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Foreign key fixes

This commit is contained in:
Clair Blacketer 2021-08-19 15:52:33 -04:00
parent 690c9edf40
commit 041291eb27
18 changed files with 45 additions and 44 deletions
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.DS_Store vendored
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.gitignore vendored
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@ -2,3 +2,4 @@
.Rhistory
.RData
.Ruserdata
extras/CodeToRun.R

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ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_constraints.sql
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@ -270,7 +270,7 @@ alter table @cdmDatabaseSchema.condition_era add constraint fpk_condition_era_co
alter table @cdmDatabaseSchema.episode add constraint fpk_episode_person_id foreign key (person_id) references @cdmDatabaseSchema.person (person_id);
alter table @cdmDatabaseSchema.episode add constraint fpk_episode_episode_concept_id foreign key (episode_concept_id) references @cdmDatabaseSchema. ();
alter table @cdmDatabaseSchema.episode add constraint fpk_episode_episode_concept_id foreign key (episode_concept_id) references @cdmDatabaseSchema.concept (concept_id);
alter table @cdmDatabaseSchema.episode add constraint fpk_episode_episode_object_concept_id foreign key (episode_object_concept_id) references @cdmDatabaseSchema.concept (concept_id);

2
ddl/5.4/impala/OMOPCDM_impala_5.4_constraints.sql
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@ -270,7 +270,7 @@ ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_co
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema. ();
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

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ddl/5.4/impala/OMOPCDM_impala_5.4_ddl.sql
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@ -395,14 +395,14 @@ CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id BIGINT,
person_id BIGINT,
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 BIGINT,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id INT,
episode_type_concept_id INT,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id BIGINT,
event_id BIGINT,
episode_id INT,
event_id INT,
episode_event_field_concept_id INT );
--HINT DISTRIBUTE ON RANDOM

2
ddl/5.4/netezza/OMOPCDM_netezza_5.4_constraints.sql
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@ -270,7 +270,7 @@ ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_co
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema. ();
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

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ddl/5.4/netezza/OMOPCDM_netezza_5.4_ddl.sql
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@ -395,14 +395,14 @@ CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_id integer NOT NULL,
person_id integer 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_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM

2
ddl/5.4/oracle/OMOPCDM_oracle_5.4_constraints.sql
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@ -270,7 +270,7 @@ ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_co
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema. ();
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

10
ddl/5.4/oracle/OMOPCDM_oracle_5.4_ddl.sql
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@ -395,14 +395,14 @@ CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id NUMBER(19) NOT NULL,
person_id NUMBER(19) NOT NULL,
episode_id integer NOT NULL,
person_id integer 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 NUMBER(19) NULL,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id NUMBER(19) NOT NULL,
event_id NUMBER(19) NOT NULL,
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM

2
ddl/5.4/pdw/OMOPCDM_pdw_5.4_constraints.sql
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@ -270,7 +270,7 @@ ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_co
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema. ();
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

10
ddl/5.4/pdw/OMOPCDM_pdw_5.4_ddl.sql
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@ -394,14 +394,14 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (con
WITH (DISTRIBUTION = HASH(person_id));
--HINT DISTRIBUTE ON KEY (person_id)
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id bigint NOT NULL,
person_id bigint NOT NULL,
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer 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_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -410,8 +410,8 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_i
WITH (DISTRIBUTION = HASH(person_id));
--HINT DISTRIBUTE ON RANDOM
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (episode_id bigint NOT NULL,
event_id bigint NOT NULL,
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL )
WITH (DISTRIBUTION = REPLICATE);

2
ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_constraints.sql
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@ -270,7 +270,7 @@ ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_co
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema. ();
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

10
ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_ddl.sql
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@ -395,14 +395,14 @@ CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_id integer NOT NULL,
person_id integer 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_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM

2
ddl/5.4/redshift/OMOPCDM_redshift_5.4_constraints.sql
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@ -270,7 +270,7 @@ ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_co
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema. ();
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

10
ddl/5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql
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@ -394,14 +394,14 @@ CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (condition_era_id integer NOT NUL
DISTKEY(person_id);
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id bigint NOT NULL,
person_id bigint NOT NULL,
CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id integer NOT NULL,
person_id integer 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_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -410,8 +410,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id bigint NOT NULL,
DISTKEY(person_id);
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (episode_id bigint NOT NULL,
event_id bigint NOT NULL,
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL )
DISTSTYLE ALL;

2
ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_constraints.sql
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@ -270,7 +270,7 @@ ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_co
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema. ();
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

10
ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_ddl.sql
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@ -395,14 +395,14 @@ CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer 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_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM

2
inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -369,7 +369,7 @@ Occurrences used to construct the
condition era.",,No,No,,,,,
EPISODE,episode_id,Yes,integer,A unique identifier for each Episode.,,Yes,No,,,,,
EPISODE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the episode is recorded.,,No,Yes,PERSON,PERSON_ID,,,
EPISODE,episode_concept_id,Yes,integer,"The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.","Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see [article] for cancers and [article] for non-cancers describing how these are defined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=)",No,Yes,,,Episode,,
EPISODE,episode_concept_id,Yes,integer,"The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.","Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see [article] for cancers and [article] for non-cancers describing how these are defined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=)",No,Yes,CONCEPT,CONCEPT_ID,,,
EPISODE,episode_start_date,Yes,date,The date when the Episode beings. ,Please see [article] for how to define an Episode start date.,No,No,,,,,
EPISODE,episode_start_datetime,No,datetime,The date and time when the Episode begins.,,No,No,,,,,
EPISODE,episode_end_date,No,date,The date when the instance of the Episode is considered to have ended.,Please see [article] for how to define an Episode end date.,,,,,,,

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
369 CONCEPT valid_start_date Yes date The date when the Concept was first recorded. The default value is 1-Jan-1970, meaning, the Concept has no (known) date of inception. No No
370 CONCEPT valid_end_date Yes date The date when the Concept became invalid because it was deleted or superseded (updated) by a new concept. The default value is 31-Dec-2099, meaning, the Concept is valid until it becomes deprecated. No No
371 CONCEPT invalid_reason No varchar(1) Reason the Concept was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value. No No
372 VOCABULARY vocabulary_id Yes varchar(20) A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. Yes No
373 VOCABULARY vocabulary_name Yes varchar(255) The name describing the vocabulary, for example, International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc. No No
374 VOCABULARY vocabulary_reference Yes varchar(255) External reference to documentation or available download of the about the vocabulary. No No
375 VOCABULARY vocabulary_version No varchar(255) Version of the Vocabulary as indicated in the source. No No