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OMOP
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Addresses cdm proposals #75 and #83

This commit is contained in:
clairblacketer 2017-07-14 12:28:57 -04:00
parent 29b0899b74
commit 17d0bfcf5f
9 changed files with 54 additions and 11 deletions
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7
Impala/OMOP_CDM_ddl_Impala.sql
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@ -330,7 +330,12 @@ CREATE TABLE visit_occurrence (
provider_id INTEGER,
care_site_id INTEGER,
visit_source_value VARCHAR(50),
visit_source_concept_id INTEGER
visit_source_concept_id INTEGER,
admitting_source_concept_id INTEGER,
admitting_source_value VARCHAR(50),
discharge_to_concept_id INTEGER(50),
discharge_to_source_value VARCHAR(50),
preceding_visit_occurrence_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")

7
Impala/OMOP_Parquet_v5.2.sql
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@ -213,7 +213,12 @@ SELECT
provider_id,
care_site_id,
visit_source_value,
visit_source_concept_id
visit_source_concept_id,
admitting_source_concept_id,
admitting_source_value,
discharge_to_concept_id,
discharge_to_source_value,
preceding_visit_occurrence_id
FROM omop_cdm.visit_occurrence;
CREATE TABLE omop_cdm_parquet.procedure_occurrence

4
Oracle/OMOP CDM constraints - Oracle.sql
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@ -323,6 +323,10 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (car
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);

7
Oracle/OMOP CDM ddl - Oracle.sql
View File

@ -312,7 +312,12 @@ CREATE TABLE visit_occurrence
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL
visit_source_concept_id INTEGER NULL,
admitting_source_concept_id INTEGER NULL ,
admitting_source_value VARCHAR(50) NULL ,
discharge_to_concept_id INTEGER(50) NULL ,
discharge_to_source_value VARCHAR(50) NULL ,
preceding_visit_occurrence_id INTEGER NULL
)
;

4
PostgreSQL/OMOP CDM constraints - PostgreSQL.sql
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@ -322,6 +322,10 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (car
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);

11
PostgreSQL/OMOP CDM ddl - PostgreSQL.sql
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@ -305,14 +305,19 @@ CREATE TABLE visit_occurrence
person_id INTEGER NOT NULL ,
visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NOT NULL ,
visit_start_datetime TIMESTAMP NULL ,
visit_start_datetime TIMESTAMP NULL ,
visit_end_date DATE NOT NULL ,
visit_end_datetime TIMESTAMP NULL ,
visit_end_datetime TIMESTAMP NULL ,
visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL
visit_source_concept_id INTEGER NULL ,
admitting_source_concept_id INTEGER NULL ,
admitting_source_value VARCHAR(50) NULL ,
discharge_to_concept_id INTEGER(50) NULL ,
discharge_to_source_value VARCHAR(50) NULL ,
preceding_visit_occurrence_id INTEGER NULL
)
;

16
README.md
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@ -7,11 +7,17 @@ See full CDM specification file on our github [wiki](https://github.com/OHDSI/Co
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
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:
* [#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
* [#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
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:
---------

4
Sql Server/OMOP CDM constraints - SQL Server.sql
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@ -322,6 +322,10 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (car
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);

5
Sql Server/OMOP CDM ddl - SQL Server.sql
View File

@ -313,6 +313,11 @@ CREATE TABLE visit_occurrence
care_site_id INTEGER NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL
admitting_source_concept_id INTEGER NULL ,
admitting_source_value VARCHAR(50) NULL ,
discharge_to_concept_id INTEGER(50) NULL ,
discharge_to_source_value VARCHAR(50) NULL ,
preceding_visit_occurrence_id INTEGER NULL
)
;