedure_end_datetime | MISSING FROM v6.0.1
provider | provider_id | IN BOTH
provider | specialty_concept_id | IN BOTH
provider | care_site_id | IN BOTH
provider | year_of_birth | IN BOTH
provider | gender_concept_id | IN BOTH
provider | specialty_source_concept_id | IN BOTH
provider | gender_source_concept_id | IN BOTH
provider | provider_name | IN BOTH
provider | npi | IN BOTH
provider | dea | IN BOTH
provider | provider_source_value | IN BOTH
provider | specialty_source_value | IN BOTH
provider | gender_source_value | IN BOTH
relationship | relationship_concept_id | IN BOTH
relationship | relationship_id | IN BOTH
relationship | relationship_name | IN BOTH
relationship | is_hierarchical | IN BOTH
relationship | defines_ancestry | IN BOTH
relationship | reverse_relationship_id | IN BOTH
source_to_concept_map | source_concept_id | IN BOTH
source_to_concept_map | target_concept_id | IN BOTH
source_to_concept_map | valid_start_date | IN BOTH
source_to_concept_map | valid_end_date | IN BOTH
source_to_concept_map | source_code | IN BOTH
source_to_concept_map | source_vocabulary_id | IN BOTH
source_to_concept_map | source_code_description | IN BOTH
source_to_concept_map | target_vocabulary_id | IN BOTH
source_to_concept_map | invalid_reason | IN BOTH
specimen | specimen_id | IN BOTH
specimen | person_id | IN BOTH
specimen | specimen_concept_id | IN BOTH
specimen | specimen_type_concept_id | IN BOTH
specimen | specimen_date | IN BOTH
specimen | specimen_datetime | IN BOTH
specimen | quantity | IN BOTH
specimen | unit_concept_id | IN BOTH
specimen | anatomic_site_concept_id | IN BOTH
specimen | disease_status_concept_id | IN BOTH
specimen | specimen_source_id | IN BOTH
specimen | specimen_source_value | IN BOTH
specimen | unit_source_value | IN BOTH
specimen | anatomic_site_source_value | IN BOTH
specimen | disease_status_source_value | IN BOTH
survey_conduct | survey_conduct_id | MISSING FROM v5.4.0
survey_conduct | person_id | MISSING FROM v5.4.0
survey_conduct | survey_concept_id | MISSING FROM v5.4.0
survey_conduct | survey_start_date | MISSING FROM v5.4.0
survey_conduct | survey_start_datetime | MISSING FROM v5.4.0
survey_conduct | survey_end_date | MISSING FROM v5.4.0
survey_conduct | survey_end_datetime | MISSING FROM v5.4.0
survey_conduct | provider_id | MISSING FROM v5.4.0
survey_conduct | assisted_concept_id | MISSING FROM v5.4.0
survey_conduct | respondent_type_concept_id | MISSING FROM v5.4.0
survey_conduct | timing_concept_id | MISSING FROM v5.4.0
survey_conduct | collection_method_concept_id | MISSING FROM v5.4.0
survey_conduct | assisted_source_value | MISSING FROM v5.4.0
survey_conduct | respondent_type_source_value | MISSING FROM v5.4.0
survey_conduct | timing_source_value | MISSING FROM v5.4.0
survey_conduct | collection_method_source_value | MISSING FROM v5.4.0
survey_conduct | survey_source_value | MISSING FROM v5.4.0
survey_conduct | survey_source_concept_id | MISSING FROM v5.4.0
survey_conduct | survey_source_identifier | MISSING FROM v5.4.0
survey_conduct | validated_survey_concept_id | MISSING FROM v5.4.0
survey_conduct | validated_survey_source_value | MISSING FROM v5.4.0
survey_conduct | survey_version_number | MISSING FROM v5.4.0
survey_conduct | visit_occurrence_id | MISSING FROM v5.4.0
survey_conduct | response_visit_occurrence_id | MISSING FROM v5.4.0
visit_detail | visit_detail_id | IN BOTH
visit_detail | person_id | IN BOTH
visit_detail | visit_detail_concept_id | IN BOTH
visit_detail | visit_detail_start_date | IN BOTH
visit_detail | visit_detail_start_datetime | IN BOTH
visit_detail | visit_detail_end_date | IN BOTH
visit_detail | visit_detail_end_datetime | IN BOTH
visit_detail | visit_detail_type_concept_id | IN BOTH
visit_detail | provider_id | IN BOTH
visit_detail | care_site_id | IN BOTH
visit_detail | preceding_visit_detail_id | IN BOTH
visit_detail | visit_detail_source_concept_id | IN BOTH
visit_detail | visit_occurrence_id | IN BOTH
visit_detail | visit_detail_source_value | IN BOTH
visit_detail | admitted_from_concept_id | IN BOTH
visit_detail | admitted_from_source_value | IN BOTH
visit_detail | discharge_to_source_value | MISSING FROM v5.4.0
visit_detail | discharge_to_concept_id | MISSING FROM v5.4.0
visit_detail | visit_detail_parent_id | MISSING FROM v5.4.0
visit_detail | discharged_to_concept_id | MISSING FROM v6.0.1
visit_detail | discharged_to_source_value | MISSING FROM v6.0.1
visit_detail | parent_visit_detail_id | MISSING FROM v6.0.1
visit_occurrence | visit_occurrence_id | IN BOTH
visit_occurrence | person_id | IN BOTH
visit_occurrence | visit_concept_id | IN BOTH
visit_occurrence | visit_start_date | IN BOTH
visit_occurrence | visit_start_datetime | IN BOTH
visit_occurrence | visit_end_date | IN BOTH
visit_occurrence | visit_end_datetime | IN BOTH
visit_occurrence | visit_type_concept_id | IN BOTH
visit_occurrence | provider_id | IN BOTH
visit_occurrence | care_site_id | IN BOTH
visit_occurrence | visit_source_concept_id | IN BOTH
visit_occurrence | preceding_visit_occurrence_id | IN BOTH
visit_occurrence | visit_source_value | IN BOTH
visit_occurrence | admitted_from_concept_id | IN BOTH
visit_occurrence | admitted_from_source_value | IN BOTH
visit_occurrence | discharge_to_concept_id | MISSING FROM v5.4.0
visit_occurrence | discharge_to_source_value | MISSING FROM v5.4.0
visit_occurrence | discharged_to_concept_id | MISSING FROM v6.0.1
visit_occurrence | discharged_to_source_value | MISSING FROM v6.0.1
vocabulary | vocabulary_id | IN BOTH
vocabulary | vocabulary_name | IN BOTH
vocabulary | vocabulary_reference | IN BOTH
vocabulary | vocabulary_version | IN BOTH
vocabulary | vocabulary_concept_id | IN BOTH

134
extras/v60_v54_conversion/redshift_v60_v54_migration.sql Normal file
View File

@ -0,0 +1,134 @@
-- DEATH
CREATE TABLE DEATH ( person_id integer NOT NULL,
death_date date NOT NULL,
death_datetime TIMESTAMP NULL,
death_type_concept_id integer NULL,
cause_concept_id integer NULL,
cause_source_value varchar(50) NULL,
cause_source_concept_id integer NULL )
DISTKEY(person_id);
-- EPISODE
CREATE TABLE EPISODE (episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id bigint NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
episode_source_value varchar(50) NULL,
episode_source_concept_id integer NULL )
DISTKEY(person_id);
-- EPISODE_EVENT
CREATE TABLE EPISODE_EVENT (episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_event_field_concept_id integer NOT NULL )
DISTSTYLE ALL;
-- PERSON
alter table person drop column death_datetime;
-- VISIT_OCCURRENCE
alter table visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
alter table visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
-- VISIT_DETAIL
alter table visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
alter table visit_detail rename column discharge_to_source_value to discharged_to_source_value;
alter table visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
-- PROCEDURE_OCCURRENCE
alter table procedure_occurrence add column procedure_end_date date;
alter table procedure_occurrence add column procedure_end_datetime timestamp;
-- DEVICE_EXPOSURE
alter table device_exposure add column production_id varchar(255);
alter table device_exposure add column unit_concept_id integer;
alter table device_exposure add column unit_source_value varchar(50);
alter table device_exposure add column unit_source_concept_id integer;
-- MEASUREMENT
alter table measurement add column unit_source_id integer;
alter table measurement add column measurement_event_id bigint;
alter table measurement add column meas_event_field_concept_id integer;
-- OBSERVATION
alter table observation add column value_source_value varchar(50);
alter table observation drop column value_as_datetime;
-- LOCATION
alter location add column country_concept_id integer;
alter location add column country_source_value varchar(80);
-- PAYER_PLAN_PERIOD
alter table payer_plan_period drop column contract_person_id;
alter table payer_plan_period drop column contract_concept_id;
alter table payer_plan_period drop column contract_source_value;
alter table payer_plan_period drop column contract_source_concept_id;
-- COST
alter table cost drop column person_id;
alter table cost drop column cost_event_field_concept_id;
alter table cost drop column cost_concept_id;
alter table cost drop column cost_source_concept_id;
alter table cost drop column cost_source_value;
alter table cost drop column cost;
alter table cost drop column incurred_date;
alter table cost drop column billed_date;
alter table cost drop column paid_date;
alter table cost drop column revenue_code_source_value;
alter cost add column total_charge float;
alter cost add column total_cost float;
alter cost add column total_paid float;
alter cost add column paid_by_payer float;
alter cost add column paid_by_patient float;
alter cost add column paid_by_primary float;
alter cost add column paid_patient_copay float;
alter cost add column paid_patient_coinsurance float;
alter cost add column paid_patient_deductible float;
alter cost add column paid_ingredient_cost float;
alter cost add column paid_dispensing_fee float;
alter cost add column amount_allowed float;
alter cost add column cost_domain_id varchar(20);
alter cost add column revenue_code_source_value varchar(50);
-- DRUG_ERA
alter table drug_era rename column drug_era_start_datetime to drug_era_start_date;
alter table drug_era rename column drug_era_end_datetime to drug_era_end_date;
alter table drug_era alter column drug_era_start_date date;
alter table drug_era alter column drug_era_end_date date;
-- DOSE_ERA
alter table dose_era rename column dose_era_start_datetime to dose_era_start_date;
alter table dose_era rename column dose_era_end_datetime to dose_era_end_date;
alter table dose_era alter column dose_era_start_date date;
alter table dose_era alter column dose_era_end_date date;
-- CONDITION_ERA
alter table condition_era rename column condition_era_start_datetime to condition_era_start_date;
alter table condition_era rename column condition_era_end_datetime to condition_era_end_date;
alter table condition_era alter column condition_era_start_date date;
alter table condition_era alter column condition_era_end_date date;
-- METADATA
alter table metadata add column metadata_id integer;
alter table metadata add column value_as_number float;
-- CDM_SOURCE
alter table cdm_source add column cdm_version_concept_id integer;

6
inst/csv/OMOP_CDMv5.4_Field_Level.csv
View File

@ -62,8 +62,8 @@ visit_detail,visit_detail_type_concept_id,Yes,integer,"Use this field to underst
visit_detail,provider_id,No,integer,"There will only be one provider per **visit** record and the ETL document should clearly state how they were chosen (attending, admitting, etc.). This is a typical reason for leveraging the VISIT_DETAIL table as even though each VISIT_DETAIL record can only have one provider, there is no limit to the number of VISIT_DETAIL records that can be associated to a VISIT_OCCURRENCE record.",The additional providers associated to a Visit can be stored in this table where each VISIT_DETAIL record represents a different provider.,No,Yes,PROVIDER,PROVIDER_ID,NA,NA,NA visit_detail,provider_id,No,integer,"There will only be one provider per **visit** record and the ETL document should clearly state how they were chosen (attending, admitting, etc.). This is a typical reason for leveraging the VISIT_DETAIL table as even though each VISIT_DETAIL record can only have one provider, there is no limit to the number of VISIT_DETAIL records that can be associated to a VISIT_OCCURRENCE record.",The additional providers associated to a Visit can be stored in this table where each VISIT_DETAIL record represents a different provider.,No,Yes,PROVIDER,PROVIDER_ID,NA,NA,NA
visit_detail,care_site_id,No,integer,This field provides information about the Care Site where the Visit Detail took place.,There should only be one Care Site associated with a Visit Detail.,No,Yes,CARE_SITE,CARE_SITE_ID,NA,NA,NA visit_detail,care_site_id,No,integer,This field provides information about the Care Site where the Visit Detail took place.,There should only be one Care Site associated with a Visit Detail.,No,Yes,CARE_SITE,CARE_SITE_ID,NA,NA,NA
visit_detail,visit_detail_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the kind of visit detail that took place (inpatient, outpatient, emergency, etc.)","If there is information about the kind of visit detail in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the VISIT_DETAIL_SOURCE_VALUE, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created.",No,No,NA,NA,NA,NA,NA visit_detail,visit_detail_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the kind of visit detail that took place (inpatient, outpatient, emergency, etc.)","If there is information about the kind of visit detail in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the VISIT_DETAIL_SOURCE_VALUE, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created.",No,No,NA,NA,NA,NA,NA
visit_detail,visit_detail_source_concept_id,No,Integer,NA,If the VISIT_DETAIL_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA visit_detail,visit_detail_source_concept_id,No,integer,NA,If the VISIT_DETAIL_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
visit_detail,admitted_from_concept_id,No,Integer,"Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example.","If available, map the admitted_from_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=). If a person was admitted from home or was self-referred, set this to 0.",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA visit_detail,admitted_from_concept_id,No,integer,"Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example.","If available, map the admitted_from_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=). If a person was admitted from home or was self-referred, set this to 0.",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA
visit_detail,admitted_from_source_value,No,varchar(50),NA,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits.",No,No,NA,NA,NA,NA,NA visit_detail,admitted_from_source_value,No,varchar(50),NA,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits.",No,No,NA,NA,NA,NA,NA
visit_detail,discharged_to_source_value,No,varchar(50),NA,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more.",No,No,NA,NA,NA,NA,NA visit_detail,discharged_to_source_value,No,varchar(50),NA,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more.",No,No,NA,NA,NA,NA,NA
visit_detail,discharged_to_concept_id,No,integer,"Use this field to determine where the patient was discharged to after a visit. This concept is part of the visit domain and can indicate if a patient was transferred to another hospital or sent to a long-term care facility, for example. It is assumed that a person is discharged to home therefore there is not a standard concept id for ""home"". Use concept id = 0 when a person is discharged to home.","If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in the Visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA visit_detail,discharged_to_concept_id,No,integer,"Use this field to determine where the patient was discharged to after a visit. This concept is part of the visit domain and can indicate if a patient was transferred to another hospital or sent to a long-term care facility, for example. It is assumed that a person is discharged to home therefore there is not a standard concept id for ""home"". Use concept id = 0 when a person is discharged to home.","If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in the Visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,NA,NA
@ -177,7 +177,7 @@ observation,observation_datetime,No,datetime,NA,If no time is given set to midni
observation,observation_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.","Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA observation,observation_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.","Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA
observation,value_as_number,No,float,"This is the numerical value of the Result of the Observation, if applicable and available. It is not expected that all Observations will have numeric results, rather, this field is here to house values should they exist.",NA,No,No,NA,NA,NA,NA,NA observation,value_as_number,No,float,"This is the numerical value of the Result of the Observation, if applicable and available. It is not expected that all Observations will have numeric results, rather, this field is here to house values should they exist.",NA,No,No,NA,NA,NA,NA,NA
observation,value_as_string,No,varchar(60),"This is the categorical value of the Result of the Observation, if applicable and available.",NA,No,No,NA,NA,NA,NA,NA observation,value_as_string,No,varchar(60),"This is the categorical value of the Result of the Observation, if applicable and available.",NA,No,No,NA,NA,NA,NA,NA
observation,value_as_concept_id,No,Integer,"It is possible that some records destined for the Observation table have two clinical ideas represented in one source code. This is common with ICD10 codes that describe a family history of some Condition, for example. In OMOP the Vocabulary breaks these two clinical ideas into two codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the VALUE_AS_CONCEPT_ID. It is important when using the Observation table to keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID field for relevant information.","Note that the value of VALUE_AS_CONCEPT_ID may be provided through mapping from a source Concept which contains the content of the Observation. In those situations, the CONCEPT_RELATIONSHIP table in addition to the 'Maps to' record contains a second record with the relationship_id set to 'Maps to value'. For example, ICD10 [Z82.4](https://athena.ohdsi.org/search-terms/terms/45581076) 'Family history of ischaemic heart disease and other diseases of the circulatory system' has a 'Maps to' relationship to [4167217](https://athena.ohdsi.org/search-terms/terms/4167217) 'Family history of clinical finding' as well as a 'Maps to value' record to [134057](https://athena.ohdsi.org/search-terms/terms/134057) 'Disorder of cardiovascular system'. If there's no categorial result in a source_data, set value_as_concept_id to NULL, if there is a categorial result in a source_data but without mapping, set value_as_concept_id to 0.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA observation,value_as_concept_id,No,integer,"It is possible that some records destined for the Observation table have two clinical ideas represented in one source code. This is common with ICD10 codes that describe a family history of some Condition, for example. In OMOP the Vocabulary breaks these two clinical ideas into two codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the VALUE_AS_CONCEPT_ID. It is important when using the Observation table to keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID field for relevant information.","Note that the value of VALUE_AS_CONCEPT_ID may be provided through mapping from a source Concept which contains the content of the Observation. In those situations, the CONCEPT_RELATIONSHIP table in addition to the 'Maps to' record contains a second record with the relationship_id set to 'Maps to value'. For example, ICD10 [Z82.4](https://athena.ohdsi.org/search-terms/terms/45581076) 'Family history of ischaemic heart disease and other diseases of the circulatory system' has a 'Maps to' relationship to [4167217](https://athena.ohdsi.org/search-terms/terms/4167217) 'Family history of clinical finding' as well as a 'Maps to value' record to [134057](https://athena.ohdsi.org/search-terms/terms/134057) 'Disorder of cardiovascular system'. If there's no categorial result in a source_data, set value_as_concept_id to NULL, if there is a categorial result in a source_data but without mapping, set value_as_concept_id to 0.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
observation,qualifier_concept_id,No,integer,"This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc.","Use your best judgement as to what Concepts to use here and if they are necessary to accurately represent the clinical record. There is no restriction on the domain of these Concepts, they just need to be Standard.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA observation,qualifier_concept_id,No,integer,"This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc.","Use your best judgement as to what Concepts to use here and if they are necessary to accurately represent the clinical record. There is no restriction on the domain of these Concepts, they just need to be Standard.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
observation,unit_concept_id,No,integer,There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.,"There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If the source unit is NULL (applicable to cases when there's no numerical value or when it doesn't require a unit), keep unit_concept_id NULL as well. If there's no mapping of a source unit, populate unit_concept_id with 0.",No,Yes,CONCEPT,CONCEPT_ID,Unit,NA,NA observation,unit_concept_id,No,integer,There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.,"There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If the source unit is NULL (applicable to cases when there's no numerical value or when it doesn't require a unit), keep unit_concept_id NULL as well. If there's no mapping of a source unit, populate unit_concept_id with 0.",No,Yes,CONCEPT,CONCEPT_ID,Unit,NA,NA
observation,provider_id,No,integer,"The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result.",The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. For example the admitting vs attending physician on an EHR record.,No,Yes,PROVIDER,PROVIDER_ID,NA,NA,NA observation,provider_id,No,integer,"The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result.",The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. For example the admitting vs attending physician on an EHR record.,No,Yes,PROVIDER,PROVIDER_ID,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
62 condition_occurrence person_id Yes integer The PERSON_ID of the PERSON for whom the condition is recorded. NA No Yes PERSON PERSON_ID NA NA NA
63 condition_occurrence condition_concept_id Yes integer The CONDITION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a condition The CONCEPT_ID that the CONDITION_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of "Condition" should go in this table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Condition NA NA
64 condition_occurrence condition_start_date Yes date Use this date to determine the start date of the condition Most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE. No No NA NA NA NA NA
65 condition_occurrence condition_start_datetime No datetime NA If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No NA NA NA NA NA
66 condition_occurrence condition_end_date No date Use this date to determine the end date of the condition Most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE. No No NA NA NA NA NA
67 condition_occurrence condition_end_datetime No datetime NA If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No NA NA NA NA NA
68 condition_occurrence condition_type_concept_id Yes integer This field can be used to determine the provenance of the Condition record, as in whether the condition was from an EHR system, insurance claim, registry, or other sources. Choose the CONDITION_TYPE_CONCEPT_ID that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept NA NA
69 condition_occurrence condition_status_concept_id No integer This concept represents the point during the visit the diagnosis was given (admitting diagnosis, final diagnosis), whether the diagnosis was determined due to laboratory findings, if the diagnosis was exclusionary, or if it was a preliminary diagnosis, among others. Choose the Concept in the Condition Status domain that best represents the point during the visit when the diagnosis was given. These can include admitting diagnosis, principal diagnosis, and secondary diagnosis. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Condition Status NA NA
177 observation observation_event_id No integer If the Observation record is related to another record in the database, this field is the primary key of the linked record. Put the primary key of the linked record, if applicable, here. See the [ETL Conventions for the OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm60.html#observation) table for more details. No No NA NA NA NA NA
178 observation obs_event_field_concept_id No integer If the Observation record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. Put the CONCEPT_ID that identifies which table and field the OBSERVATION_EVENT_ID came from. No Yes CONCEPT CONCEPT_ID NA NA NA
179 death person_id Yes integer NA NA No Yes PERSON PERSON_ID NA NA NA
180 death death_date Yes date The date the person was deceased. If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day. For additional conventions related to this field, please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_death_date.html). No No NA NA NA NA NA
181 death death_datetime No datetime NA If you have date and time of death, populate death_datetime, otherwise leave NULL No No NA NA NA NA NA
182 death death_type_concept_id No integer This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc. Use the type concept that reflects the source of the death record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept NA NA
183 death cause_concept_id No integer This is the Standard Concept representing the Person's cause of death, if available. There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death. No Yes CONCEPT CONCEPT_ID NA NA NA