310 lines
14 KiB
MySQL
310 lines
14 KiB
MySQL
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/*********************************************************************************
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# Copyright 2015 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.4
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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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script to create OMOP common data model, version 5.0 for Oracle database
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last revised: 1 Mar 2015
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author: Christian Reich
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*************************/
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CREATE TABLE concept
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(
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concept_id INTEGER NOT NULL,
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concept_name VARCHAR2(256 BYTE) NOT NULL,
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concept_level NUMBER NOT NULL,
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concept_class VARCHAR2(60 BYTE) NOT NULL,
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vocabulary_id INTEGER NOT NULL,
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concept_code VARCHAR2(40 BYTE) NOT NULL,
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valid_start_date DATE NOT NULL,
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valid_end_date DATE DEFAULT '31-Dec-2099' NOT NULL,
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invalid_reason CHAR(1 BYTE)
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) NOLOGGING;
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COMMENT ON TABLE concept IS 'A list of all valid terminology concepts across domains and their attributes. Concepts are derived from existing standards.';
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COMMENT ON COLUMN concept.concept_id IS 'A system-generated identifier to uniquely identify each concept across all concept types.';
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COMMENT ON COLUMN concept.concept_name IS 'An unambiguous, meaningful and descriptive name for the concept.';
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COMMENT ON COLUMN concept.concept_level IS 'The level of hierarchy associated with the concept. Different concept levels are assigned to concepts to depict their seniority in a clearly defined hierarchy, such as drugs, conditions, etc. A concept level of 0 is assigned to concepts that are not part of a standard vocabulary, but are part of the vocabulary for reference purposes (e.g. drug form).';
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COMMENT ON COLUMN concept.concept_class IS 'The category or class of the concept along both the hierarchical tree as well as different domains within a vocabulary. Examples are ''Clinical Drug'', ''Ingredient'', ''Clinical Finding'' etc.';
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COMMENT ON COLUMN concept.vocabulary_id IS 'A foreign key to the vocabulary table indicating from which source the concept has been adapted.';
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COMMENT ON COLUMN concept.concept_code IS 'The concept code represents the identifier of the concept in the source data it originates from, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that concept codes are not unique across vocabularies.';
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COMMENT ON COLUMN concept.valid_start_date IS 'The date when the was first recorded.';
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COMMENT ON COLUMN concept.valid_end_date IS 'The date when the concept became invalid because it was deleted or superseded (updated) by a new concept. The default value is 31-Dec-2099.';
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COMMENT ON COLUMN concept.invalid_reason IS 'Concepts that are replaced with a new concept are designated "Updated" (U) and concepts that are removed without replacement are "Deprecated" (D).';
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CREATE INDEX concept_code ON concept (concept_code, vocabulary_id);
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CREATE UNIQUE INDEX XPKconcept ON concept (concept_id);
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ALTER TABLE concept ADD (
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CHECK ( invalid_reason IN ('D', 'U'))
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ENABLE VALIDATE,
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CONSTRAINT XPKCONCEPT
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PRIMARY KEY
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(concept_id)
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USING INDEX XPKCONCEPT
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ENABLE VALIDATE);
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--add table RELATIONSHIP
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CREATE TABLE relationship
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(
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relationship_id INTEGER NOT NULL,
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relationship_name VARCHAR2(256 BYTE) NOT NULL,
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is_hierarchical INTEGER NOT NULL,
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defines_ancestry INTEGER DEFAULT 1 NOT NULL,
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reverse_relationship INTEGER
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) NOLOGGING;
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COMMENT ON TABLE relationship IS 'A list of relationship between concepts. Some of these relationships are generic (e.g. "Subsumes" relationship), others are domain-specific.';
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COMMENT ON COLUMN relationship.relationship_id IS 'The type of relationship captured by the relationship record.';
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COMMENT ON COLUMN relationship.relationship_name IS 'The text that describes the relationship type.';
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COMMENT ON COLUMN relationship.is_hierarchical IS 'Defines whether a relationship defines concepts into classes or hierarchies. Values are Y for hierarchical relationship or NULL if not';
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COMMENT ON COLUMN relationship.defines_ancestry IS 'Defines whether a hierarchical relationship contributes to the concept_ancestor table. These are subsets of the hierarchical relationships. Valid values are Y or NULL.';
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COMMENT ON COLUMN relationship.reverse_relationship IS 'relationship ID of the reverse relationship to this one. Corresponding records of reverse relationships have their concept_id_1 and concept_id_2 swapped.';
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CREATE UNIQUE INDEX XPKRELATIONHIP_TYPE ON relationship
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(relationship_id);
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ALTER TABLE relationship ADD (
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CONSTRAINT xpkrelationship_type
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PRIMARY KEY
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(relationship_id)
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USING INDEX xpkrelationship_type
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ENABLE VALIDATE);
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--add table concept_relationship
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CREATE TABLE concept_relationship
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(
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concept_id_1 INTEGER NOT NULL,
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concept_id_2 INTEGER NOT NULL,
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relationship_id INTEGER NOT NULL,
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valid_start_date DATE NOT NULL,
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valid_end_date DATE DEFAULT '31-Dec-2099' NOT NULL,
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invalid_reason CHAR(1 BYTE)
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) NOLOGGING;
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COMMENT ON TABLE concept_relationship IS 'A list of relationship between concepts. Some of these relationships are generic (e.g. ''Subsumes'' relationship), others are domain-specific.';
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COMMENT ON COLUMN concept_relationship.concept_id_1 IS 'A foreign key to the concept in the concept table associated with the relationship. relationships are directional, and this field represents the source concept designation.';
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COMMENT ON COLUMN concept_relationship.concept_id_2 IS 'A foreign key to the concept in the concept table associated with the relationship. relationships are directional, and this field represents the destination concept designation.';
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COMMENT ON COLUMN concept_relationship.relationship_id IS 'The type of relationship as defined in the relationship table.';
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COMMENT ON COLUMN concept_relationship.valid_start_date IS 'The date when the the relationship was first recorded.';
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COMMENT ON COLUMN concept_relationship.valid_end_date IS 'The date when the relationship became invalid because it was deleted or superseded (updated) by a new relationship. Default value is 31-Dec-2099.';
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COMMENT ON COLUMN concept_relationship.invalid_reason IS 'Reason the relationship was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value.';
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CREATE UNIQUE INDEX xpkconcept_relationship ON concept_relationship
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(concept_id_1, concept_id_2, relationship_id);
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ALTER TABLE concept_relationship ADD (
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CHECK ( invalid_reason IN ('D', 'U'))
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ENABLE VALIDATE,
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CHECK ( invalid_reason IN ('D', 'U'))
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ENABLE VALIDATE,
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CHECK (invalid_reason in ('D', 'U'))
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ENABLE VALIDATE,
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CONSTRAINT xpkconcept_relationship
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PRIMARY KEY
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(concept_id_1, concept_id_2, relationship_id)
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USING INDEX xpkconcept_relationship
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ENABLE VALIDATE);
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ALTER TABLE concept_relationship ADD (
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CONSTRAINT concept_REL_CHILD_FK
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FOREIGN KEY (concept_id_2)
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REFERENCES concept (concept_id)
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ENABLE VALIDATE,
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CONSTRAINT concept_REL_PARENT_FK
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FOREIGN KEY (concept_id_1)
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REFERENCES concept (concept_id)
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ENABLE VALIDATE,
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CONSTRAINT concept_REL_REL_type_FK
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FOREIGN KEY (relationship_id)
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REFERENCES relationship (relationship_id)
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ENABLE VALIDATE);
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--add table concept_ancestor
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CREATE TABLE concept_ancestor
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(
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ancestor_concept_id INTEGER NOT NULL,
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descendant_concept_id INTEGER NOT NULL,
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max_levels_of_separation NUMBER,
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min_levels_of_separation NUMBER
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) NOLOGGING;
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COMMENT ON TABLE concept_ancestor IS 'A specialized table containing only hierarchical relationship between concepts that may span several generations.';
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COMMENT ON COLUMN concept_ancestor.ancestor_concept_id IS 'A foreign key to the concept code in the concept table for the higher-level concept that forms the ancestor in the relationship.';
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COMMENT ON COLUMN concept_ancestor.descendant_concept_id IS 'A foreign key to the concept code in the concept table for the lower-level concept that forms the descendant in the relationship.';
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COMMENT ON COLUMN concept_ancestor.max_levels_of_separation IS 'The maximum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an optional attribute that is used to simplify hierarchic analysis. ';
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COMMENT ON COLUMN concept_ancestor.min_levels_of_separation IS 'The minimum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an optional attribute that is used to simplify hierarchic analysis.';
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CREATE UNIQUE INDEX xpkconcept_ancestor ON concept_ancestor
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(ancestor_concept_id, descendant_concept_id);
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ALTER TABLE concept_ancestor ADD (
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CONSTRAINT xpkconcept_ancestor
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PRIMARY KEY
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(ancestor_concept_id, descendant_concept_id)
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USING INDEX xpkconcept_ancestor
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ENABLE VALIDATE);
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ALTER TABLE concept_ancestor ADD (
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CONSTRAINT concept_ancestor_FK
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FOREIGN KEY (ancestor_concept_id)
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REFERENCES concept (concept_id)
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ENABLE VALIDATE,
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CONSTRAINT concept_descendant_FK
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FOREIGN KEY (descendant_concept_id)
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REFERENCES concept (concept_id)
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ENABLE VALIDATE);
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--add table concept_synonym
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CREATE TABLE concept_synonym
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(
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concept_synonym_id INTEGER NOT NULL,
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concept_id INTEGER NOT NULL,
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concept_synonym_name VARCHAR2(1000 BYTE) NOT NULL
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) NOLOGGING;
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COMMENT ON TABLE concept_synonym IS 'A table with synonyms for concepts that have more than one valid name or description.';
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COMMENT ON COLUMN concept_synonym.concept_synonym_id IS 'A system-generated unique identifier for each concept synonym.';
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COMMENT ON COLUMN concept_synonym.concept_id IS 'A foreign key to the concept in the concept table. ';
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COMMENT ON COLUMN concept_synonym.concept_synonym_name IS 'The alternative name for the concept.';
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CREATE UNIQUE INDEX xpkconcept_synonym ON concept_synonym
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(concept_synonym_id);
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ALTER TABLE concept_synonym ADD (
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CONSTRAINT xpkconcept_synonym
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PRIMARY KEY
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(concept_synonym_id)
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USING INDEX xpkconcept_synonym
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ENABLE VALIDATE);
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ALTER TABLE concept_synonym ADD (
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CONSTRAINT concept_synonym_concept_FK
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FOREIGN KEY (concept_id)
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REFERENCES concept (concept_id)
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ENABLE VALIDATE);
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--add table source_to_concept_map
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CREATE TABLE source_to_concept_map
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(
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source_code VARCHAR2(40 BYTE) NOT NULL,
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source_vocabulary_id INTEGER NOT NULL,
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source_code_description VARCHAR2(256 BYTE),
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target_concept_id INTEGER NOT NULL,
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target_vocabulary_id INTEGER NOT NULL,
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mapping_type VARCHAR2(256 BYTE),
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primary_map CHAR(1 BYTE),
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valid_start_date DATE NOT NULL,
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valid_end_date DATE NOT NULL,
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invalid_reason CHAR(1 BYTE)
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) NOLOGGING;
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CREATE INDEX SOURCE_TO_concept_SOURCE_idX ON source_to_concept_map
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(SOURCE_CODE);
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CREATE UNIQUE INDEX xpksource_to_concept_map ON source_to_concept_map
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(SOURCE_vocabulary_id, TARGET_concept_id, SOURCE_CODE, valid_end_date);
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ALTER TABLE source_to_concept_map ADD (
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CHECK (primary_map in ('Y'))
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ENABLE VALIDATE,
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CHECK (invalid_reason in ('D', 'U'))
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ENABLE VALIDATE,
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CONSTRAINT xpksource_to_concept_map
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PRIMARY KEY
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(SOURCE_vocabulary_id, TARGET_concept_id, SOURCE_CODE, valid_end_date)
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USING INDEX xpksource_to_concept_map
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ENABLE VALIDATE);
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ALTER TABLE source_to_concept_map ADD (
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CONSTRAINT SOURCE_TO_concept_concept
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FOREIGN KEY (TARGET_concept_id)
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REFERENCES concept (concept_id)
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ENABLE VALIDATE);
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--add table drug_strength
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CREATE TABLE drug_strength
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(
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drug_concept_id INTEGER NOT NULL,
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ingredient_concept_id INTEGER NOT NULL,
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amount_value NUMBER,
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amount_unit VARCHAR2 (60 BYTE),
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concentration_value NUMBER,
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concentration_enum_unit VARCHAR2 (60 BYTE),
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concentration_denom_unit VARCHAR2 (60 BYTE),
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valid_start_date DATE NOT NULL,
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valid_end_date DATE NOT NULL,
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invalid_reason VARCHAR2 (1 BYTE)
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);
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--add table vocabulary
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CREATE TABLE VOCABULARY
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(
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VOCABULARY_ID INTEGER NOT NULL,
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VOCABULARY_NAME VARCHAR2 (256 BYTE) NOT NULL
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);
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