From 19150d2720cfeba409ee964e66e2159dc0f5141c Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Fri, 14 Jul 2017 13:12:23 -0400 Subject: [PATCH] Addresses cdm proposal #84 --- Impala/OMOP_CDM_ddl_Impala.sql | 4 +++- Impala/OMOP_Parquet_v5.2.sql | 4 +++- Oracle/OMOP CDM constraints - Oracle.sql | 2 ++ Oracle/OMOP CDM ddl - Oracle.sql | 4 +++- PostgreSQL/OMOP CDM constraints - PostgreSQL.sql | 2 ++ PostgreSQL/OMOP CDM ddl - PostgreSQL.sql | 4 +++- README.md | 5 ++++- Sql Server/OMOP CDM constraints - SQL Server.sql | 2 ++ Sql Server/OMOP CDM ddl - SQL Server.sql | 4 +++- 9 files changed, 25 insertions(+), 6 deletions(-) diff --git a/Impala/OMOP_CDM_ddl_Impala.sql b/Impala/OMOP_CDM_ddl_Impala.sql index 6f2a881..c01a171 100644 --- a/Impala/OMOP_CDM_ddl_Impala.sql +++ b/Impala/OMOP_CDM_ddl_Impala.sql @@ -420,7 +420,9 @@ CREATE TABLE condition_occurrence ( provider_id INTEGER, visit_occurrence_id INTEGER, condition_source_value VARCHAR(50), - condition_source_concept_id INTEGER + condition_source_concept_id INTEGER, + condition_status_source_value VARCHAR(50), + condition_status_concept_id INTEGER ) ROW FORMAT DELIMITED FIELDS TERMINATED BY ',' TBLPROPERTIES ("skip.header.line.count"="1") diff --git a/Impala/OMOP_Parquet_v5.2.sql b/Impala/OMOP_Parquet_v5.2.sql index 83c17e5..7afd312 100644 --- a/Impala/OMOP_Parquet_v5.2.sql +++ b/Impala/OMOP_Parquet_v5.2.sql @@ -304,7 +304,9 @@ SELECT provider_id, visit_occurrence_id, condition_source_value, - condition_source_concept_id + condition_source_concept_id, + condition_status_source_value, + condition_status_concept_id FROM omop_cdm.condition_occurrence; CREATE TABLE omop_cdm_parquet.measurement diff --git a/Oracle/OMOP CDM constraints - Oracle.sql b/Oracle/OMOP CDM constraints - Oracle.sql index b211730..a1e3207 100644 --- a/Oracle/OMOP CDM constraints - Oracle.sql +++ b/Oracle/OMOP CDM constraints - Oracle.sql @@ -385,6 +385,8 @@ ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id); +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_status_concept FOREIGN KEY (condition_status_concept_id) REFERENCES concept (concept_id); + ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id); diff --git a/Oracle/OMOP CDM ddl - Oracle.sql b/Oracle/OMOP CDM ddl - Oracle.sql index d8cc713..5f7a4f1 100644 --- a/Oracle/OMOP CDM ddl - Oracle.sql +++ b/Oracle/OMOP CDM ddl - Oracle.sql @@ -405,7 +405,9 @@ CREATE TABLE condition_occurrence provider_id INTEGER NULL , visit_occurrence_id INTEGER NULL , condition_source_value VARCHAR(50) NULL , - condition_source_concept_id INTEGER NULL + condition_source_concept_id INTEGER NULL , + condition_status_source_value VARCHAR(50) NULL , + condition_status_concept_id INTEGER NULL ) ; diff --git a/PostgreSQL/OMOP CDM constraints - PostgreSQL.sql b/PostgreSQL/OMOP CDM constraints - PostgreSQL.sql index d5405d9..429c111 100644 --- a/PostgreSQL/OMOP CDM constraints - PostgreSQL.sql +++ b/PostgreSQL/OMOP CDM constraints - PostgreSQL.sql @@ -384,6 +384,8 @@ ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id); +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_status_concept FOREIGN KEY (condition_status_concept_id) REFERENCES concept (concept_id); + ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id); diff --git a/PostgreSQL/OMOP CDM ddl - PostgreSQL.sql b/PostgreSQL/OMOP CDM ddl - PostgreSQL.sql index 39cc4cd..af5e54e 100644 --- a/PostgreSQL/OMOP CDM ddl - PostgreSQL.sql +++ b/PostgreSQL/OMOP CDM ddl - PostgreSQL.sql @@ -405,7 +405,9 @@ CREATE TABLE condition_occurrence provider_id INTEGER NULL , visit_occurrence_id INTEGER NULL , condition_source_value VARCHAR(50) NULL , - condition_source_concept_id INTEGER NULL + condition_source_concept_id INTEGER NULL , + condition_status_source_value VARCHAR(50) NULL , + condition_status_concept_id INTEGER NULL ) ; diff --git a/README.md b/README.md index 087ec34..2bd8ef3 100644 --- a/README.md +++ b/README.md @@ -9,13 +9,16 @@ Release Notes for v5.2.0 This version is based on the CDM working group proposals: * [#71](https://github.com/OHDSI/CommonDataModel/issues/71) Adds the field VERBATIM_END_DATE to DRUG_EXPOSURE and makes DRUG_EXPOSURE_END_DATE a required field * [#73](https://github.com/OHDSI/CommonDataModel/issues/73) Removes EFFECTIVE_DRUG_DOSE and DOSE_UNIT_CONCEPT_ID from DRUG_EXPOSURE -* [#75] (https://github.com/OHDSI/CommonDataModel/issues/75) Adds the field BOX_SIZE to DRUG_STRENGTH +* [#75](https://github.com/OHDSI/CommonDataModel/issues/75) Adds the field BOX_SIZE to DRUG_STRENGTH * [#83](https://github.com/OHDSI/CommonDataModel/issues/83) Adds the following fields to VISIT_OCCURRENCE: * ADMITTING_SOURCE_CONCEPT_ID * ADMITTING_SOURCE_VALUE * DISCHARGE_TO_CONCEPT_ID * DISCHARGE_TO_SOURCE_VALUE * PRECEDING_VISIT_OCCURRENCE_ID +* [#84](https://github.com/OHDSI/CommonDataModel/issues/84) Adds the following fields to CONDITION_OCCURRENCE: + * CONDITION_STATUS_CONCEPT_ID + * CONDITION_STATUS_SOURCE_VALUE and is **backwards compatibile with v5.0.1**. The proposed and accepted changes include adding a datetime field to every table that had a date column and adding field DENOMINATOR_VALUE to the DRUG_STRENGTH table. These were the new columns added: diff --git a/Sql Server/OMOP CDM constraints - SQL Server.sql b/Sql Server/OMOP CDM constraints - SQL Server.sql index b0c5754..4ee15d2 100644 --- a/Sql Server/OMOP CDM constraints - SQL Server.sql +++ b/Sql Server/OMOP CDM constraints - SQL Server.sql @@ -384,6 +384,8 @@ ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id); +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_status_concept FOREIGN KEY (condition_status_concept_id) REFERENCES concept (concept_id); + ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id); diff --git a/Sql Server/OMOP CDM ddl - SQL Server.sql b/Sql Server/OMOP CDM ddl - SQL Server.sql index 16e5e4a..20e2f1d 100644 --- a/Sql Server/OMOP CDM ddl - SQL Server.sql +++ b/Sql Server/OMOP CDM ddl - SQL Server.sql @@ -405,7 +405,9 @@ CREATE TABLE condition_occurrence provider_id INTEGER NULL , visit_occurrence_id INTEGER NULL , condition_source_value VARCHAR(50) NULL , - condition_source_concept_id INTEGER NULL + condition_source_concept_id INTEGER NULL , + condition_status_source_value VARCHAR(50) NULL , + condition_status_concept_id INTEGER NULL ) ;