Instructions and DDL for instantiating the CDM v6.0 data model in Snowflake.
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Kathryn Watson
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/*********************************************************************************
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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********************************************************************************/
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/************************
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snowflake script to create OMOP common data model results schema version 6.0
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last revised: 05-Aug-2019
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Authors: Kathryn Watson
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*************************/
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CREATE TABLE cohort_definition (
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cohort_definition_id INTEGER NOT NULL,
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cohort_definition_name VARCHAR NOT NULL,
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cohort_definition_description VARCHAR NULL,
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definition_type_concept_id INTEGER NOT NULL,
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cohort_definition_syntax VARCHAR NULL,
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subject_concept_id INTEGER NOT NULL,
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cohort_initiation_date DATE NULL
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)
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;
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CREATE TABLE cohort
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(
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cohort_definition_id INTEGER NOT NULL,
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subject_id INTEGER NOT NULL,
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cohort_start_date DATE NOT NULL ,
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cohort_end_date DATE NOT NULL
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)
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;
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/*********************************************************************************
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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********************************************************************************/
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/************************
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# # # # # # # ###### # # # # # # # # ###### # # ###### ### ### # # # # # # # # ##### ####
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# # # # # # # # # # # # # # # # ### # # # # # # # # # # # # # # # # # #
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# # # # # # # # # # # # # # # # # ### # # # # # # # # # ## # # # # # # # #
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####### # # ####### # ##### ###### # # ## ##### ### ### # # # ### # ### # # ##### # #### ###### ####
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snowflake script to create suggested cluster keys within the OMOP common data model, version 6.0
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last revised: 05-Aug-2019
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author: Kathryn Watson
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description: These cluster keys are optional and should be evaluated on a table by table basis in each environment. Cluster keys increase compute costs and should only be implemented as needed for performance improvements.
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*************************/
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/************************
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*************************
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*************************
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*************************
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Cluster Keys
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*************************
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*************************
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*************************
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************************/
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/************************
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Standardized vocabulary
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************************/
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ALTER TABLE concept CLUSTER BY (concept_code,vocabulary_id,domain_id,concept_class_id);
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ALTER TABLE concept_relationship CLUSTER BY (concept_id_1,concept_id_2,relationship_id);
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ALTER TABLE concept_synonym CLUSTER BY (concept_id);
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ALTER TABLE concept_ancestor CLUSTER BY (ancestor_concept_id,descendant_concept_id);
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ALTER TABLE source_to_concept_map CLUSTER BY (target_concept_id,target_vocabulary_id,source_vocabulary_id,source_code);
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ALTER TABLE drug_strength CLUSTER BY (drug_concept_id,ingredient_concept_id);
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/**************************
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Standardized meta-data
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***************************/
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/************************
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Standardized clinical data
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************************/
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ALTER TABLE observation_period CLUSTER BY (person_id);
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ALTER TABLE specimen CLUSTER BY (person_id,specimen_concept_id);
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ALTER TABLE visit_occurrence CLUSTER BY (person_id,visit_concept_id);
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ALTER TABLE visit_detail CLUSTER BY (person_id,visit_detail_concept_id);
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ALTER TABLE procedure_occurrence CLUSTER BY (person_id,procedure_concept_id,visit_occurrence_id);
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ALTER TABLE drug_exposure CLUSTER BY (person_id,drug_concept_id,visit_occurrence_id);
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ALTER TABLE device_exposure CLUSTER BY (person_id,device_concept_id,visit_occurrence_id);
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ALTER TABLE condition_occurrence CLUSTER BY (person_id,condition_concept_id,visit_occurrence_id);
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ALTER TABLE measurement CLUSTER BY (person_id,measurement_concept_id,visit_occurrence_id);
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ALTER TABLE note CLUSTER BY (person_id,note_type_concept_id,visit_occurrence_id);
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ALTER TABLE note_nlp CLUSTER BY (note_id,note_nlp_concept_id);
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ALTER TABLE observation CLUSTER BY (person_id,observation_concept_id,visit_occurrence_id);
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ALTER TABLE survey_conduct CLUSTER BY (person_id);
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ALTER TABLE fact_relationship CLUSTER BY (domain_concept_id_1,domain_concept_id_2,relationship_concept_id);
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/************************
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Standardized health system data
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************************/
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/************************
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Standardized health economics
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************************/
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ALTER TABLE payer_plan_period CLUSTER BY (person_id);
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ALTER TABLE cost CLUSTER BY (person_id);
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/************************
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Standardized derived elements
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************************/
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ALTER TABLE drug_era CLUSTER BY (person_id,drug_concept_id);
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ALTER TABLE dose_era CLUSTER BY (person_id,drug_concept_id);
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ALTER TABLE condition_era CLUSTER BY (person_id,condition_concept_id);
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/************************
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Results elements
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************************/
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ALTER TABLE cohort CLUSTER BY (subject_id);
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/*********************************************************************************
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
|
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#
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# Unless required by applicable law or agreed to in writing, software
|
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# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
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# See the License for the specific language governing permissions and
|
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# limitations under the License.
|
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********************************************************************************/
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/************************
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####### # # ####### ###### ##### ###### # # ##### ### #####
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# # ## ## # # # # # # # # ## ## # # # # # # # # #### # # #### ##### ##### ## # # # ##### ####
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# # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
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# # # # # # # ###### # # # # # # # # ###### # # # # # # # # #### # # # # # # # # # # ####
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# # # # # # # # # # # # # # # # ### # # # # # # # # # # ##### ###### # # # # # #
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# # # # # # # # # # # # # # # # # ### # # # # # # # ## # # # # # # # # # ## # # #
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####### # # ####### # ##### ###### # # ## ##### ### ### ##### #### # # #### # # # # # # # # # ####
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snowflake script to create foreign key and unique constraints within the OMOP common data model, version 6.0
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last revised: 05-Aug-2019
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author: Kathryn Watson
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*************************/
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/************************
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*************************
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*************************
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*************************
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Foreign key constraints
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*************************
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*************************
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*************************
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************************/
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/************************
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Standardized vocabulary
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************************/
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
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ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
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ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_synonym ADD CONSTRAINT fpk_synonym_language FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
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/**************************
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Standardized meta-data
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***************************/
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ALTER TABLE metadata ADD CONSTRAINT fpk_metadata_concept FOREIGN KEY (metadata_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE metadata ADD CONSTRAINT fpk_metadata_type_concept FOREIGN KEY (metadata_type_concept_id) REFERENCES concept (concept_id);
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/************************
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Standardized clinical data
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************************/
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ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitted_from_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_preceding FOREIGN KEY (preceding_visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept FOREIGN KEY (visit_detail_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_type_concept FOREIGN KEY (visit_detail_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitted_from_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_detail_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_preceding FOREIGN KEY (preceding_visit_detail_id) REFERENCES visit_detail (visit_detail_id);
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ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_parent FOREIGN KEY (visit_detail_parent_id) REFERENCES visit_detail (visit_detail_id);
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||||
ALTER TABLE visit_detail ADD CONSTRAINT fpd_v_detail_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_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 condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_class_concept FOREIGN KEY (note_class_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_encoding_concept FOREIGN KEY (encoding_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_language_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
|
||||
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_note FOREIGN KEY (note_id) REFERENCES note (note_id);
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_section_concept FOREIGN KEY (section_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_concept FOREIGN KEY (note_nlp_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_concept_s FOREIGN KEY (note_nlp_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAint fpk_observation_v_detail FOREIGN KEY (visit_detail_id) REFERENCES visit_detail (visit_detail_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_concept FOREIGN KEY (survey_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE survey_conduct ADD CONSTRAINT fpk_survey_assist FOREIGN KEY (assisted_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_conduct ADD CONSTRAINT fpk_survey_timing FOREIGN KEY (timing_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_conduct ADD CONSTRAINT fpk_survey_source FOREIGN KEY (survey_source_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_conduct ADD CONSTRAINT fpk_survey_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_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_conduct ADD CONSTRAINT fpk_response_visit FOREIGN KEY (response_visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
ALTER TABLE location_history ADD CONSTRAINT fpk_location_history FOREIGN KEY ( location_id ) REFERENCES location ( location_id ) ;
|
||||
|
||||
ALTER TABLE location_history ADD CONSTRAINT fpk_relationship_type FOREIGN KEY (relationship_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_contract_person FOREIGN KEY (contract_person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_concept FOREIGN KEY (payer_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_plan_concept_id FOREIGN KEY (plan_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_contract_concept FOREIGN KEY (contract_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_sponsor_concept FOREIGN KEY (sponsor_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_stop_reason_concept FOREIGN KEY (stop_reason_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_s FOREIGN KEY (payer_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_plan_s FOREIGN KEY (plan_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_contract_s FOREIGN KEY (contract_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_sponsor_s FOREIGN KEY (sponsor_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_stop_reason_s FOREIGN KEY (stop_reason_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_cost_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_cost_concept FOREIGN KEY (cost_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_cost_type FOREIGN KEY (cost_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_revenue_concept FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_drg_concept FOREIGN KEY (drg_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_cost_s FOREIGN KEY (cost_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
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);
|
||||
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Results elements
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
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 );
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
Unique constraints
|
||||
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
************************/
|
||||
|
||||
ALTER TABLE concept_synonym ADD CONSTRAINT uq_concept_synonym UNIQUE (concept_id, concept_synonym_name, language_concept_id);
|
||||
|
|
@ -0,0 +1,706 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2019 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.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ##### ###
|
||||
# # ## ## # # # # # # # # ## ## # # # # # #
|
||||
# # # # # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # #
|
||||
# # # # # # # # # # # # # # # # ### # #
|
||||
# # # # # # # # # # # # # # # # # ### # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ### ###
|
||||
|
||||
snowflake script to create OMOP common data model version 6.0
|
||||
|
||||
last revised: 05-Aug-2019
|
||||
|
||||
Authors: Kathryn Watson
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE concept (
|
||||
concept_id INTEGER NOT NULL ,
|
||||
concept_name VARCHAR NOT NULL ,
|
||||
domain_id VARCHAR NOT NULL ,
|
||||
vocabulary_id VARCHAR NOT NULL ,
|
||||
concept_class_id VARCHAR NOT NULL ,
|
||||
standard_concept VARCHAR NULL ,
|
||||
concept_code VARCHAR NOT NULL ,
|
||||
valid_start_date DATE NOT NULL ,
|
||||
valid_end_date DATE NOT NULL ,
|
||||
invalid_reason VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE vocabulary (
|
||||
vocabulary_id VARCHAR NOT NULL,
|
||||
vocabulary_name VARCHAR NOT NULL,
|
||||
vocabulary_reference VARCHAR NOT NULL,
|
||||
vocabulary_version VARCHAR NULL,
|
||||
vocabulary_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE domain (
|
||||
domain_id VARCHAR NOT NULL,
|
||||
domain_name VARCHAR NOT NULL,
|
||||
domain_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_class (
|
||||
concept_class_id VARCHAR NOT NULL,
|
||||
concept_class_name VARCHAR NOT NULL,
|
||||
concept_class_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_relationship (
|
||||
concept_id_1 INTEGER NOT NULL,
|
||||
concept_id_2 INTEGER NOT NULL,
|
||||
relationship_id VARCHAR NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE relationship (
|
||||
relationship_id VARCHAR NOT NULL,
|
||||
relationship_name VARCHAR NOT NULL,
|
||||
is_hierarchical VARCHAR NOT NULL,
|
||||
defines_ancestry VARCHAR NOT NULL,
|
||||
reverse_relationship_id VARCHAR NOT NULL,
|
||||
relationship_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_synonym (
|
||||
concept_id INTEGER NOT NULL,
|
||||
concept_synonym_name VARCHAR NOT NULL,
|
||||
language_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_ancestor (
|
||||
ancestor_concept_id INTEGER NOT NULL,
|
||||
descendant_concept_id INTEGER NOT NULL,
|
||||
min_levels_of_separation INTEGER NOT NULL,
|
||||
max_levels_of_separation INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE source_to_concept_map (
|
||||
source_code VARCHAR NOT NULL,
|
||||
source_concept_id INTEGER NOT NULL,
|
||||
source_vocabulary_id VARCHAR NOT NULL,
|
||||
source_code_description VARCHAR NULL,
|
||||
target_concept_id INTEGER NOT NULL,
|
||||
target_vocabulary_id VARCHAR NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE drug_strength (
|
||||
drug_concept_id INTEGER NOT NULL,
|
||||
ingredient_concept_id INTEGER NOT NULL,
|
||||
amount_value FLOAT NULL,
|
||||
amount_unit_concept_id INTEGER NULL,
|
||||
numerator_value FLOAT NULL,
|
||||
numerator_unit_concept_id INTEGER NULL,
|
||||
denominator_value FLOAT NULL,
|
||||
denominator_unit_concept_id INTEGER NULL,
|
||||
box_size INTEGER NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
CREATE TABLE cdm_source
|
||||
(
|
||||
cdm_source_name VARCHAR NOT NULL ,
|
||||
cdm_source_abbreviation VARCHAR NULL ,
|
||||
cdm_holder VARCHAR NULL ,
|
||||
source_description VARCHAR NULL ,
|
||||
source_documentation_reference VARCHAR NULL ,
|
||||
cdm_etl_reference VARCHAR NULL ,
|
||||
source_release_date DATE NULL ,
|
||||
cdm_release_date DATE NULL ,
|
||||
cdm_version VARCHAR NULL ,
|
||||
vocabulary_version VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE metadata
|
||||
(
|
||||
metadata_concept_id INTEGER NOT NULL ,
|
||||
metadata_type_concept_id INTEGER NOT NULL ,
|
||||
name VARCHAR NOT NULL ,
|
||||
value_as_string VARCHAR NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
metadata_date DATE NULL ,
|
||||
metadata_datetime TIMESTAMP NULL
|
||||
)
|
||||
;
|
||||
|
||||
INSERT INTO metadata (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, metadata_datetime) --Added cdm version record
|
||||
VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
|
||||
;
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE person
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
gender_concept_id INTEGER NOT NULL ,
|
||||
year_of_birth INTEGER NOT NULL ,
|
||||
month_of_birth INTEGER NULL,
|
||||
day_of_birth INTEGER NULL,
|
||||
birth_datetime TIMESTAMP NULL,
|
||||
death_datetime TIMESTAMP NULL,
|
||||
race_concept_id INTEGER NOT NULL,
|
||||
ethnicity_concept_id INTEGER NOT NULL,
|
||||
location_id INTEGER NULL,
|
||||
provider_id INTEGER NULL,
|
||||
care_site_id INTEGER NULL,
|
||||
person_source_value VARCHAR NULL,
|
||||
gender_source_value VARCHAR NULL,
|
||||
gender_source_concept_id INTEGER NOT NULL,
|
||||
race_source_value VARCHAR NULL,
|
||||
race_source_concept_id INTEGER NOT NULL,
|
||||
ethnicity_source_value VARCHAR NULL,
|
||||
ethnicity_source_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE observation_period
|
||||
(
|
||||
observation_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_period_start_date DATE NOT NULL ,
|
||||
observation_period_end_date DATE NOT NULL ,
|
||||
period_type_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE specimen
|
||||
(
|
||||
specimen_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
specimen_concept_id INTEGER NOT NULL ,
|
||||
specimen_type_concept_id INTEGER NOT NULL ,
|
||||
specimen_date DATE NULL ,
|
||||
specimen_datetime TIMESTAMP NOT NULL ,
|
||||
quantity FLOAT NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
anatomic_site_concept_id INTEGER NOT NULL ,
|
||||
disease_status_concept_id INTEGER NOT NULL ,
|
||||
specimen_source_id VARCHAR NULL ,
|
||||
specimen_source_value VARCHAR NULL ,
|
||||
unit_source_value VARCHAR NULL ,
|
||||
anatomic_site_source_value VARCHAR NULL ,
|
||||
disease_status_source_value VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE visit_occurrence
|
||||
(
|
||||
visit_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
visit_concept_id INTEGER NOT NULL ,
|
||||
visit_start_date DATE NULL ,
|
||||
visit_start_datetime TIMESTAMP NOT NULL ,
|
||||
visit_end_date DATE NULL ,
|
||||
visit_end_datetime TIMESTAMP NOT NULL ,
|
||||
visit_type_concept_id INTEGER NOT NULL ,
|
||||
provider_id INTEGER NULL,
|
||||
care_site_id INTEGER NULL,
|
||||
visit_source_value VARCHAR NULL,
|
||||
visit_source_concept_id INTEGER NOT NULL ,
|
||||
admitted_from_concept_id INTEGER NOT NULL ,
|
||||
admitted_from_source_value VARCHAR NULL ,
|
||||
discharge_to_source_value VARCHAR NULL ,
|
||||
discharge_to_concept_id INTEGER NOT NULL ,
|
||||
preceding_visit_occurrence_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE visit_detail
|
||||
(
|
||||
visit_detail_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
visit_detail_concept_id INTEGER NOT NULL ,
|
||||
visit_detail_start_date DATE NULL ,
|
||||
visit_detail_start_datetime TIMESTAMP NOT NULL ,
|
||||
visit_detail_end_date DATE NULL ,
|
||||
visit_detail_end_datetime TIMESTAMP NOT NULL ,
|
||||
visit_detail_type_concept_id INTEGER NOT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
care_site_id INTEGER NULL ,
|
||||
discharge_to_concept_id INTEGER NOT NULL ,
|
||||
admitted_from_concept_id INTEGER NOT NULL ,
|
||||
admitted_from_source_value VARCHAR NULL ,
|
||||
visit_detail_source_value VARCHAR NULL ,
|
||||
visit_detail_source_concept_id INTEGER NOT NULL ,
|
||||
discharge_to_source_value VARCHAR NULL ,
|
||||
preceding_visit_detail_id INTEGER NULL ,
|
||||
visit_detail_parent_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE procedure_occurrence
|
||||
(
|
||||
procedure_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
procedure_concept_id INTEGER NOT NULL ,
|
||||
procedure_date DATE NULL ,
|
||||
procedure_datetime TIMESTAMP NOT NULL ,
|
||||
procedure_type_concept_id INTEGER NOT NULL ,
|
||||
modifier_concept_id INTEGER NOT NULL ,
|
||||
quantity INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
visit_detail_id INTEGER NULL ,
|
||||
procedure_source_value VARCHAR NULL ,
|
||||
procedure_source_concept_id INTEGER NOT NULL ,
|
||||
modifier_source_value VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE drug_exposure
|
||||
(
|
||||
drug_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_exposure_start_date DATE NULL ,
|
||||
drug_exposure_start_datetime TIMESTAMP NOT NULL ,
|
||||
drug_exposure_end_date DATE NULL ,
|
||||
drug_exposure_end_datetime TIMESTAMP NOT NULL ,
|
||||
verbatim_end_date DATE NULL ,
|
||||
drug_type_concept_id INTEGER NOT NULL ,
|
||||
stop_reason VARCHAR NULL ,
|
||||
refills INTEGER NULL ,
|
||||
quantity FLOAT NULL ,
|
||||
days_supply INTEGER NULL ,
|
||||
sig VARCHAR NULL ,
|
||||
route_concept_id INTEGER NOT NULL ,
|
||||
lot_number VARCHAR NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
visit_detail_id INTEGER NULL ,
|
||||
drug_source_value VARCHAR NULL ,
|
||||
drug_source_concept_id INTEGER NOT NULL ,
|
||||
route_source_value VARCHAR NULL ,
|
||||
dose_unit_source_value VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE device_exposure
|
||||
(
|
||||
device_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
device_concept_id INTEGER NOT NULL ,
|
||||
device_exposure_start_date DATE NULL ,
|
||||
device_exposure_start_datetime TIMESTAMP NOT NULL ,
|
||||
device_exposure_end_date DATE NULL ,
|
||||
device_exposure_end_datetime TIMESTAMP NULL ,
|
||||
device_type_concept_id INTEGER NOT NULL ,
|
||||
unique_device_id VARCHAR NULL ,
|
||||
quantity INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
visit_detail_id INTEGER NULL ,
|
||||
device_source_value VARCHAR NULL ,
|
||||
device_source_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE condition_occurrence
|
||||
(
|
||||
condition_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_start_date DATE NULL ,
|
||||
condition_start_datetime TIMESTAMP NOT NULL ,
|
||||
condition_end_date DATE NULL ,
|
||||
condition_end_datetime TIMESTAMP NULL ,
|
||||
condition_type_concept_id INTEGER NOT NULL ,
|
||||
condition_status_concept_id INTEGER NOT NULL ,
|
||||
stop_reason VARCHAR NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
visit_detail_id INTEGER NULL ,
|
||||
condition_source_value VARCHAR NULL ,
|
||||
condition_source_concept_id INTEGER NOT NULL ,
|
||||
condition_status_source_value VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE measurement
|
||||
(
|
||||
measurement_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
measurement_concept_id INTEGER NOT NULL ,
|
||||
measurement_date DATE NULL ,
|
||||
measurement_datetime TIMESTAMP NOT NULL ,
|
||||
measurement_time VARCHAR NULL,
|
||||
measurement_type_concept_id INTEGER NOT NULL ,
|
||||
operator_concept_id INTEGER NULL ,
|
||||
value_as_number FLOAT NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
range_low FLOAT NULL ,
|
||||
range_high FLOAT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
visit_detail_id INTEGER NULL ,
|
||||
measurement_source_value VARCHAR NULL ,
|
||||
measurement_source_concept_id INTEGER NOT NULL ,
|
||||
unit_source_value VARCHAR NULL ,
|
||||
value_source_value VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE note
|
||||
(
|
||||
note_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
note_event_id INTEGER NULL ,
|
||||
note_event_field_concept_id INTEGER NOT NULL ,
|
||||
note_date DATE NULL ,
|
||||
note_datetime TIMESTAMP NOT NULL ,
|
||||
note_type_concept_id INTEGER NOT NULL ,
|
||||
note_class_concept_id INTEGER NOT NULL ,
|
||||
note_title VARCHAR NULL ,
|
||||
note_text VARCHAR NULL ,
|
||||
encoding_concept_id INTEGER NOT NULL ,
|
||||
language_concept_id INTEGER NOT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
visit_detail_id INTEGER NULL ,
|
||||
note_source_value VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE note_nlp
|
||||
(
|
||||
note_nlp_id INTEGER NOT NULL ,
|
||||
note_id INTEGER NOT NULL ,
|
||||
section_concept_id INTEGER NOT NULL ,
|
||||
snippet VARCHAR NULL ,
|
||||
"offset" VARCHAR NULL ,
|
||||
lexical_variant VARCHAR NOT NULL ,
|
||||
note_nlp_concept_id INTEGER NOT NULL ,
|
||||
nlp_system VARCHAR NULL ,
|
||||
nlp_date DATE NOT NULL ,
|
||||
nlp_datetime TIMESTAMP NULL ,
|
||||
term_exists VARCHAR NULL ,
|
||||
term_temporal VARCHAR NULL ,
|
||||
term_modifiers VARCHAR NULL ,
|
||||
note_nlp_source_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE observation
|
||||
(
|
||||
observation_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_concept_id INTEGER NOT NULL ,
|
||||
observation_date DATE NULL ,
|
||||
observation_datetime TIMESTAMP NOT NULL ,
|
||||
observation_type_concept_id INTEGER NOT NULL ,
|
||||
value_as_number FLOAT NULL ,
|
||||
value_as_string VARCHAR NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
qualifier_concept_id INTEGER NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
visit_detail_id INTEGER NULL ,
|
||||
observation_source_value VARCHAR NULL ,
|
||||
observation_source_concept_id INTEGER NOT NULL ,
|
||||
unit_source_value VARCHAR NULL ,
|
||||
qualifier_source_value VARCHAR NULL ,
|
||||
observation_event_id INTEGER NULL ,
|
||||
obs_event_field_concept_id INTEGER NOT NULL ,
|
||||
value_as_datetime TIMESTAMP NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE survey_conduct --Table added
|
||||
(
|
||||
survey_conduct_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
survey_concept_id INTEGER NOT NULL ,
|
||||
survey_start_date DATE NULL ,
|
||||
survey_start_datetime TIMESTAMP NULL ,
|
||||
survey_end_date DATE NULL ,
|
||||
survey_end_datetime TIMESTAMP NOT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
assisted_concept_id INTEGER NOT NULL ,
|
||||
respondent_type_concept_id INTEGER NOT NULL ,
|
||||
timing_concept_id INTEGER NOT NULL ,
|
||||
collection_method_concept_id INTEGER NOT NULL ,
|
||||
assisted_source_value VARCHAR NULL ,
|
||||
respondent_type_source_value VARCHAR NULL ,
|
||||
timing_source_value VARCHAR NULL ,
|
||||
collection_method_source_value VARCHAR NULL ,
|
||||
survey_source_value VARCHAR NULL ,
|
||||
survey_source_concept_id INTEGER NOT NULL ,
|
||||
survey_source_identifier VARCHAR NULL ,
|
||||
validated_survey_concept_id INTEGER NOT NULL ,
|
||||
validated_survey_source_value VARCHAR NULL ,
|
||||
survey_version_number VARCHAR NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
visit_detail_id INTEGER NULL ,
|
||||
response_visit_occurrence_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE fact_relationship
|
||||
(
|
||||
domain_concept_id_1 INTEGER NOT NULL ,
|
||||
fact_id_1 INTEGER NOT NULL ,
|
||||
domain_concept_id_2 INTEGER NOT NULL ,
|
||||
fact_id_2 INTEGER NOT NULL ,
|
||||
relationship_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE location
|
||||
(
|
||||
location_id INTEGER NOT NULL ,
|
||||
address_1 VARCHAR NULL ,
|
||||
address_2 VARCHAR NULL ,
|
||||
city VARCHAR NULL ,
|
||||
state VARCHAR NULL ,
|
||||
zip VARCHAR NULL ,
|
||||
county VARCHAR NULL ,
|
||||
country VARCHAR NULL ,
|
||||
location_source_value VARCHAR NULL ,
|
||||
latitude FLOAT NULL ,
|
||||
longitude FLOAT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE location_history --Table added
|
||||
(
|
||||
location_history_id INTEGER NOT NULL ,
|
||||
location_id INTEGER NOT NULL ,
|
||||
relationship_type_concept_id INTEGER NOT NULL ,
|
||||
domain_id VARCHAR NOT NULL ,
|
||||
entity_id INTEGER NOT NULL ,
|
||||
start_date DATE NOT NULL ,
|
||||
end_date DATE NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE care_site
|
||||
(
|
||||
care_site_id INTEGER NOT NULL ,
|
||||
care_site_name VARCHAR NULL ,
|
||||
place_of_service_concept_id INTEGER NOT NULL ,
|
||||
location_id INTEGER NULL ,
|
||||
care_site_source_value VARCHAR NULL ,
|
||||
place_of_service_source_value VARCHAR NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE provider
|
||||
(
|
||||
provider_id INTEGER NOT NULL ,
|
||||
provider_name VARCHAR NULL ,
|
||||
NPI VARCHAR NULL ,
|
||||
DEA VARCHAR NULL ,
|
||||
specialty_concept_id INTEGER NOT NULL ,
|
||||
care_site_id INTEGER NULL ,
|
||||
year_of_birth INTEGER NULL ,
|
||||
gender_concept_id INTEGER NULL ,
|
||||
provider_source_value VARCHAR NULL ,
|
||||
specialty_source_value VARCHAR NULL ,
|
||||
specialty_source_concept_id INTEGER NOT NULL ,
|
||||
gender_source_value VARCHAR NULL ,
|
||||
gender_source_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE payer_plan_period
|
||||
(
|
||||
payer_plan_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
contract_person_id INTEGER NULL ,
|
||||
payer_plan_period_start_date DATE NOT NULL ,
|
||||
payer_plan_period_end_date DATE NOT NULL ,
|
||||
payer_concept_id INTEGER NOT NULL ,
|
||||
plan_concept_id INTEGER NOT NULL ,
|
||||
contract_concept_id INTEGER NOT NULL ,
|
||||
sponsor_concept_id INTEGER NOT NULL ,
|
||||
stop_reason_concept_id INTEGER NOT NULL ,
|
||||
payer_source_value VARCHAR NULL ,
|
||||
payer_source_concept_id INTEGER NOT NULL ,
|
||||
plan_source_value VARCHAR NULL ,
|
||||
plan_source_concept_id INTEGER NOT NULL ,
|
||||
contract_source_value VARCHAR NULL ,
|
||||
contract_source_concept_id INTEGER NOT NULL ,
|
||||
sponsor_source_value VARCHAR NULL ,
|
||||
sponsor_source_concept_id INTEGER NOT NULL ,
|
||||
family_source_value VARCHAR NULL ,
|
||||
stop_reason_source_value VARCHAR NULL ,
|
||||
stop_reason_source_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE cost
|
||||
(
|
||||
cost_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL,
|
||||
cost_event_id INTEGER 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 NOT NULL ,
|
||||
cost FLOAT NULL ,
|
||||
incurred_date DATE NOT NULL ,
|
||||
billed_date DATE NULL ,
|
||||
paid_date DATE NULL ,
|
||||
revenue_code_concept_id INTEGER NOT NULL ,
|
||||
drg_concept_id INTEGER NOT NULL ,
|
||||
cost_source_value VARCHAR NULL ,
|
||||
cost_source_concept_id INTEGER NOT NULL ,
|
||||
revenue_code_source_value VARCHAR NULL ,
|
||||
drg_source_value VARCHAR NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE drug_era
|
||||
(
|
||||
drug_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_era_start_datetime TIMESTAMP NOT NULL ,
|
||||
drug_era_end_datetime TIMESTAMP NOT NULL ,
|
||||
drug_exposure_count INTEGER NULL ,
|
||||
gap_days INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE dose_era
|
||||
(
|
||||
dose_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
unit_concept_id INTEGER NOT NULL ,
|
||||
dose_value FLOAT NOT NULL ,
|
||||
dose_era_start_datetime TIMESTAMP NOT NULL ,
|
||||
dose_era_end_datetime TIMESTAMP NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE condition_era
|
||||
(
|
||||
condition_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_era_start_datetime TIMESTAMP NOT NULL ,
|
||||
condition_era_end_datetime TIMESTAMP NOT NULL ,
|
||||
condition_occurrence_count INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
|
@ -0,0 +1,177 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2019 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.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ##### ### ###### # # ## ###
|
||||
# # ## ## # # # # # # # # ## ## # # # # # # # # # # # # # # # ##### # #### ###### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # # # # # ## # ## # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # # ###### ### ### # # # # # # # # ##### ####
|
||||
# # # # # # # # # # # # # # # # ### # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # # # # # # # # # # # ### # # # # # # # # # ## # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ### ### # # # ### # ### # # ##### # #### ###### ####
|
||||
|
||||
|
||||
snowflake script to create the required primary keys within the OMOP common data model, version 6.0
|
||||
|
||||
last revised: 05-Aug-2019
|
||||
|
||||
author: Kathryn Watson
|
||||
|
||||
description: These primary keys are considered a minimal requirement to ensure adequate performance of analyses.
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
Primary key constraints
|
||||
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);
|
||||
|
||||
ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);
|
||||
|
||||
ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);
|
||||
|
||||
ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);
|
||||
|
||||
ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id);
|
||||
|
||||
ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);
|
||||
|
||||
ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id);
|
||||
|
||||
ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
|
||||
|
||||
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
/**PRIMARY KEY NONCLUSTERED constraints**/
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ;
|
||||
|
||||
ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ;
|
||||
|
||||
ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ;
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ;
|
||||
|
||||
ALTER TABLE visit_detail ADD CONSTRAINT xpk_visit_detail PRIMARY KEY ( visit_detail_id ) ;
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ;
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ;
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ;
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ;
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ;
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;
|
||||
|
||||
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_conduct ADD CONSTRAINT xpk_survey_conduct PRIMARY KEY ( survey_conduct_id ) ;
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
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 ) ;
|
||||
|
||||
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ;
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ;
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( cost_id ) ;
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
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 ) ;
|
||||
|
||||
ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ;
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Results elements
|
||||
|
||||
************************/
|
||||
|
||||
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 );
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
Common-Data-Model / Snowflake
|
||||
=================
|
||||
|
||||
This folder contains the SQL scripts for Snowflake.
|
||||
|
||||
In order to create your instantiation of the Common Data Model, we recommend following these steps:
|
||||
|
||||
1. Create a database for all OHDSI assets, if one does not already exist within your Snowflake account.
|
||||
|
||||
2. Within the OHDSI database, create a schema for the Common Data Model.
|
||||
|
||||
3. Open a Snowflake session and set the session context to use the database and schema referenced in Steps 1 and 2.
|
||||
|
||||
4. Set the session context to use an available Warehouse.
|
||||
|
||||
5. Execute the scripts `OMOP CDM snowflake ddl.txt` and `OMOP CDM Results snowflake ddl.txt` to create the tables and fields.
|
||||
|
||||
6. Execute the script `OMOP CDM snowflake primary keys.txt` to add the minimum set of primary keys we recommend.
|
||||
|
||||
7. Execute the script `OMOP CDM snowflake constraints.txt` to add the foreign key constraints.
|
||||
|
||||
8. Load your data into the schema.
|
||||
|
||||
Optionally, before loading your data into the schema, execute the `OMOP CDM snowflake cluster keys.txt` in full or for individual tables to add cluster keys where indexes are used in other technologies.
|
||||
|
||||
Note: adding cluster keys will result in additional compute costs in Snowflake and should be considered carefully with respect to performance SLAs vs. compute costs.
|
||||
Loading…
Reference in New Issue