mz-health/OMOP
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OMOP
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Impala, Oracle, and Netezza edits from testers

This commit is contained in:
clairblacketer 2018-09-24 12:00:16 -04:00
parent 8c6ebe5f95
commit eee81f61ad
9 changed files with 1069 additions and 1315 deletions
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2
Impala/DataImport/OMOP_CDM_synpuf_load_Impala.sql
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@ -1,6 +1,6 @@
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CARE_SITE.csv' OVERWRITE INTO TABLE care_site; LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CARE_SITE.csv' OVERWRITE INTO TABLE care_site;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CONDITION_OCCURRENCE.csv' OVERWRITE INTO TABLE condition_occurrence; LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CONDITION_OCCURRENCE.csv' OVERWRITE INTO TABLE condition_occurrence;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEATH.csv' OVERWRITE INTO TABLE death; --LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEATH.csv' OVERWRITE INTO TABLE death;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DRUG_EXPOSURE.csv' OVERWRITE INTO TABLE drug_exposure; LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DRUG_EXPOSURE.csv' OVERWRITE INTO TABLE drug_exposure;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEVICE_EXPOSURE.csv' OVERWRITE INTO TABLE device_exposure; LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEVICE_EXPOSURE.csv' OVERWRITE INTO TABLE device_exposure;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_LOCATION.csv' OVERWRITE INTO TABLE `location`; LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_LOCATION.csv' OVERWRITE INTO TABLE `location`;

665
Impala/OMOP CDM impala ddl.txt
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@ -43,14 +43,14 @@ Standardized vocabulary
CREATE TABLE concept ( CREATE TABLE concept (
concept_id INTEGER , concept_id INTEGER ,
concept_name VARCHAR(255) , concept_name VARCHAR(255) ,
domain_id VARCHAR(20) , domain_id VARCHAR(20) ,
vocabulary_id VARCHAR(20) , vocabulary_id VARCHAR(20) ,
concept_class_id VARCHAR(20) , concept_class_id VARCHAR(20) ,
standard_concept VARCHAR(1) , standard_concept VARCHAR(1) ,
concept_code VARCHAR(50) , concept_code VARCHAR(50) ,
valid_start_date TIMESTAMP , valid_start_date TIMESTAMP ,
valid_end_date TIMESTAMP , valid_end_date TIMESTAMP ,
invalid_reason VARCHAR(1) invalid_reason VARCHAR(1)
) )
@ -58,10 +58,10 @@ CREATE TABLE concept (
CREATE TABLE vocabulary ( CREATE TABLE vocabulary (
vocabulary_id VARCHAR(20), vocabulary_id VARCHAR(20),
vocabulary_name VARCHAR(255), vocabulary_name VARCHAR(255),
vocabulary_reference VARCHAR(255), vocabulary_reference VARCHAR(255),
vocabulary_version VARCHAR(255), vocabulary_version VARCHAR(255),
vocabulary_concept_id INTEGER vocabulary_concept_id INTEGER
) )
; ;
@ -70,7 +70,7 @@ CREATE TABLE vocabulary (
CREATE TABLE domain ( CREATE TABLE domain (
domain_id VARCHAR(20), domain_id VARCHAR(20),
domain_name VARCHAR(255), domain_name VARCHAR(255),
domain_concept_id INTEGER domain_concept_id INTEGER
) )
; ;
@ -78,7 +78,7 @@ CREATE TABLE domain (
CREATE TABLE concept_class ( CREATE TABLE concept_class (
concept_class_id VARCHAR(20), concept_class_id VARCHAR(20),
concept_class_name VARCHAR(255), concept_class_name VARCHAR(255),
concept_class_concept_id INTEGER concept_class_concept_id INTEGER
) )
; ;
@ -87,7 +87,7 @@ CREATE TABLE concept_relationship (
concept_id_1 INTEGER , concept_id_1 INTEGER ,
concept_id_2 INTEGER , concept_id_2 INTEGER ,
relationship_id VARCHAR(20), relationship_id VARCHAR(20),
valid_start_date TIMESTAMP, valid_start_date TIMESTAMP,
valid_end_date TIMESTAMP, valid_end_date TIMESTAMP,
invalid_reason VARCHAR(1) invalid_reason VARCHAR(1)
) )
@ -95,10 +95,10 @@ CREATE TABLE concept_relationship (
CREATE TABLE relationship ( CREATE TABLE relationship (
relationship_id VARCHAR(20), relationship_id VARCHAR(20),
relationship_name VARCHAR(255), relationship_name VARCHAR(255),
is_hierarchical VARCHAR(1), is_hierarchical VARCHAR(1),
defines_ancestry VARCHAR(1), defines_ancestry VARCHAR(1),
reverse_relationship_id VARCHAR(20), reverse_relationship_id VARCHAR(20),
relationship_concept_id INTEGER relationship_concept_id INTEGER
) )
@ -106,16 +106,16 @@ CREATE TABLE relationship (
CREATE TABLE concept_synonym ( CREATE TABLE concept_synonym (
concept_id INTEGER , concept_id INTEGER ,
concept_synonym_name STRING, concept_synonym_name STRING,
language_concept_id INTEGER language_concept_id INTEGER
) )
; ;
CREATE TABLE concept_ancestor ( CREATE TABLE concept_ancestor (
ancestor_concept_id INTEGER , ancestor_concept_id INTEGER ,
descendant_concept_id INTEGER , descendant_concept_id INTEGER ,
min_levels_of_separation INTEGER , min_levels_of_separation INTEGER ,
max_levels_of_separation INTEGER max_levels_of_separation INTEGER
) )
@ -123,54 +123,32 @@ CREATE TABLE concept_ancestor (
CREATE TABLE source_to_concept_map ( CREATE TABLE source_to_concept_map (
source_code VARCHAR(50), source_code VARCHAR(50),
source_concept_id INTEGER , source_concept_id INTEGER ,
source_vocabulary_id VARCHAR(20), source_vocabulary_id VARCHAR(20),
source_code_description VARCHAR(255), source_code_description VARCHAR(255),
target_concept_id INTEGER , target_concept_id INTEGER ,
target_vocabulary_id VARCHAR(20), target_vocabulary_id VARCHAR(20),
valid_start_date TIMESTAMP, valid_start_date TIMESTAMP,
valid_end_date TIMESTAMP, valid_end_date TIMESTAMP,
invalid_reason VARCHAR(1) invalid_reason VARCHAR(1)
) )
; ;
CREATE TABLE drug_strength ( CREATE TABLE drug_strength (
drug_concept_id INTEGER , drug_concept_id INTEGER ,
ingredient_concept_id INTEGER , ingredient_concept_id INTEGER ,
amount_value FLOAT, amount_value FLOAT,
amount_unit_concept_id INTEGER , amount_unit_concept_id INTEGER ,
numerator_value FLOAT, numerator_value FLOAT,
numerator_unit_concept_id INTEGER , numerator_unit_concept_id INTEGER ,
denominator_value FLOAT, denominator_value FLOAT,
denominator_unit_concept_id INTEGER , denominator_unit_concept_id INTEGER ,
box_size INTEGER , box_size INTEGER ,
valid_start_date TIMESTAMP, valid_start_date TIMESTAMP,
valid_end_date TIMESTAMP, valid_end_date TIMESTAMP,
invalid_reason VARCHAR(1) invalid_reason VARCHAR(1)
)
;
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER ,
cohort_definition_name VARCHAR(255),
cohort_definition_description STRING,
definition_type_concept_id INTEGER ,
cohort_definition_syntax STRING,
subject_concept_id INTEGER ,
cohort_initiation_date TIMESTAMP
)
;
CREATE TABLE attribute_definition (
attribute_definition_id INTEGER ,
attribute_name VARCHAR(255),
attribute_description STRING,
attribute_type_concept_id INTEGER ,
attribute_syntax STRING
) )
; ;
@ -184,16 +162,16 @@ Standardized meta-data
CREATE TABLE cdm_source CREATE TABLE cdm_source
( (
cdm_source_name VARCHAR(255) , cdm_source_name VARCHAR(255) ,
cdm_source_abbreviation VARCHAR(25) , cdm_source_abbreviation VARCHAR(25) ,
cdm_holder VARCHAR(255) , cdm_holder VARCHAR(255) ,
source_description STRING , source_description STRING ,
source_documentation_reference VARCHAR(255) , source_documentation_reference VARCHAR(255) ,
cdm_etl_reference VARCHAR(255) , cdm_etl_reference VARCHAR(255) ,
source_release_date TIMESTAMP , source_release_date TIMESTAMP ,
cdm_release_date TIMESTAMP , cdm_release_date TIMESTAMP ,
cdm_version VARCHAR(10) , cdm_version VARCHAR(10) ,
vocabulary_version VARCHAR(20) vocabulary_version VARCHAR(20)
) )
; ;
@ -210,8 +188,8 @@ CREATE TABLE `metadata`
) )
; ;
INSERT INTO metadata (name, value_as_string) --Added cdm version record 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 ('CDM Version', '6.0') VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
; ;
@ -225,24 +203,24 @@ Standardized clinical data
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE person CREATE TABLE person
( (
person_id BIGINT , --BIGINTs added person_id BIGINT , --BIGINTs added
gender_concept_id INTEGER , gender_concept_id INTEGER ,
year_of_birth INTEGER , year_of_birth INTEGER ,
month_of_birth INTEGER , month_of_birth INTEGER ,
day_of_birth INTEGER , day_of_birth INTEGER ,
birth_datetime TIMESTAMP , birth_datetime TIMESTAMP ,
race_concept_id INTEGER , race_concept_id INTEGER ,
ethnicity_concept_id INTEGER , ethnicity_concept_id INTEGER ,
location_id INTEGER , location_id BIGINT ,
provider_id INTEGER , provider_id BIGINT ,
care_site_id INTEGER , care_site_id BIGINT ,
person_source_value VARCHAR(50), person_source_value VARCHAR(50),
gender_source_value VARCHAR(50), gender_source_value VARCHAR(50),
gender_source_concept_id INTEGER , gender_source_concept_id INTEGER ,
race_source_value VARCHAR(50), race_source_value VARCHAR(50),
race_source_concept_id INTEGER , race_source_concept_id INTEGER ,
ethnicity_source_value VARCHAR(50), ethnicity_source_value VARCHAR(50),
ethnicity_source_concept_id INTEGER ethnicity_source_concept_id INTEGER
) )
; ;
@ -250,11 +228,11 @@ CREATE TABLE person
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE observation_period CREATE TABLE observation_period
( (
observation_period_id BIGINT , observation_period_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
observation_period_start_date TIMESTAMP , observation_period_start_date TIMESTAMP ,
observation_period_end_date TIMESTAMP , observation_period_end_date TIMESTAMP ,
period_type_concept_id INTEGER period_type_concept_id INTEGER
) )
; ;
@ -262,35 +240,21 @@ CREATE TABLE observation_period
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE specimen CREATE TABLE specimen
( (
specimen_id BIGINT , specimen_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
specimen_concept_id INTEGER , specimen_concept_id INTEGER ,
specimen_type_concept_id INTEGER , specimen_type_concept_id INTEGER ,
specimen_date TIMESTAMP , specimen_date TIMESTAMP ,
specimen_datetime TIMESTAMP , specimen_datetime TIMESTAMP ,
quantity FLOAT , quantity FLOAT ,
unit_concept_id INTEGER , unit_concept_id INTEGER ,
anatomic_site_concept_id INTEGER , anatomic_site_concept_id INTEGER ,
disease_status_concept_id INTEGER , disease_status_concept_id INTEGER ,
specimen_source_id VARCHAR(50) , specimen_source_id VARCHAR(50) ,
specimen_source_value VARCHAR(50) , specimen_source_value VARCHAR(50) ,
unit_source_value VARCHAR(50) , unit_source_value VARCHAR(50) ,
anatomic_site_source_value VARCHAR(50) , anatomic_site_source_value VARCHAR(50) ,
disease_status_source_value VARCHAR(50) disease_status_source_value VARCHAR(50)
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE death
(
person_id BIGINT ,
death_date TIMESTAMP ,
death_datetime TIMESTAMP ,
death_type_concept_id INTEGER ,
cause_concept_id INTEGER ,
cause_source_value VARCHAR(50),
cause_source_concept_id INTEGER
) )
; ;
@ -298,27 +262,27 @@ CREATE TABLE death
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_occurrence CREATE TABLE visit_occurrence
( (
visit_occurrence_id BIGINT , visit_occurrence_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
visit_concept_id INTEGER , visit_concept_id INTEGER ,
visit_start_date TIMESTAMP , visit_start_date TIMESTAMP ,
visit_start_datetime TIMESTAMP , visit_start_datetime TIMESTAMP ,
visit_end_date TIMESTAMP , visit_end_date TIMESTAMP ,
visit_end_datetime TIMESTAMP , visit_end_datetime TIMESTAMP ,
visit_type_concept_id INTEGER , visit_type_concept_id INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
care_site_id INTEGER , care_site_id BIGINT ,
visit_source_value VARCHAR(50), visit_source_value VARCHAR(50),
visit_source_concept_id INTEGER , visit_source_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */ admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
admitted_from_source_value VARCHAR(50), admitted_from_source_value VARCHAR(50),
discharge_to_source_value VARCHAR(50) , discharge_to_source_value VARCHAR(50) ,
discharge_to_concept_id INTEGER , discharge_to_concept_id INTEGER ,
preceding_visit_occurrence_id INTEGER preceding_visit_occurrence_id INTEGER
) )
; ;
--todo admitting 'source'
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_detail CREATE TABLE visit_detail
( (
@ -330,8 +294,8 @@ CREATE TABLE visit_detail
visit_detail_end_date TIMESTAMP , visit_detail_end_date TIMESTAMP ,
visit_detail_end_datetime TIMESTAMP , visit_detail_end_datetime TIMESTAMP ,
visit_detail_type_concept_id INTEGER , visit_detail_type_concept_id INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
care_site_id INTEGER , care_site_id BIGINT ,
discharge_to_concept_id INTEGER , discharge_to_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */ admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
admitted_from_source_value VARCHAR(50) , admitted_from_source_value VARCHAR(50) ,
@ -348,20 +312,20 @@ CREATE TABLE visit_detail
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE procedure_occurrence CREATE TABLE procedure_occurrence
( (
procedure_occurrence_id BIGINT , procedure_occurrence_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
procedure_concept_id INTEGER , procedure_concept_id INTEGER ,
procedure_date TIMESTAMP , procedure_date TIMESTAMP ,
procedure_datetime TIMESTAMP , procedure_datetime TIMESTAMP ,
procedure_type_concept_id INTEGER , procedure_type_concept_id INTEGER ,
modifier_concept_id INTEGER , modifier_concept_id INTEGER ,
quantity INTEGER , quantity INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
procedure_source_value VARCHAR(50) , procedure_source_value VARCHAR(50) ,
procedure_source_concept_id INTEGER , procedure_source_concept_id INTEGER ,
modifier_source_value VARCHAR(50) , modifier_source_value VARCHAR(50)
) )
; ;
@ -369,29 +333,29 @@ CREATE TABLE procedure_occurrence
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_exposure CREATE TABLE drug_exposure
( (
drug_exposure_id BIGINT , drug_exposure_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
drug_concept_id INTEGER , drug_concept_id INTEGER ,
drug_exposure_start_date TIMESTAMP , drug_exposure_start_date TIMESTAMP ,
drug_exposure_start_datetime TIMESTAMP , drug_exposure_start_datetime TIMESTAMP ,
drug_exposure_end_date TIMESTAMP , drug_exposure_end_date TIMESTAMP ,
drug_exposure_end_datetime TIMESTAMP , drug_exposure_end_datetime TIMESTAMP ,
verbatim_end_date TIMESTAMP , verbatim_end_date TIMESTAMP ,
drug_type_concept_id INTEGER , drug_type_concept_id INTEGER ,
stop_reason VARCHAR(20) , stop_reason VARCHAR(20) ,
refills INTEGER , refills INTEGER ,
quantity FLOAT , quantity FLOAT ,
days_supply INTEGER , days_supply INTEGER ,
sig STRING , sig STRING ,
route_concept_id INTEGER , route_concept_id INTEGER ,
lot_number VARCHAR(50) , lot_number VARCHAR(50) ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
drug_source_value VARCHAR(50) , drug_source_value VARCHAR(50) ,
drug_source_concept_id INTEGER , drug_source_concept_id INTEGER ,
route_source_value VARCHAR(50) , route_source_value VARCHAR(50) ,
dose_unit_source_value VARCHAR(50) dose_unit_source_value VARCHAR(50)
) )
; ;
@ -399,21 +363,21 @@ CREATE TABLE drug_exposure
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE device_exposure CREATE TABLE device_exposure
( (
device_exposure_id BIGINT , device_exposure_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
device_concept_id INTEGER , device_concept_id INTEGER ,
device_exposure_start_date TIMESTAMP , device_exposure_start_date TIMESTAMP ,
device_exposure_start_datetime TIMESTAMP , device_exposure_start_datetime TIMESTAMP ,
device_exposure_end_date TIMESTAMP , device_exposure_end_date TIMESTAMP ,
device_exposure_end_datetime TIMESTAMP , device_exposure_end_datetime TIMESTAMP ,
device_type_concept_id INTEGER , device_type_concept_id INTEGER ,
unique_device_id VARCHAR(50) , unique_device_id VARCHAR(50) ,
quantity INTEGER , quantity INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
device_source_value VARCHAR(100) , device_source_value VARCHAR(100) ,
device_source_concept_id INTEGER device_source_concept_id INTEGER
) )
; ;
@ -422,21 +386,21 @@ CREATE TABLE device_exposure
CREATE TABLE condition_occurrence CREATE TABLE condition_occurrence
( (
condition_occurrence_id BIGINT , condition_occurrence_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
condition_concept_id INTEGER , condition_concept_id INTEGER ,
condition_start_date TIMESTAMP , condition_start_date TIMESTAMP ,
condition_start_datetime TIMESTAMP , condition_start_datetime TIMESTAMP ,
condition_end_date TIMESTAMP , condition_end_date TIMESTAMP ,
condition_end_datetime TIMESTAMP , condition_end_datetime TIMESTAMP ,
condition_type_concept_id INTEGER , condition_type_concept_id INTEGER ,
condition_status_concept_id INTEGER , condition_status_concept_id INTEGER ,
stop_reason VARCHAR(20) , stop_reason VARCHAR(20) ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
condition_source_value VARCHAR(50) , condition_source_value VARCHAR(50) ,
condition_source_concept_id INTEGER , condition_source_concept_id INTEGER ,
condition_status_source_value VARCHAR(50) condition_status_source_value VARCHAR(50)
) )
; ;
@ -444,26 +408,26 @@ CREATE TABLE condition_occurrence
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE measurement CREATE TABLE measurement
( (
measurement_id BIGINT , measurement_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
measurement_concept_id INTEGER , measurement_concept_id INTEGER ,
measurement_date TIMESTAMP , measurement_date TIMESTAMP ,
measurement_datetime TIMESTAMP , measurement_datetime TIMESTAMP ,
measurement_time VARCHAR(10), measurement_time VARCHAR(10),
measurement_type_concept_id INTEGER , measurement_type_concept_id INTEGER ,
operator_concept_id INTEGER , operator_concept_id INTEGER ,
value_as_number FLOAT , value_as_number FLOAT ,
value_as_concept_id INTEGER , value_as_concept_id INTEGER ,
unit_concept_id INTEGER , unit_concept_id INTEGER ,
range_low FLOAT , range_low FLOAT ,
range_high FLOAT , range_high FLOAT ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
measurement_source_value VARCHAR(50) , measurement_source_value VARCHAR(50) ,
measurement_source_concept_id INTEGER , measurement_source_concept_id INTEGER ,
unit_source_value VARCHAR(50) , unit_source_value VARCHAR(50) ,
value_source_value VARCHAR(50) value_source_value VARCHAR(50)
) )
; ;
@ -471,44 +435,42 @@ CREATE TABLE measurement
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE note CREATE TABLE note
( (
note_id BIGINT , note_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
note_event_id BIGINT , --This and the field below added note_event_id BIGINT ,
note_domain_id VARCHAR(20) , --This field may be removed in favor of the one below note_event_field_concept_id INTEGER ,
--note_event_table_concept_id INTEGER , --This may be added based on 9/4 meeting note_date TIMESTAMP ,
note_date TIMESTAMP ,
note_datetime TIMESTAMP , note_datetime TIMESTAMP ,
note_type_concept_id INTEGER , note_type_concept_id INTEGER ,
note_class_concept_id INTEGER , note_class_concept_id INTEGER ,
note_title VARCHAR(250) , note_title VARCHAR(250) ,
note_text STRING , note_text STRING ,
encoding_concept_id INTEGER , encoding_concept_id INTEGER ,
language_concept_id INTEGER , language_concept_id INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
note_source_value VARCHAR(50) note_source_value VARCHAR(50)
) )
; ;
CREATE TABLE note_nlp CREATE TABLE note_nlp
( (
note_nlp_id BIGINT , note_nlp_id BIGINT ,
note_id BIGINT , note_id BIGINT ,
section_concept_id INTEGER , section_concept_id INTEGER ,
snippet VARCHAR(250) , snippet VARCHAR(250) ,
`offset` VARCHAR(250) , `offset` VARCHAR(250) ,
lexical_variant VARCHAR(250) , lexical_variant VARCHAR(250) ,
note_nlp_concept_id INTEGER , note_nlp_concept_id INTEGER ,
nlp_system VARCHAR(250) , nlp_system VARCHAR(250) ,
nlp_date TIMESTAMP , nlp_date TIMESTAMP ,
nlp_datetime TIMESTAMP , nlp_datetime TIMESTAMP ,
term_exists VARCHAR(1) , term_exists VARCHAR(1) ,
term_temporal VARCHAR(50) , term_temporal VARCHAR(50) ,
term_modifiers VARCHAR(2000) , term_modifiers VARCHAR(2000) ,
note_nlp_source_concept_id INTEGER note_nlp_source_concept_id INTEGER
) )
; ;
@ -516,57 +478,56 @@ CREATE TABLE note_nlp
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE observation CREATE TABLE observation
( (
observation_id BIGINT , observation_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
observation_concept_id INTEGER , observation_concept_id INTEGER ,
observation_date TIMESTAMP , observation_date TIMESTAMP ,
observation_datetime TIMESTAMP , observation_datetime TIMESTAMP ,
observation_type_concept_id INTEGER , observation_type_concept_id INTEGER ,
value_as_number FLOAT , value_as_number FLOAT ,
value_as_string VARCHAR(60) , value_as_string VARCHAR(60) ,
value_as_concept_id INTEGER , value_as_concept_id INTEGER ,
qualifier_concept_id INTEGER , qualifier_concept_id INTEGER ,
unit_concept_id INTEGER , unit_concept_id INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id BIGINT , visit_occurrence_id BIGINT ,
visit_detail_id BIGINT , visit_detail_id BIGINT ,
observation_source_value VARCHAR(50) , observation_source_value VARCHAR(50) ,
observation_source_concept_id INTEGER , observation_source_concept_id INTEGER ,
unit_source_value VARCHAR(50) , unit_source_value VARCHAR(50) ,
qualifier_source_value VARCHAR(50) , qualifier_source_value VARCHAR(50) ,
observation_event_id BIGINT , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/ observation_event_id BIGINT , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
observation_event_domain_id VARCHAR(20) , obs_event_field_concept_id INTEGER , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/
--obs_event_table_concept_id INTEGER , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/ value_as_datetime TIMESTAMP
value_as_datetime TIMESTAMP
) )
; ;
CREATE TABLE survey_conduct CREATE TABLE survey_conduct
( (
survey_conduct_id BIGINT , survey_conduct_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
survey_concept_id INTEGER , survey_concept_id INTEGER ,
survey_start_date TIMESTAMP , survey_start_date TIMESTAMP ,
survey_start_datetime TIMESTAMP , survey_start_datetime TIMESTAMP ,
survey_end_date TIMESTAMP , survey_end_date TIMESTAMP ,
survey_end_datetime TIMESTAMP , survey_end_datetime TIMESTAMP ,
provider_id BIGINT , provider_id BIGINT ,
assisted_concept_id INTEGER , assisted_concept_id INTEGER ,
respondent_type_concept_id INTEGER , respondent_type_concept_id INTEGER ,
timing_concept_id INTEGER , timing_concept_id INTEGER ,
collection_method_concept_id INTEGER , collection_method_concept_id INTEGER ,
assisted_source_value VARCHAR(50) , assisted_source_value VARCHAR(50) ,
respondent_type_source_value VARCHAR(100) , respondent_type_source_value VARCHAR(100) ,
timing_source_value VARCHAR(100) , timing_source_value VARCHAR(100) ,
collection_method_source_value VARCHAR(100) , collection_method_source_value VARCHAR(100) ,
survey_source_value VARCHAR(100) , survey_source_value VARCHAR(100) ,
survey_source_concept_id INTEGER , survey_source_concept_id INTEGER ,
survey_source_identifier VARCHAR(100) , survey_source_identifier VARCHAR(100) ,
validated_survey_concept_id INTEGER , validated_survey_concept_id INTEGER ,
validated_survey_source_value VARCHAR(100) , validated_survey_source_value VARCHAR(100) ,
survey_version_number VARCHAR(20) , survey_version_number VARCHAR(20) ,
visit_occurrence_id BIGINT , visit_occurrence_id BIGINT ,
visit_detail_id BIGINT , visit_detail_id BIGINT ,
response_to_visit_occurrence_id BIGINT response_to_visit_occurrence_id BIGINT
) )
@ -577,10 +538,10 @@ CREATE TABLE survey_conduct
CREATE TABLE fact_relationship CREATE TABLE fact_relationship
( (
domain_concept_id_1 INTEGER , domain_concept_id_1 INTEGER ,
fact_id_1 BIGINT , fact_id_1 BIGINT ,
domain_concept_id_2 INTEGER , domain_concept_id_2 INTEGER ,
fact_id_2 BIGINT , fact_id_2 BIGINT ,
relationship_concept_id INTEGER relationship_concept_id INTEGER
) )
; ;
@ -593,17 +554,17 @@ Standardized health system data
************************/ ************************/
CREATE TABLE location CREATE TABLE `location`
( (
location_id BIGINT , location_id BIGINT ,
address_1 VARCHAR(50) , address_1 VARCHAR(50) ,
address_2 VARCHAR(50) , address_2 VARCHAR(50) ,
city VARCHAR(50) , city VARCHAR(50) ,
state VARCHAR(2) , state VARCHAR(2) ,
zip VARCHAR(9) , zip VARCHAR(9) ,
county VARCHAR(20) , county VARCHAR(20) ,
country VARCHAR(100) , country VARCHAR(100) ,
location_source_value VARCHAR(50) , location_source_value VARCHAR(50) ,
latitude FLOAT , latitude FLOAT ,
longitude FLOAT longitude FLOAT
) )
@ -612,42 +573,42 @@ CREATE TABLE location
CREATE TABLE location_history CREATE TABLE location_history
( (
location_history_id BIGINT , location_history_id BIGINT ,
location_id BIGINT , location_id BIGINT ,
relationship_type_concept_id INTEGER , --Recent addition based on github discussion relationship_type_concept_id INTEGER , --Recent addition based on github discussion
domain_id VARCHAR(50) , domain_id VARCHAR(50) ,
entity_id BIGINT , entity_id BIGINT ,
start_date TIMESTAMP , start_date TIMESTAMP ,
end_date TIMESTAMP end_date TIMESTAMP
) )
; ;
CREATE TABLE care_site CREATE TABLE care_site
( (
care_site_id BIGINT , care_site_id BIGINT ,
care_site_name VARCHAR(255) , care_site_name VARCHAR(255) ,
place_of_service_concept_id INTEGER , place_of_service_concept_id INTEGER ,
location_id BIGINT , location_id BIGINT ,
care_site_source_value VARCHAR(50) , care_site_source_value VARCHAR(50) ,
place_of_service_source_value VARCHAR(50) place_of_service_source_value VARCHAR(50)
) )
; ;
CREATE TABLE provider CREATE TABLE provider
( (
provider_id BIGINT , provider_id BIGINT ,
provider_name VARCHAR(255) , provider_name VARCHAR(255) ,
NPI VARCHAR(20) , NPI VARCHAR(20) ,
DEA VARCHAR(20) , DEA VARCHAR(20) ,
specialty_concept_id INTEGER , specialty_concept_id INTEGER ,
care_site_id BIGINT , care_site_id BIGINT ,
year_of_birth INTEGER , year_of_birth INTEGER ,
gender_concept_id INTEGER , gender_concept_id INTEGER ,
provider_source_value VARCHAR(50) , provider_source_value VARCHAR(50) ,
specialty_source_value VARCHAR(50) , specialty_source_value VARCHAR(50) ,
specialty_source_concept_id INTEGER , specialty_source_concept_id INTEGER ,
gender_source_value VARCHAR(50) , gender_source_value VARCHAR(50) ,
gender_source_concept_id INTEGER gender_source_concept_id INTEGER
) )
; ;
@ -663,25 +624,25 @@ Standardized health economics
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE payer_plan_period CREATE TABLE payer_plan_period
( (
payer_plan_period_id BIGINT , payer_plan_period_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
contract_person_id BIGINT , contract_person_id BIGINT ,
payer_plan_period_start_date TIMESTAMP , payer_plan_period_start_date TIMESTAMP ,
payer_plan_period_end_date TIMESTAMP , payer_plan_period_end_date TIMESTAMP ,
payer_concept_id INTEGER , payer_concept_id INTEGER ,
plan_concept_id INTEGER , plan_concept_id INTEGER ,
contract_concept_id INTEGER , contract_concept_id INTEGER ,
sponsor_concept_id INTEGER , sponsor_concept_id INTEGER ,
stop_reason_concept_id INTEGER , stop_reason_concept_id INTEGER ,
payer_source_value VARCHAR(50) , payer_source_value VARCHAR(50) ,
payer_source_concept_id INTEGER , payer_source_concept_id INTEGER ,
plan_source_value VARCHAR(50) , plan_source_value VARCHAR(50) ,
plan_source_concept_id INTEGER , plan_source_concept_id INTEGER ,
contract_source_value VARCHAR(50) , contract_source_value VARCHAR(50) ,
contract_source_concept_id INTEGER , contract_source_concept_id INTEGER ,
sponsor_source_value VARCHAR(50) , sponsor_source_value VARCHAR(50) ,
sponsor_source_concept_id INTEGER , sponsor_source_concept_id INTEGER ,
family_source_value VARCHAR(50) , family_source_value VARCHAR(50) ,
stop_reason_source_value VARCHAR(50) , stop_reason_source_value VARCHAR(50) ,
stop_reason_source_concept_id INTEGER stop_reason_source_concept_id INTEGER
) )
@ -690,23 +651,22 @@ CREATE TABLE payer_plan_period
CREATE TABLE cost CREATE TABLE cost
( (
cost_id BIGINT , cost_id BIGINT ,
person_id BIGINT, person_id BIGINT,
cost_event_id BIGINT , cost_event_id BIGINT ,
cost_domain_id VARCHAR(20) , cost_event_field_concept_id INTEGER , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
--cost_event_table_concept_id INTEGER , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/ cost_concept_id INTEGER ,
cost_concept_id INTEGER , cost_type_concept_id INTEGER ,
cost_type_concept_id INTEGER , currency_concept_id INTEGER ,
currency_concept_id INTEGER , cost FLOAT ,
cost FLOAT , incurred_date TIMESTAMP ,
incurred_date TIMESTAMP , billed_date TIMESTAMP ,
billed_date TIMESTAMP , paid_date TIMESTAMP ,
paid_date TIMESTAMP ,
revenue_code_concept_id INTEGER , revenue_code_concept_id INTEGER ,
drg_concept_id INTEGER , drg_concept_id INTEGER ,
cost_source_value VARCHAR(50) , cost_source_value VARCHAR(50) ,
cost_source_concept_id INTEGER , cost_source_concept_id INTEGER ,
revenue_code_source_value VARCHAR(50) , revenue_code_source_value VARCHAR(50) ,
drg_source_value VARCHAR(3) , drg_source_value VARCHAR(3) ,
payer_plan_period_id BIGINT payer_plan_period_id BIGINT
) )
@ -720,41 +680,16 @@ Standardized derived elements
************************/ ************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id BIGINT ,
subject_id BIGINT ,
cohort_start_date TIMESTAMP ,
cohort_end_date TIMESTAMP
)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort_attribute
(
cohort_definition_id BIGINT ,
subject_id BIGINT ,
cohort_start_date TIMESTAMP ,
cohort_end_date TIMESTAMP ,
attribute_definition_id BIGINT ,
value_as_number FLOAT ,
value_as_concept_id INTEGER
)
;
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era CREATE TABLE drug_era
( (
drug_era_id BIGINT , drug_era_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
drug_concept_id INTEGER , drug_concept_id INTEGER ,
drug_era_start_date TIMESTAMP , drug_era_start_date TIMESTAMP ,
drug_era_end_date TIMESTAMP , drug_era_end_date TIMESTAMP ,
drug_exposure_count INTEGER , drug_exposure_count INTEGER ,
gap_days INTEGER gap_days INTEGER
) )
; ;
@ -762,12 +697,12 @@ CREATE TABLE drug_era
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE dose_era CREATE TABLE dose_era
( (
dose_era_id BIGINT , dose_era_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
drug_concept_id INTEGER , drug_concept_id INTEGER ,
unit_concept_id INTEGER , unit_concept_id INTEGER ,
dose_value FLOAT , dose_value FLOAT ,
dose_era_start_date TIMESTAMP , dose_era_start_date TIMESTAMP ,
dose_era_end_date TIMESTAMP dose_era_end_date TIMESTAMP
) )
; ;
@ -776,11 +711,11 @@ CREATE TABLE dose_era
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE condition_era CREATE TABLE condition_era
( (
condition_era_id BIGINT , condition_era_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
condition_concept_id INTEGER , condition_concept_id INTEGER ,
condition_era_start_date TIMESTAMP , condition_era_start_date TIMESTAMP ,
condition_era_end_date TIMESTAMP , condition_era_end_date TIMESTAMP ,
condition_occurrence_count INTEGER condition_occurrence_count INTEGER
) )
; ;

4
Impala/README.md
View File

@ -11,10 +11,11 @@ In order to create your instantiation of the Common Data Model, we recommend fol
impala-shell -q 'CREATE DATABASE omop_cdm' impala-shell -q 'CREATE DATABASE omop_cdm'
``` ```
2. Execute the script `OMOP CDM impala ddl.txt` (you will need to convert it to a sql file first) to create the tables and fields. 2. Execute the scripts `OMOP CDM impala ddl.txt` and `OMOP CDM Results impala ddl.txt` (you will need to convert them to sql files first) to create the tables and fields.
```bash ```bash
impala-shell -d omop_cdm -f OMOP_CDM_impala_ddl.sql impala-shell -d omop_cdm -f OMOP_CDM_impala_ddl.sql
impala-shell -d omop_cdm -f OMOP_CDM_Results_impala_ddl.sql
``` ```
3. Load your data into the schema. 3. Load your data into the schema.
@ -42,6 +43,7 @@ hadoop fs -put synpuf synpuf
hadoop fs -chmod +w synpuf hadoop fs -chmod +w synpuf
impala-shell -d omop_cdm -f DataImport/OMOP_CDM_synpuf_load_Impala.sql --var=OMOP_SYNPUF_PATH=/user/$USER/synpuf impala-shell -d omop_cdm -f DataImport/OMOP_CDM_synpuf_load_Impala.sql --var=OMOP_SYNPUF_PATH=/user/$USER/synpuf
``` ```
* Note that these tables are in CDM v5.2.2 format
4. Convert to Parquet format. 4. Convert to Parquet format.

864
Netezza/OMOP CDM netezza ddl.txt
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13
Netezza/OMOP CDM netezza primary keys.txt
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@ -77,11 +77,6 @@ ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMA
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id); ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
/************************** /**************************
Standardized meta-data Standardized meta-data
@ -127,7 +122,7 @@ ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ; ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY ( survey_occurrence_id ) ; ALTER TABLE survey_conduct ADD CONSTRAINT xpk_survey_conduct PRIMARY KEY ( survey_conduct_id ) ;
/************************ /************************
@ -139,7 +134,7 @@ Standardized health system data
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ; 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 ) ; -- May need to remove this one 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 care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
@ -165,10 +160,6 @@ Standardized derived elements
************************/ ************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ; ALTER TABLE 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 dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;

28
Oracle/OMOP CDM oracle constraints.txt
View File

@ -28,7 +28,7 @@
oracle script to create foreign key, unique, and check constraints within the OMOP common data model, version 6.0 oracle script to create foreign key, unique, and check constraints within the OMOP common data model, version 6.0
last revised: 30-Aug┌-2018 last revised: 30-Aug-2018
author: Patrick Ryan, Clair Blacketer author: Patrick Ryan, Clair Blacketer
@ -86,7 +86,7 @@ ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (re
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id); ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id); ALTER TABLE concept_synonym ADD CONSTRAINT fpk_synonym_language FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id); ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
@ -112,14 +112,6 @@ ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (n
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id); ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
ALTER TABLE attribute_definition ADD CONSTRAINT fpk_attribute_type_concept FOREIGN KEY (attribute_type_concept_id) REFERENCES concept (concept_id);
/************************** /**************************
Standardized meta-data Standardized meta-data
@ -194,9 +186,9 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (prov
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_ visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id); ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitted_from_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
@ -215,7 +207,7 @@ ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitted_from_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_detail_source_concept_id) REFERENCES concept (concept_id); ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_detail_source_concept_id) REFERENCES concept (concept_id);
@ -476,16 +468,6 @@ Standardized derived elements
************************/ ************************/
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_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 drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);

784
Oracle/OMOP CDM oracle ddl.txt
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22
Oracle/OMOP CDM oracle pk indexes.txt
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@ -77,10 +77,6 @@ ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMA
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id); ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
/************************** /**************************
@ -127,7 +123,7 @@ ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ; ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY ( survey_occurrence_id ) ; ALTER TABLE survey_conduct ADD CONSTRAINT xpk_survey_conduct PRIMARY KEY ( survey_conduct_id ) ;
/************************ /************************
@ -139,7 +135,7 @@ Standardized health system data
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ; ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ; --Assuming this should be added ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ; ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
@ -165,10 +161,6 @@ Standardized derived elements
************************/ ************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ; ALTER TABLE 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 dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
@ -260,10 +252,6 @@ CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_cod
CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC); CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC); CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
/************************** /**************************
@ -370,12 +358,6 @@ Standardized derived elements
************************/ ************************/
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC); CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC); CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);

2
Oracle/README.md
View File

@ -7,7 +7,7 @@ In order to create your instantiation of the Common Data Model, we recommend fol
1. Create an empty schema. 1. Create an empty schema.
2. Execute the script `OMOP CDM oracle ddl.txt` to create the tables and fields. 2. Execute the script `OMOP CDM oracle ddl.txt` and `OMOP CDM Results oracle ddl.txt` to create the tables and fields.
3. Load your data into the schema. 3. Load your data into the schema.