mz-health/OMOP
mz-health
/
OMOP
mirror of https://github.com/OHDSI/CommonDataModel.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fixes from testers for pdw, redshit, postgres and sql server and survey -> survey_conduct changes.

This commit is contained in:
clairblacketer 2018-09-25 12:40:53 -04:00
parent 62207c4309
commit 86dbcec3e0
22 changed files with 1720 additions and 1704 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
Impala/OMOP CDM impala ddl.txt
View File

@ -203,7 +203,7 @@ Standardized clinical data
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE person
(
person_id BIGINT , --BIGINTs added
person_id BIGINT ,
gender_concept_id INTEGER ,
year_of_birth INTEGER ,
month_of_birth INTEGER ,
@ -274,7 +274,7 @@ CREATE TABLE visit_occurrence
care_site_id BIGINT ,
visit_source_value VARCHAR(50),
visit_source_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
admitted_from_concept_id INTEGER ,
admitted_from_source_value VARCHAR(50),
discharge_to_source_value VARCHAR(50) ,
discharge_to_concept_id INTEGER ,
@ -297,7 +297,7 @@ CREATE TABLE visit_detail
provider_id BIGINT ,
care_site_id BIGINT ,
discharge_to_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
admitted_from_concept_id INTEGER ,
admitted_from_source_value VARCHAR(50) ,
visit_detail_source_value VARCHAR(50) ,
visit_detail_source_concept_id INTEGER ,
@ -496,8 +496,8 @@ CREATE TABLE observation
observation_source_concept_id INTEGER ,
unit_source_value VARCHAR(50) ,
qualifier_source_value VARCHAR(50) ,
observation_event_id BIGINT , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
obs_event_field_concept_id INTEGER , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/
observation_event_id BIGINT ,
obs_event_field_concept_id INTEGER ,
value_as_datetime TIMESTAMP
)
;
@ -529,12 +529,11 @@ CREATE TABLE survey_conduct
survey_version_number VARCHAR(20) ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
response_to_visit_occurrence_id BIGINT
response_visit_occurrence_id BIGINT
)
;
CREATE TABLE fact_relationship
(
domain_concept_id_1 INTEGER ,
@ -546,7 +545,6 @@ CREATE TABLE fact_relationship
;
/************************
Standardized health system data
@ -574,7 +572,7 @@ CREATE TABLE location_history
(
location_history_id BIGINT ,
location_id BIGINT ,
relationship_type_concept_id INTEGER , --Recent addition based on github discussion
relationship_type_concept_id INTEGER ,
domain_id VARCHAR(50) ,
entity_id BIGINT ,
start_date TIMESTAMP ,
@ -654,7 +652,7 @@ CREATE TABLE cost
cost_id BIGINT ,
person_id BIGINT,
cost_event_id BIGINT ,
cost_event_field_concept_id INTEGER , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_event_field_concept_id INTEGER ,
cost_concept_id INTEGER ,
cost_type_concept_id INTEGER ,
currency_concept_id INTEGER ,

10
Netezza/OMOP CDM netezza ddl.txt
View File

@ -227,7 +227,7 @@ Standardized clinical data
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE person
(
person_id BIGINT NOT NULL , --BIGINTs added
person_id BIGINT NOT NULL ,
gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL,
@ -542,7 +542,7 @@ DISTRIBUTE ON (person_id)
--HINT DISTRIBUTE ON KEY(person_id)
CREATE TABLE survey_conduct /*Should this be SURVEY_OCCURRENCE instead to comply with the other tables?*/
CREATE TABLE survey_conduct
(
survey_conduct_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
@ -568,7 +568,7 @@ CREATE TABLE survey_conduct /*Should this be SURVEY_OCCURRENCE instead to comply
survey_version_number VARCHAR(20) NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
response_to_visit_occurrence_id BIGINT NULL
response_visit_occurrence_id BIGINT NULL
)
DISTRIBUTE ON (person_id)
;
@ -616,9 +616,9 @@ DISTRIBUTE ON RANDOM
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE location_history
(
location_history_id BIGINT NOT NULL , --unauthorized addition based on CDM conventions
location_history_id BIGINT NOT NULL ,
location_id BIGINT NOT NULL ,
relationship_type_concept_id INTEGER NULL , --Recent addition based on github discussion
relationship_type_concept_id INTEGER NULL ,
domain_id VARCHAR(50) NOT NULL ,
entity_id BIGINT NOT NULL ,
start_date DATE NOT NULL ,

24
Oracle/OMOP CDM oracle constraints.txt
View File

@ -352,29 +352,29 @@ ALTER TABLE observation ADD CONSTRAint fpk_observation_v_detail FOREIGN KEY (vis
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_respondent_type FOREIGN KEY (respondent_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_respondent_type FOREIGN KEY (respondent_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_collection_method FOREIGN KEY (collection_method_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_collection_method FOREIGN KEY (collection_method_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_validation FOREIGN KEY (validated_survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_validation FOREIGN KEY (validated_survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
ALTER TABLE survey ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_to_visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);

12
Oracle/OMOP CDM oracle ddl.txt
View File

@ -215,7 +215,7 @@ Standardized clinical data
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE person
(
person_id NUMBER(19) NOT NULL , --BIGINTs added
person_id NUMBER(19) NOT NULL ,
gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL,
@ -309,7 +309,7 @@ CREATE TABLE visit_detail
provider_id NUMBER(19) NULL ,
care_site_id NUMBER(19) NULL ,
discharge_to_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL , /*Changed from admitting_source_* */
admitted_from_concept_id INTEGER NULL ,
admitted_from_source_value VARCHAR(50) NULL ,
visit_detail_source_value VARCHAR(50) NULL ,
visit_detail_source_concept_id INTEGER NULL ,
@ -509,8 +509,8 @@ CREATE TABLE observation
observation_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL ,
observation_event_id NUMBER(19) NULL , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
obs_event_field_concept_id INTEGER NULL , /* Changed name to comply with COST and NOTE. Had to use 'obs' for oracle restriction, may be added on 9/4*/
observation_event_id NUMBER(19) NULL ,
obs_event_field_concept_id INTEGER NULL ,
value_as_datetime TIMESTAMP NULL
)
;
@ -543,7 +543,7 @@ CREATE TABLE survey_conduct --Table added
survey_version_number VARCHAR(20) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
response_visit_occurrence_id NUMBER(19) NULL
response_visit_occurrence_id NUMBER(19) NULL
)
;
@ -591,7 +591,7 @@ CREATE TABLE location_history --Table added
(
location_history_id NUMBER(19) NOT NULL ,
location_id NUMBER(19) NOT NULL ,
relationship_type_concept_id INTEGER NULL , --Recent addition based on github discussion
relationship_type_concept_id INTEGER NULL ,
domain_id VARCHAR(50) NOT NULL ,
entity_id NUMBER(19) NOT NULL ,
start_date DATE NOT NULL ,

78
ParallelDataWarehouse/OMOP CDM Results pdw ddl.txt Normal file
View File

@ -0,0 +1,78 @@
/*********************************************************************************
# Copyright 2018-08 Observational Health Data Sciences and Informatics
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
********************************************************************************/
/************************
####### # # ####### ###### ##### ###### # # ##### ###
# # ## ## # # # # # # # # ## ## # # # # # #
# # # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # #
# # # # # # # # # # # # # # # # ### # #
# # # # # # # # # # # # # # # # # ### # #
####### # # ####### # ##### ###### # # ## ##### ### ###
pdw script to create OMOP common data model results schema version 6.0
last revised: 27-Aug-2018
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
*************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
IF XACT_STATE() = 1 COMMIT; CREATE TABLE
cohort (
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
WITH (DISTRIBUTION = HASH(subject_id));
--HINT DISTRIBUTE ON RANDOM
IF XACT_STATE() = 1 COMMIT; CREATE TABLE
cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description VARCHAR(1000) NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax VARCHAR(1000) NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
WITH (DISTRIBUTION = REPLICATE);
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);

52
ParallelDataWarehouse/OMOP CDM pdw constraints.txt
View File

@ -28,7 +28,7 @@
pdw script to create foreign key, unique, and check constraints within the OMOP common data model, version 6.0
last revised: 30-Aug┌-2018
last revised: 30-Aug-2018
author: Patrick Ryan, Clair Blacketer
@ -86,7 +86,7 @@ ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (re
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_synonym_language FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
@ -112,14 +112,6 @@ ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (n
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
ALTER TABLE attribute_definition ADD CONSTRAINT fpk_attribute_type_concept FOREIGN KEY (attribute_type_concept_id) REFERENCES concept (concept_id);
/**************************
Standardized meta-data
@ -194,9 +186,9 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (prov
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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_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_admitting_s FOREIGN KEY (admitted_frome_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);
@ -215,7 +207,7 @@ ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitted_from_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_detail_source_concept_id) REFERENCES concept (concept_id);
@ -360,29 +352,29 @@ ALTER TABLE observation ADD CONSTRAint fpk_observation_v_detail FOREIGN KEY (vis
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_respondent_type FOREIGN KEY (respondent_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_respondent_type FOREIGN KEY (respondent_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_collection_method FOREIGN KEY (collection_method_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_collection_method FOREIGN KEY (collection_method_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_validation FOREIGN KEY (validated_survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_validation FOREIGN KEY (validated_survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
ALTER TABLE survey ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_to_visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
@ -476,16 +468,6 @@ Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);

891
ParallelDataWarehouse/OMOP CDM pdw ddl.txt
View File

File diff suppressed because it is too large Load Diff

18
ParallelDataWarehouse/OMOP CDM pdw pk indexes.txt
View File

@ -77,10 +77,6 @@ ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMA
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY NONCLUSTERED (drug_concept_id, ingredient_concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY NONCLUSTERED (attribute_definition_id);
/**************************
@ -127,7 +123,7 @@ ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY NONCLUSTERED ( note
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY NONCLUSTERED ( observation_id ) ;
ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY NONCLUSTERED ( survey_occurrence_id ) ;
ALTER TABLE survey_conduct ADD CONSTRAINT xpk_survey PRIMARY KEY NONCLUSTERED ( survey_conduct_id ) ;
/************************
@ -165,9 +161,6 @@ Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY NONCLUSTERED ( drug_era_id ) ;
@ -225,9 +218,6 @@ CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_cod
CREATE CLUSTERED INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
CREATE CLUSTERED INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CREATE CLUSTERED INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
/**************************
@ -328,12 +318,6 @@ Standardized derived elements
************************/
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
CREATE CLUSTERED INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);

4
ParallelDataWarehouse/README.md
View File

@ -14,3 +14,7 @@ n order to create your instantiation of the Common Data Model, we recommend foll
4. Execute the script `OMOP CDM pdw indexes.txt` to add the minimum set of indices and primary keys we recommend.
5. Execute the script `OMOP CDM pdw constraints.txt` to add the foreign key constraints.
6. Create an empty schema for results.
7. Execute the script `OMOP CDM Results pdw ddl.txt` to create the tables and fields in the results schema.

90
PostgreSQL/OMOP CDM Results postgresql ddl.txt Normal file
View File

@ -0,0 +1,90 @@
/*********************************************************************************
# Copyright 2018-08 Observational Health Data Sciences and Informatics
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
********************************************************************************/
/************************
####### # # ####### ###### ##### ###### # # ##### ###
# # ## ## # # # # # # # # ## ## # # # # # #
# # # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # #
# # # # # # # # # # # # # # # # ### # #
# # # # # # # # # # # # # # # # # ### # #
####### # # ####### # ##### ###### # # ## ##### ### ###
postgresql script to create OMOP common data model results schema version 6.0
last revised: 27-Aug-2018
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
*************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description TEXT NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax TEXT NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
;
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CLUSTER cohort_definition USING idx_cohort_definition_id ;
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);

46
PostgreSQL/OMOP CDM postgresql constraints.txt
View File

@ -28,7 +28,7 @@
postgresql script to create foreign key, unique, and check constraints within the OMOP common data model, version 6.0
last revised: 30-Aug┌-2018
last revised: 30-Aug-2018
author: Patrick Ryan, Clair Blacketer
@ -112,14 +112,6 @@ ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (n
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
ALTER TABLE attribute_definition ADD CONSTRAINT fpk_attribute_type_concept FOREIGN KEY (attribute_type_concept_id) REFERENCES concept (concept_id);
/**************************
Standardized meta-data
@ -194,7 +186,7 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (prov
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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_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);
@ -360,29 +352,29 @@ ALTER TABLE observation ADD CONSTRAint fpk_observation_v_detail FOREIGN KEY (vis
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_respondent_type FOREIGN KEY (respondent_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_respondent_type FOREIGN KEY (respondent_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_collection_method FOREIGN KEY (collection_method_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_collection_method FOREIGN KEY (collection_method_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_validation FOREIGN KEY (validated_survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_validation FOREIGN KEY (validated_survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
ALTER TABLE survey ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_to_visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
@ -476,16 +468,6 @@ Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);

801
PostgreSQL/OMOP CDM postgresql ddl.txt
View File

File diff suppressed because it is too large Load Diff

28
PostgreSQL/OMOP CDM postgresql pk indexes.txt
View File

@ -77,10 +77,6 @@ ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMA
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
/**************************
@ -127,7 +123,7 @@ ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY ( survey_occurrence_id ) ;
ALTER TABLE survey_conduct ADD CONSTRAINT xpk_survey PRIMARY KEY ( survey_conduct_id ) ;
/************************
@ -139,7 +135,7 @@ Standardized health system data
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ; --Assuming this should be added
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
@ -165,10 +161,6 @@ Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
@ -234,12 +226,6 @@ CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CLUSTER drug_strength USING idx_drug_strength_id_1 ;
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CLUSTER cohort_definition USING idx_cohort_definition_id ;
CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
CLUSTER attribute_definition USING idx_attribute_definition_id ;
/**************************
@ -317,8 +303,8 @@ CLUSTER observation USING idx_observation_person_id ;
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
CREATE INDEX idx_survey_person_id ON survey (person_id ASC);
CLUSTER survey USING idx_survey_person_id ;
CREATE INDEX idx_survey_person_id ON survey_conduct (person_id ASC);
CLUSTER survey_conduct USING idx_survey_person_id ;
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
@ -356,12 +342,6 @@ Standardized derived elements
************************/
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CLUSTER drug_era USING idx_drug_era_person_id ;
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);

2
PostgreSQL/README.md
View File

@ -16,3 +16,5 @@ In order to create your instantiation of the Common Data Model, we recommend fol
5. Execute the script `OMOP CDM postgresql constraints.txt` to add the constraints (foreign keys).
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.
6. Repeat steps 1-3, executing the script `OMOP CDM Results postgresql ddl.txt`

59
Redshift/OMOP CDM Results redshift ddl.txt Normal file
View File

@ -0,0 +1,59 @@
/*********************************************************************************
# Copyright 2018-08 Observational Health Data Sciences and Informatics
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
********************************************************************************/
/************************
####### # # ####### ###### ##### ###### # # ##### ###
# # ## ## # # # # # # # # ## ## # # # # # #
# # # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # #
# # # # # # # # # # # # # # # # ### # #
# # # # # # # # # # # # # # # # # ### # #
####### # # ####### # ##### ###### # # ## ##### ### ###
redshift script to create OMOP common data model results schema version 6.0
last revised: 27-Aug-2018
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
*************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort (
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
DISTKEY(subject_id);
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description VARCHAR(MAX) NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax VARCHAR(MAX) NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
DISTSTYLE ALL;

847
Redshift/OMOP CDM redshift ddl.txt
View File

File diff suppressed because it is too large Load Diff

4
Redshift/README.md
View File

@ -11,4 +11,6 @@ In order to create your instantiation of the Common Data Model, we recommend fol
3. Execute the script `OMOP CDM redshift ddl.txt` to create the tables and fields.
4. Load your data into the schema using COPY commands from Amazon S3.
4. Load your data into the schema using COPY commands from Amazon S3.
5. Repeat to create the results schema, executing the script `OMOP CDM Results redshift ddl.txt`

37
Sql Server/OMOP CDM Results sql server.txt
View File

@ -41,6 +41,18 @@ Standardized vocabulary
************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
@ -52,3 +64,28 @@ CREATE TABLE cohort_definition (
cohort_initiation_date DATE NULL
)
;
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
CREATE CLUSTERED INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);

44
Sql Server/OMOP CDM sql server constraints.txt
View File

@ -112,14 +112,6 @@ ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (n
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
ALTER TABLE attribute_definition ADD CONSTRAINT fpk_attribute_type_concept FOREIGN KEY (attribute_type_concept_id) REFERENCES concept (concept_id);
/**************************
Standardized meta-data
@ -194,7 +186,7 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (prov
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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_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);
@ -360,29 +352,29 @@ ALTER TABLE observation ADD CONSTRAint fpk_observation_v_detail FOREIGN KEY (vis
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_respondent_type FOREIGN KEY (respondent_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_respondent_type FOREIGN KEY (respondent_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_collection_method FOREIGN KEY (collection_method_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_collection_method FOREIGN KEY (collection_method_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_validation FOREIGN KEY (validated_survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_validation FOREIGN KEY (validated_survey_concept_id) REFERENCES concept (concept_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey ADD CONSTRAINT fpk_survey_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
ALTER TABLE survey ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_to_visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_to_visit_occurrence_id) REFERENCES visit (visit_occurrence_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
@ -476,16 +468,6 @@ Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);

331
Sql Server/OMOP CDM sql server ddl.txt
View File

@ -215,7 +215,7 @@ Standardized clinical data
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE person
(
person_id BIGINT NOT NULL , --BIGINTs added
person_id BIGINT NOT NULL ,
gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL,
@ -271,20 +271,6 @@ CREATE TABLE specimen
;
--HINT DISTRIBUTE_ON_KEY(person_id)
/*CREATE TABLE death
(
person_id BIGINT NOT NULL ,
death_date DATE NULL ,
death_datetime DATETIME2 NOT NULL ,
death_type_concept_id INTEGER NOT NULL ,
cause_concept_id INTEGER NULL ,
cause_source_value VARCHAR(50) NULL,
cause_source_concept_id INTEGER NULL
)
;*/
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_occurrence
(
@ -300,7 +286,7 @@ CREATE TABLE visit_occurrence
care_site_id BIGINT NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL , /*Changed from admitting_source_* */
admitted_from_concept_id INTEGER NULL ,
admitted_from_source_value VARCHAR(50) NULL ,
discharge_to_source_value VARCHAR(50) NULL ,
discharge_to_concept_id INTEGER NULL ,
@ -323,7 +309,7 @@ CREATE TABLE visit_detail
provider_id BIGINT NULL ,
care_site_id BIGINT NULL ,
discharge_to_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL , /*Changed from admitting_source_* */
admitted_from_concept_id INTEGER NULL ,
admitted_from_source_value VARCHAR(50) NULL ,
visit_detail_source_value VARCHAR(50) NULL ,
visit_detail_source_concept_id INTEGER NULL ,
@ -464,7 +450,7 @@ CREATE TABLE note
note_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
note_event_id BIGINT NULL ,
note_event_domain_id VARCHAR(20) NULL ,
note_event_domain_id VARCHAR(20) NULL ,
note_event_field_concept_id INTEGER NULL ,
note_date DATE NULL ,
note_datetime DATETIME2 NOT NULL ,
@ -506,60 +492,59 @@ CREATE TABLE note_nlp
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE observation
(
observation_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
observation_concept_id INTEGER NOT NULL ,
observation_date DATE NULL ,
observation_datetime DATETIME2 NOT NULL ,
observation_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
observation_concept_id INTEGER NOT NULL ,
observation_date DATE NULL ,
observation_datetime DATETIME2 NOT NULL ,
observation_type_concept_id INTEGER NOT NULL ,
value_as_number FLOAT NULL ,
value_as_string VARCHAR(60) NULL ,
value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
observation_source_value VARCHAR(50) NULL ,
value_as_number FLOAT NULL ,
value_as_string VARCHAR(60) NULL ,
value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
observation_source_value VARCHAR(50) NULL ,
observation_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL ,
observation_event_id BIGINT NULL , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
observation_event_domain_id VARCHAR(20) NULL ,
--obs_event_table_concept_id INTEGER NULL , /* Changed name to comply with COST and NOTE. Had to use 'obs' for oracle restriction, may be added on 9/4*/
value_as_datetime DATETIME2 NULL
unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL ,
observation_event_id BIGINT NULL ,
obs_event_field_concept_id INTEGER NULL ,
value_as_datetime DATETIME2 NULL
)
;
--HINT DISTRIBUTE ON KEY(person_id)
CREATE TABLE survey_conduct --Table added
CREATE TABLE survey_conduct
(
survey_conduct_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
survey_concept_id INTEGER NOT NULL ,
survey_start_date DATE NULL ,
survey_start_datetime DATETIME2 NULL ,
survey_end_date DATE NULL ,
survey_end_datetime DATETIME2 NOT NULL ,
provider_id BIGINT NULL ,
assisted_concept_id INTEGER NULL ,
respondent_type_concept_id INTEGER NULL ,
timing_concept_id INTEGER NULL ,
collection_method_concept_id INTEGER NULL ,
assisted_source_value VARCHAR(50) NULL ,
respondent_type_source_value VARCHAR(100) NULL ,
timing_source_value VARCHAR(100) NULL ,
survey_conduct_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
survey_concept_id INTEGER NOT NULL ,
survey_start_date DATE NULL ,
survey_start_datetime DATETIME2 NULL ,
survey_end_date DATE NULL ,
survey_end_datetime DATETIME2 NOT NULL ,
provider_id BIGINT NULL ,
assisted_concept_id INTEGER NULL ,
respondent_type_concept_id INTEGER NULL ,
timing_concept_id INTEGER NULL ,
collection_method_concept_id INTEGER NULL ,
assisted_source_value VARCHAR(50) NULL ,
respondent_type_source_value VARCHAR(100) NULL ,
timing_source_value VARCHAR(100) NULL ,
collection_method_source_value VARCHAR(100) NULL ,
survey_source_value VARCHAR(100) NULL ,
survey_source_concept_id INTEGER NULL ,
survey_source_identifier VARCHAR(100) NULL ,
validated_survey_concept_id INTEGER NULL ,
survey_source_value VARCHAR(100) NULL ,
survey_source_concept_id INTEGER NULL ,
survey_source_identifier VARCHAR(100) NULL ,
validated_survey_concept_id INTEGER NULL ,
validated_survey_source_value VARCHAR(100) NULL ,
survey_version_number VARCHAR(20) NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
response_to_visit_occurrence_id BIGINT NULL
survey_version_number VARCHAR(20) NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
response_visit_occurrence_id BIGINT NULL
)
;
@ -567,10 +552,10 @@ CREATE TABLE survey_conduct --Table added
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE fact_relationship
(
domain_concept_id_1 INTEGER NOT NULL ,
fact_id_1 BIGINT NOT NULL ,
domain_concept_id_2 INTEGER NOT NULL ,
fact_id_2 BIGINT NOT NULL ,
domain_concept_id_1 INTEGER NOT NULL ,
fact_id_1 BIGINT NOT NULL ,
domain_concept_id_2 INTEGER NOT NULL ,
fact_id_2 BIGINT NOT NULL ,
relationship_concept_id INTEGER NOT NULL
)
;
@ -587,31 +572,31 @@ Standardized health system data
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE location
(
location_id BIGINT NOT NULL ,
address_1 VARCHAR(50) NULL ,
address_2 VARCHAR(50) NULL ,
city VARCHAR(50) NULL ,
state VARCHAR(2) NULL ,
zip VARCHAR(9) NULL ,
county VARCHAR(20) NULL ,
country VARCHAR(100) NULL ,
location_id BIGINT NOT NULL ,
address_1 VARCHAR(50) NULL ,
address_2 VARCHAR(50) NULL ,
city VARCHAR(50) NULL ,
state VARCHAR(2) NULL ,
zip VARCHAR(9) NULL ,
county VARCHAR(20) NULL ,
country VARCHAR(100) NULL ,
location_source_value VARCHAR(50) NULL ,
latitude FLOAT NULL ,
longitude FLOAT NULL
latitude FLOAT NULL ,
longitude FLOAT NULL
)
;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE location_history --Table added
CREATE TABLE location_history
(
location_history_id BIGINT NOT NULL ,
location_id BIGINT NOT NULL ,
relationship_type_concept_id INTEGER NULL , --Recent addition based on github discussion
domain_id VARCHAR(50) NOT NULL ,
entity_id BIGINT NOT NULL ,
start_date DATE NOT NULL ,
end_date DATE NULL
location_history_id BIGINT NOT NULL ,
location_id BIGINT NOT NULL ,
relationship_type_concept_id INTEGER NULL ,
domain_id VARCHAR(50) NOT NULL ,
entity_id BIGINT NOT NULL ,
start_date DATE NOT NULL ,
end_date DATE NULL
)
;
@ -619,12 +604,12 @@ CREATE TABLE location_history --Table added
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE care_site
(
care_site_id BIGINT NOT NULL ,
care_site_name VARCHAR(255) NULL ,
place_of_service_concept_id INTEGER NULL ,
location_id BIGINT NULL ,
care_site_source_value VARCHAR(50) NULL ,
place_of_service_source_value VARCHAR(50) NULL
care_site_id BIGINT NOT NULL ,
care_site_name VARCHAR(255) NULL ,
place_of_service_concept_id INTEGER NULL ,
location_id BIGINT NULL ,
care_site_source_value VARCHAR(50) NULL ,
place_of_service_source_value VARCHAR(50) NULL
)
;
@ -632,19 +617,19 @@ CREATE TABLE care_site
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE provider
(
provider_id BIGINT NOT NULL ,
provider_name VARCHAR(255) NULL ,
NPI VARCHAR(20) NULL ,
DEA VARCHAR(20) NULL ,
specialty_concept_id INTEGER NULL ,
care_site_id BIGINT NULL ,
year_of_birth INTEGER NULL ,
gender_concept_id INTEGER NULL ,
provider_source_value VARCHAR(50) NULL ,
specialty_source_value VARCHAR(50) NULL ,
specialty_source_concept_id INTEGER NULL ,
gender_source_value VARCHAR(50) NULL ,
gender_source_concept_id INTEGER NULL
provider_id BIGINT NOT NULL ,
provider_name VARCHAR(255) NULL ,
NPI VARCHAR(20) NULL ,
DEA VARCHAR(20) NULL ,
specialty_concept_id INTEGER NULL ,
care_site_id BIGINT NULL ,
year_of_birth INTEGER NULL ,
gender_concept_id INTEGER NULL ,
provider_source_value VARCHAR(50) NULL ,
specialty_source_value VARCHAR(50) NULL ,
specialty_source_concept_id INTEGER NULL ,
gender_source_value VARCHAR(50) NULL ,
gender_source_concept_id INTEGER NULL
)
;
@ -659,27 +644,27 @@ Standardized health economics
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE payer_plan_period
(
payer_plan_period_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
contract_person_id BIGINT NULL ,
payer_plan_period_start_date DATE NOT NULL ,
payer_plan_period_end_date DATE NOT NULL ,
payer_concept_id INTEGER NULL ,
plan_concept_id INTEGER NULL ,
contract_concept_id INTEGER NULL ,
sponsor_concept_id INTEGER NULL ,
stop_reason_concept_id INTEGER NULL ,
payer_source_value VARCHAR(50) NULL ,
payer_source_concept_id INTEGER NULL ,
plan_source_value VARCHAR(50) NULL ,
plan_source_concept_id INTEGER NULL ,
contract_source_value VARCHAR(50) NULL ,
contract_source_concept_id INTEGER NULL ,
sponsor_source_value VARCHAR(50) NULL ,
sponsor_source_concept_id INTEGER NULL ,
family_source_value VARCHAR(50) NULL ,
stop_reason_source_value VARCHAR(50) NULL ,
stop_reason_source_concept_id INTEGER NULL
payer_plan_period_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
contract_person_id BIGINT NULL ,
payer_plan_period_start_date DATE NOT NULL ,
payer_plan_period_end_date DATE NOT NULL ,
payer_concept_id INTEGER NULL ,
plan_concept_id INTEGER NULL ,
contract_concept_id INTEGER NULL ,
sponsor_concept_id INTEGER NULL ,
stop_reason_concept_id INTEGER NULL ,
payer_source_value VARCHAR(50) NULL ,
payer_source_concept_id INTEGER NULL ,
plan_source_value VARCHAR(50) NULL ,
plan_source_concept_id INTEGER NULL ,
contract_source_value VARCHAR(50) NULL ,
contract_source_concept_id INTEGER NULL ,
sponsor_source_value VARCHAR(50) NULL ,
sponsor_source_concept_id INTEGER NULL ,
family_source_value VARCHAR(50) NULL ,
stop_reason_source_value VARCHAR(50) NULL ,
stop_reason_source_concept_id INTEGER NULL
)
;
@ -687,25 +672,24 @@ CREATE TABLE payer_plan_period
--HINT DISTRIBUTE ON KEY(person_id)
CREATE TABLE cost
(
cost_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL,
cost_event_id BIGINT NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL ,
--cost_event_table_concept_id INTEGER NOT NULL , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_concept_id INTEGER NOT NULL ,
cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
cost FLOAT NULL ,
incurred_date DATE NOT NULL ,
billed_date DATE NULL ,
paid_date DATE NULL ,
revenue_code_concept_id INTEGER NULL ,
drg_concept_id INTEGER NULL ,
cost_source_value VARCHAR(50) NULL ,
cost_source_concept_id INTEGER NULL ,
revenue_code_source_value VARCHAR(50) NULL ,
drg_source_value VARCHAR(3) NULL ,
payer_plan_period_id BIGINT NULL
cost_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL,
cost_event_id BIGINT NOT NULL ,
cost_event_field_concept_id INTEGER NOT NULL ,
cost_concept_id INTEGER NOT NULL ,
cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
cost FLOAT NULL ,
incurred_date DATE NOT NULL ,
billed_date DATE NULL ,
paid_date DATE NULL ,
revenue_code_concept_id INTEGER NULL ,
drg_concept_id INTEGER NULL ,
cost_source_value VARCHAR(50) NULL ,
cost_source_concept_id INTEGER NULL ,
revenue_code_source_value VARCHAR(50) NULL ,
drg_source_value VARCHAR(3) NULL ,
payer_plan_period_id BIGINT NULL
)
;
@ -717,41 +701,16 @@ Standardized derived elements
************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort_attribute
(
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL ,
attribute_definition_id BIGINT NOT NULL ,
value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era
(
drug_era_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_era_start_date DATE NOT NULL ,
drug_era_end_date DATE NOT NULL ,
drug_exposure_count INTEGER NULL ,
gap_days INTEGER NULL
drug_era_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_era_start_date DATE NOT NULL ,
drug_era_end_date DATE NOT NULL ,
drug_exposure_count INTEGER NULL ,
gap_days INTEGER NULL
)
;
@ -759,12 +718,12 @@ CREATE TABLE drug_era
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE dose_era
(
dose_era_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
unit_concept_id INTEGER NOT NULL ,
dose_value FLOAT NOT NULL ,
dose_era_start_date DATE NOT NULL ,
dose_era_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
unit_concept_id INTEGER NOT NULL ,
dose_value FLOAT NOT NULL ,
dose_era_start_date DATE NOT NULL ,
dose_era_end_date DATE NOT NULL
)
;
@ -773,11 +732,11 @@ CREATE TABLE dose_era
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE condition_era
(
condition_era_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_era_start_date DATE NOT NULL ,
condition_era_end_date DATE NOT NULL ,
condition_era_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_era_start_date DATE NOT NULL ,
condition_era_end_date DATE NOT NULL ,
condition_occurrence_count INTEGER NULL
)
;

26
Sql Server/OMOP CDM sql server pk indexes.txt
View File

@ -77,10 +77,6 @@ ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMA
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY NONCLUSTERED (drug_concept_id, ingredient_concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY NONCLUSTERED (attribute_definition_id);
/**************************
@ -127,7 +123,7 @@ ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY NONCLUSTERED ( note
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY NONCLUSTERED ( observation_id ) ;
ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY NONCLUSTERED ( survey_occurrence_id ) ;
ALTER TABLE survey_conduct ADD CONSTRAINT xpk_survey PRIMARY KEY NONCLUSTERED ( survey_conduct_id ) ;
/************************
@ -139,7 +135,7 @@ Standardized health system data
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ;
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY NONCLUSTERED ( location_history_id ) ; --Assuming this should be added
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY NONCLUSTERED ( location_history_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY NONCLUSTERED ( care_site_id ) ;
@ -165,10 +161,6 @@ Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY NONCLUSTERED ( drug_era_id ) ;
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY NONCLUSTERED ( dose_era_id ) ;
@ -225,10 +217,6 @@ CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_cod
CREATE CLUSTERED INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
CREATE CLUSTERED INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CREATE CLUSTERED INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
/**************************
@ -292,7 +280,7 @@ CREATE CLUSTERED INDEX idx_observation_person_id ON observation (person_id ASC);
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
CREATE CLUSTERED INDEX idx_survey_person_id ON survey (person_id ASC);
CREATE CLUSTERED INDEX idx_survey_person_id ON survey_conduct (person_id ASC);
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
@ -328,13 +316,7 @@ Standardized derived elements
************************/
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
CREATE CLUSTERED INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
REATE CLUSTERED INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
CREATE CLUSTERED INDEX idx_dose_era_person_id ON dose_era (person_id ASC);

2
Sql Server/README.md
View File

@ -16,3 +16,5 @@ In order to create your instantiation of the Common Data Model, we recommend fol
5. Execute the script `OMOP CDM sql server constraints.txt` to add the foreign key constraints.
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.
6. Repeat steps 1-3, executing the script `OMOP CDM Results sql server ddl.txt` to create the results schema