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
View File

@ -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_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_DEVICE_EXPOSURE.csv' OVERWRITE INTO TABLE device_exposure;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_LOCATION.csv' OVERWRITE INTO TABLE `location`;

665
Impala/OMOP CDM impala ddl.txt
View File

@ -43,14 +43,14 @@ Standardized vocabulary
CREATE TABLE concept (
concept_id INTEGER ,
concept_id INTEGER ,
concept_name VARCHAR(255) ,
domain_id VARCHAR(20) ,
domain_id VARCHAR(20) ,
vocabulary_id VARCHAR(20) ,
concept_class_id VARCHAR(20) ,
standard_concept VARCHAR(1) ,
concept_class_id VARCHAR(20) ,
standard_concept VARCHAR(1) ,
concept_code VARCHAR(50) ,
valid_start_date TIMESTAMP ,
valid_start_date TIMESTAMP ,
valid_end_date TIMESTAMP ,
invalid_reason VARCHAR(1)
)
@ -58,10 +58,10 @@ CREATE TABLE concept (
CREATE TABLE vocabulary (
vocabulary_id VARCHAR(20),
vocabulary_name VARCHAR(255),
vocabulary_id VARCHAR(20),
vocabulary_name VARCHAR(255),
vocabulary_reference VARCHAR(255),
vocabulary_version VARCHAR(255),
vocabulary_version VARCHAR(255),
vocabulary_concept_id INTEGER
)
;
@ -70,7 +70,7 @@ CREATE TABLE vocabulary (
CREATE TABLE domain (
domain_id VARCHAR(20),
domain_name VARCHAR(255),
domain_concept_id INTEGER
domain_concept_id INTEGER
)
;
@ -78,7 +78,7 @@ CREATE TABLE domain (
CREATE TABLE concept_class (
concept_class_id VARCHAR(20),
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_2 INTEGER ,
relationship_id VARCHAR(20),
valid_start_date TIMESTAMP,
valid_start_date TIMESTAMP,
valid_end_date TIMESTAMP,
invalid_reason VARCHAR(1)
)
@ -95,10 +95,10 @@ CREATE TABLE concept_relationship (
CREATE TABLE relationship (
relationship_id VARCHAR(20),
relationship_name VARCHAR(255),
is_hierarchical VARCHAR(1),
defines_ancestry VARCHAR(1),
relationship_id VARCHAR(20),
relationship_name VARCHAR(255),
is_hierarchical VARCHAR(1),
defines_ancestry VARCHAR(1),
reverse_relationship_id VARCHAR(20),
relationship_concept_id INTEGER
)
@ -106,16 +106,16 @@ CREATE TABLE relationship (
CREATE TABLE concept_synonym (
concept_id INTEGER ,
concept_synonym_name STRING,
concept_id INTEGER ,
concept_synonym_name STRING,
language_concept_id INTEGER
)
;
CREATE TABLE concept_ancestor (
ancestor_concept_id INTEGER ,
descendant_concept_id INTEGER ,
ancestor_concept_id INTEGER ,
descendant_concept_id INTEGER ,
min_levels_of_separation INTEGER ,
max_levels_of_separation INTEGER
)
@ -123,54 +123,32 @@ CREATE TABLE concept_ancestor (
CREATE TABLE source_to_concept_map (
source_code VARCHAR(50),
source_concept_id INTEGER ,
source_code VARCHAR(50),
source_concept_id INTEGER ,
source_vocabulary_id VARCHAR(20),
source_code_description VARCHAR(255),
target_concept_id INTEGER ,
target_concept_id INTEGER ,
target_vocabulary_id VARCHAR(20),
valid_start_date TIMESTAMP,
valid_end_date TIMESTAMP,
invalid_reason VARCHAR(1)
valid_start_date TIMESTAMP,
valid_end_date TIMESTAMP,
invalid_reason VARCHAR(1)
)
;
CREATE TABLE drug_strength (
drug_concept_id INTEGER ,
drug_concept_id INTEGER ,
ingredient_concept_id INTEGER ,
amount_value FLOAT,
amount_value FLOAT,
amount_unit_concept_id INTEGER ,
numerator_value FLOAT,
numerator_unit_concept_id INTEGER ,
denominator_value FLOAT,
denominator_unit_concept_id INTEGER ,
box_size INTEGER ,
valid_start_date TIMESTAMP,
valid_end_date TIMESTAMP,
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
numerator_value FLOAT,
numerator_unit_concept_id INTEGER ,
denominator_value FLOAT,
denominator_unit_concept_id INTEGER ,
box_size INTEGER ,
valid_start_date TIMESTAMP,
valid_end_date TIMESTAMP,
invalid_reason VARCHAR(1)
)
;
@ -184,16 +162,16 @@ Standardized meta-data
CREATE TABLE cdm_source
(
cdm_source_name VARCHAR(255) ,
cdm_source_name VARCHAR(255) ,
cdm_source_abbreviation VARCHAR(25) ,
cdm_holder VARCHAR(255) ,
source_description STRING ,
source_documentation_reference VARCHAR(255) ,
cdm_etl_reference VARCHAR(255) ,
source_release_date TIMESTAMP ,
cdm_release_date TIMESTAMP ,
cdm_version VARCHAR(10) ,
vocabulary_version VARCHAR(20)
cdm_holder VARCHAR(255) ,
source_description STRING ,
source_documentation_reference VARCHAR(255) ,
cdm_etl_reference VARCHAR(255) ,
source_release_date TIMESTAMP ,
cdm_release_date TIMESTAMP ,
cdm_version VARCHAR(10) ,
vocabulary_version VARCHAR(20)
)
;
@ -210,8 +188,8 @@ CREATE TABLE `metadata`
)
;
INSERT INTO metadata (name, value_as_string) --Added cdm version record
VALUES ('CDM Version', '6.0')
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)
;
@ -225,24 +203,24 @@ Standardized clinical data
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE person
(
person_id BIGINT , --BIGINTs added
person_id BIGINT , --BIGINTs added
gender_concept_id INTEGER ,
year_of_birth INTEGER ,
month_of_birth INTEGER ,
day_of_birth INTEGER ,
birth_datetime TIMESTAMP ,
race_concept_id INTEGER ,
ethnicity_concept_id INTEGER ,
location_id INTEGER ,
provider_id INTEGER ,
care_site_id INTEGER ,
year_of_birth INTEGER ,
month_of_birth INTEGER ,
day_of_birth INTEGER ,
birth_datetime TIMESTAMP ,
race_concept_id INTEGER ,
ethnicity_concept_id INTEGER ,
location_id BIGINT ,
provider_id BIGINT ,
care_site_id BIGINT ,
person_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_concept_id INTEGER ,
ethnicity_source_value VARCHAR(50),
ethnicity_source_concept_id INTEGER
race_source_concept_id INTEGER ,
ethnicity_source_value VARCHAR(50),
ethnicity_source_concept_id INTEGER
)
;
@ -250,11 +228,11 @@ CREATE TABLE person
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE observation_period
(
observation_period_id BIGINT ,
person_id BIGINT ,
observation_period_id BIGINT ,
person_id BIGINT ,
observation_period_start_date TIMESTAMP ,
observation_period_end_date TIMESTAMP ,
period_type_concept_id INTEGER
observation_period_end_date TIMESTAMP ,
period_type_concept_id INTEGER
)
;
@ -262,35 +240,21 @@ CREATE TABLE observation_period
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE specimen
(
specimen_id BIGINT ,
person_id BIGINT ,
specimen_concept_id INTEGER ,
specimen_id BIGINT ,
person_id BIGINT ,
specimen_concept_id INTEGER ,
specimen_type_concept_id INTEGER ,
specimen_date TIMESTAMP ,
specimen_datetime TIMESTAMP ,
quantity FLOAT ,
unit_concept_id INTEGER ,
specimen_date TIMESTAMP ,
specimen_datetime TIMESTAMP ,
quantity FLOAT ,
unit_concept_id INTEGER ,
anatomic_site_concept_id INTEGER ,
disease_status_concept_id INTEGER ,
specimen_source_id VARCHAR(50) ,
specimen_source_value VARCHAR(50) ,
unit_source_value VARCHAR(50) ,
specimen_source_id VARCHAR(50) ,
specimen_source_value VARCHAR(50) ,
unit_source_value VARCHAR(50) ,
anatomic_site_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
disease_status_source_value VARCHAR(50)
)
;
@ -298,27 +262,27 @@ CREATE TABLE death
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_occurrence
(
visit_occurrence_id BIGINT ,
person_id BIGINT ,
visit_concept_id INTEGER ,
visit_start_date TIMESTAMP ,
visit_start_datetime TIMESTAMP ,
visit_end_date TIMESTAMP ,
visit_end_datetime TIMESTAMP ,
visit_type_concept_id INTEGER ,
provider_id INTEGER ,
care_site_id INTEGER ,
visit_source_value VARCHAR(50),
visit_source_concept_id INTEGER ,
visit_occurrence_id BIGINT ,
person_id BIGINT ,
visit_concept_id INTEGER ,
visit_start_date TIMESTAMP ,
visit_start_datetime TIMESTAMP ,
visit_end_date TIMESTAMP ,
visit_end_datetime TIMESTAMP ,
visit_type_concept_id INTEGER ,
provider_id BIGINT ,
care_site_id BIGINT ,
visit_source_value VARCHAR(50),
visit_source_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
admitted_from_source_value VARCHAR(50),
discharge_to_source_value VARCHAR(50) ,
discharge_to_concept_id INTEGER ,
discharge_to_source_value VARCHAR(50) ,
discharge_to_concept_id INTEGER ,
preceding_visit_occurrence_id INTEGER
)
;
--todo admitting 'source'
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_detail
(
@ -330,8 +294,8 @@ CREATE TABLE visit_detail
visit_detail_end_date TIMESTAMP ,
visit_detail_end_datetime TIMESTAMP ,
visit_detail_type_concept_id INTEGER ,
provider_id INTEGER ,
care_site_id INTEGER ,
provider_id BIGINT ,
care_site_id BIGINT ,
discharge_to_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
admitted_from_source_value VARCHAR(50) ,
@ -348,20 +312,20 @@ CREATE TABLE visit_detail
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE procedure_occurrence
(
procedure_occurrence_id BIGINT ,
person_id BIGINT ,
procedure_concept_id INTEGER ,
procedure_date TIMESTAMP ,
procedure_datetime TIMESTAMP ,
procedure_occurrence_id BIGINT ,
person_id BIGINT ,
procedure_concept_id INTEGER ,
procedure_date TIMESTAMP ,
procedure_datetime TIMESTAMP ,
procedure_type_concept_id INTEGER ,
modifier_concept_id INTEGER ,
quantity INTEGER ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
procedure_source_value VARCHAR(50) ,
modifier_concept_id INTEGER ,
quantity INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
procedure_source_value VARCHAR(50) ,
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)
CREATE TABLE drug_exposure
(
drug_exposure_id BIGINT ,
person_id BIGINT ,
drug_concept_id INTEGER ,
drug_exposure_start_date TIMESTAMP ,
drug_exposure_id BIGINT ,
person_id BIGINT ,
drug_concept_id INTEGER ,
drug_exposure_start_date TIMESTAMP ,
drug_exposure_start_datetime TIMESTAMP ,
drug_exposure_end_date TIMESTAMP ,
drug_exposure_end_datetime TIMESTAMP ,
verbatim_end_date TIMESTAMP ,
drug_type_concept_id INTEGER ,
stop_reason VARCHAR(20) ,
refills INTEGER ,
quantity FLOAT ,
days_supply INTEGER ,
sig STRING ,
route_concept_id INTEGER ,
lot_number VARCHAR(50) ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
drug_source_value VARCHAR(50) ,
drug_source_concept_id INTEGER ,
route_source_value VARCHAR(50) ,
dose_unit_source_value VARCHAR(50)
drug_exposure_end_date TIMESTAMP ,
drug_exposure_end_datetime TIMESTAMP ,
verbatim_end_date TIMESTAMP ,
drug_type_concept_id INTEGER ,
stop_reason VARCHAR(20) ,
refills INTEGER ,
quantity FLOAT ,
days_supply INTEGER ,
sig STRING ,
route_concept_id INTEGER ,
lot_number VARCHAR(50) ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
drug_source_value VARCHAR(50) ,
drug_source_concept_id INTEGER ,
route_source_value VARCHAR(50) ,
dose_unit_source_value VARCHAR(50)
)
;
@ -399,21 +363,21 @@ CREATE TABLE drug_exposure
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE device_exposure
(
device_exposure_id BIGINT ,
person_id BIGINT ,
device_concept_id INTEGER ,
device_exposure_start_date TIMESTAMP ,
device_exposure_id BIGINT ,
person_id BIGINT ,
device_concept_id INTEGER ,
device_exposure_start_date TIMESTAMP ,
device_exposure_start_datetime TIMESTAMP ,
device_exposure_end_date TIMESTAMP ,
device_exposure_end_date TIMESTAMP ,
device_exposure_end_datetime TIMESTAMP ,
device_type_concept_id INTEGER ,
unique_device_id VARCHAR(50) ,
quantity INTEGER ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
device_source_value VARCHAR(100) ,
device_source_concept_id INTEGER
device_type_concept_id INTEGER ,
unique_device_id VARCHAR(50) ,
quantity INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
device_source_value VARCHAR(100) ,
device_source_concept_id INTEGER
)
;
@ -422,21 +386,21 @@ CREATE TABLE device_exposure
CREATE TABLE condition_occurrence
(
condition_occurrence_id BIGINT ,
person_id BIGINT ,
person_id BIGINT ,
condition_concept_id INTEGER ,
condition_start_date TIMESTAMP ,
condition_start_datetime TIMESTAMP ,
condition_end_date TIMESTAMP ,
condition_start_datetime TIMESTAMP ,
condition_end_date TIMESTAMP ,
condition_end_datetime TIMESTAMP ,
condition_type_concept_id INTEGER ,
condition_status_concept_id INTEGER ,
stop_reason VARCHAR(20) ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
condition_type_concept_id INTEGER ,
condition_status_concept_id INTEGER ,
stop_reason VARCHAR(20) ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
condition_source_value VARCHAR(50) ,
condition_source_concept_id INTEGER ,
condition_status_source_value VARCHAR(50)
condition_source_concept_id INTEGER ,
condition_status_source_value VARCHAR(50)
)
;
@ -444,26 +408,26 @@ CREATE TABLE condition_occurrence
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE measurement
(
measurement_id BIGINT ,
person_id BIGINT ,
measurement_id BIGINT ,
person_id BIGINT ,
measurement_concept_id INTEGER ,
measurement_date TIMESTAMP ,
measurement_date TIMESTAMP ,
measurement_datetime TIMESTAMP ,
measurement_time VARCHAR(10),
measurement_type_concept_id INTEGER ,
operator_concept_id INTEGER ,
value_as_number FLOAT ,
value_as_concept_id INTEGER ,
unit_concept_id INTEGER ,
range_low FLOAT ,
range_high FLOAT ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
measurement_source_value VARCHAR(50) ,
measurement_source_concept_id INTEGER ,
unit_source_value VARCHAR(50) ,
value_source_value VARCHAR(50)
measurement_time VARCHAR(10),
measurement_type_concept_id INTEGER ,
operator_concept_id INTEGER ,
value_as_number FLOAT ,
value_as_concept_id INTEGER ,
unit_concept_id INTEGER ,
range_low FLOAT ,
range_high FLOAT ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
measurement_source_value VARCHAR(50) ,
measurement_source_concept_id INTEGER ,
unit_source_value VARCHAR(50) ,
value_source_value VARCHAR(50)
)
;
@ -471,44 +435,42 @@ CREATE TABLE measurement
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE note
(
note_id BIGINT ,
person_id BIGINT ,
note_event_id BIGINT , --This and the field below added
note_domain_id VARCHAR(20) , --This field may be removed in favor of the one below
--note_event_table_concept_id INTEGER , --This may be added based on 9/4 meeting
note_date TIMESTAMP ,
note_id BIGINT ,
person_id BIGINT ,
note_event_id BIGINT ,
note_event_field_concept_id INTEGER ,
note_date TIMESTAMP ,
note_datetime TIMESTAMP ,
note_type_concept_id INTEGER ,
note_class_concept_id INTEGER ,
note_title VARCHAR(250) ,
note_text STRING ,
encoding_concept_id INTEGER ,
language_concept_id INTEGER ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
note_source_value VARCHAR(50)
note_type_concept_id INTEGER ,
note_class_concept_id INTEGER ,
note_title VARCHAR(250) ,
note_text STRING ,
encoding_concept_id INTEGER ,
language_concept_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
note_source_value VARCHAR(50)
)
;
CREATE TABLE note_nlp
(
note_nlp_id BIGINT ,
note_id BIGINT ,
section_concept_id INTEGER ,
snippet VARCHAR(250) ,
`offset` VARCHAR(250) ,
lexical_variant VARCHAR(250) ,
note_nlp_concept_id INTEGER ,
nlp_system VARCHAR(250) ,
nlp_date TIMESTAMP ,
nlp_datetime TIMESTAMP ,
term_exists VARCHAR(1) ,
term_temporal VARCHAR(50) ,
term_modifiers VARCHAR(2000) ,
note_nlp_source_concept_id INTEGER
note_nlp_id BIGINT ,
note_id BIGINT ,
section_concept_id INTEGER ,
snippet VARCHAR(250) ,
`offset` VARCHAR(250) ,
lexical_variant VARCHAR(250) ,
note_nlp_concept_id INTEGER ,
nlp_system VARCHAR(250) ,
nlp_date TIMESTAMP ,
nlp_datetime TIMESTAMP ,
term_exists VARCHAR(1) ,
term_temporal VARCHAR(50) ,
term_modifiers VARCHAR(2000) ,
note_nlp_source_concept_id INTEGER
)
;
@ -516,57 +478,56 @@ CREATE TABLE note_nlp
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE observation
(
observation_id BIGINT ,
person_id BIGINT ,
observation_concept_id INTEGER ,
observation_date TIMESTAMP ,
observation_datetime TIMESTAMP ,
observation_id BIGINT ,
person_id BIGINT ,
observation_concept_id INTEGER ,
observation_date TIMESTAMP ,
observation_datetime TIMESTAMP ,
observation_type_concept_id INTEGER ,
value_as_number FLOAT ,
value_as_string VARCHAR(60) ,
value_as_concept_id INTEGER ,
qualifier_concept_id INTEGER ,
unit_concept_id INTEGER ,
provider_id INTEGER ,
visit_occurrence_id BIGINT ,
value_as_number FLOAT ,
value_as_string VARCHAR(60) ,
value_as_concept_id INTEGER ,
qualifier_concept_id INTEGER ,
unit_concept_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
observation_source_value VARCHAR(50) ,
observation_source_concept_id INTEGER ,
unit_source_value VARCHAR(50) ,
qualifier_source_value VARCHAR(50) ,
observation_event_id BIGINT , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
observation_event_domain_id VARCHAR(20) ,
--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
unit_source_value VARCHAR(50) ,
qualifier_source_value VARCHAR(50) ,
observation_event_id BIGINT , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
obs_event_field_concept_id INTEGER , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/
value_as_datetime TIMESTAMP
)
;
CREATE TABLE survey_conduct
(
survey_conduct_id BIGINT ,
person_id BIGINT ,
survey_concept_id INTEGER ,
survey_start_date TIMESTAMP ,
survey_start_datetime TIMESTAMP ,
survey_end_date TIMESTAMP ,
survey_end_datetime TIMESTAMP ,
provider_id BIGINT ,
assisted_concept_id INTEGER ,
respondent_type_concept_id INTEGER ,
timing_concept_id INTEGER ,
survey_conduct_id BIGINT ,
person_id BIGINT ,
survey_concept_id INTEGER ,
survey_start_date TIMESTAMP ,
survey_start_datetime TIMESTAMP ,
survey_end_date TIMESTAMP ,
survey_end_datetime TIMESTAMP ,
provider_id BIGINT ,
assisted_concept_id INTEGER ,
respondent_type_concept_id INTEGER ,
timing_concept_id INTEGER ,
collection_method_concept_id INTEGER ,
assisted_source_value VARCHAR(50) ,
assisted_source_value VARCHAR(50) ,
respondent_type_source_value VARCHAR(100) ,
timing_source_value VARCHAR(100) ,
timing_source_value VARCHAR(100) ,
collection_method_source_value VARCHAR(100) ,
survey_source_value VARCHAR(100) ,
survey_source_concept_id INTEGER ,
survey_source_identifier VARCHAR(100) ,
validated_survey_concept_id INTEGER ,
survey_source_value VARCHAR(100) ,
survey_source_concept_id INTEGER ,
survey_source_identifier VARCHAR(100) ,
validated_survey_concept_id INTEGER ,
validated_survey_source_value VARCHAR(100) ,
survey_version_number VARCHAR(20) ,
visit_occurrence_id BIGINT ,
survey_version_number VARCHAR(20) ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
response_to_visit_occurrence_id BIGINT
)
@ -577,10 +538,10 @@ CREATE TABLE survey_conduct
CREATE TABLE fact_relationship
(
domain_concept_id_1 INTEGER ,
fact_id_1 BIGINT ,
fact_id_1 BIGINT ,
domain_concept_id_2 INTEGER ,
fact_id_2 BIGINT ,
relationship_concept_id INTEGER
fact_id_2 BIGINT ,
relationship_concept_id INTEGER
)
;
@ -593,17 +554,17 @@ Standardized health system data
************************/
CREATE TABLE location
CREATE TABLE `location`
(
location_id BIGINT ,
address_1 VARCHAR(50) ,
address_2 VARCHAR(50) ,
city VARCHAR(50) ,
state VARCHAR(2) ,
zip VARCHAR(9) ,
county VARCHAR(20) ,
country VARCHAR(100) ,
location_source_value VARCHAR(50) ,
city VARCHAR(50) ,
state VARCHAR(2) ,
zip VARCHAR(9) ,
county VARCHAR(20) ,
country VARCHAR(100) ,
location_source_value VARCHAR(50) ,
latitude FLOAT ,
longitude FLOAT
)
@ -612,42 +573,42 @@ CREATE TABLE location
CREATE TABLE location_history
(
location_history_id BIGINT ,
location_id BIGINT ,
location_id BIGINT ,
relationship_type_concept_id INTEGER , --Recent addition based on github discussion
domain_id VARCHAR(50) ,
entity_id BIGINT ,
start_date TIMESTAMP ,
end_date TIMESTAMP
domain_id VARCHAR(50) ,
entity_id BIGINT ,
start_date TIMESTAMP ,
end_date TIMESTAMP
)
;
CREATE TABLE care_site
(
care_site_id BIGINT ,
care_site_name VARCHAR(255) ,
place_of_service_concept_id INTEGER ,
location_id BIGINT ,
care_site_source_value VARCHAR(50) ,
place_of_service_source_value VARCHAR(50)
care_site_id BIGINT ,
care_site_name VARCHAR(255) ,
place_of_service_concept_id INTEGER ,
location_id BIGINT ,
care_site_source_value VARCHAR(50) ,
place_of_service_source_value VARCHAR(50)
)
;
CREATE TABLE provider
(
provider_id BIGINT ,
provider_name VARCHAR(255) ,
NPI VARCHAR(20) ,
DEA VARCHAR(20) ,
specialty_concept_id INTEGER ,
care_site_id BIGINT ,
year_of_birth INTEGER ,
gender_concept_id INTEGER ,
provider_source_value VARCHAR(50) ,
specialty_source_value VARCHAR(50) ,
provider_id BIGINT ,
provider_name VARCHAR(255) ,
NPI VARCHAR(20) ,
DEA VARCHAR(20) ,
specialty_concept_id INTEGER ,
care_site_id BIGINT ,
year_of_birth INTEGER ,
gender_concept_id INTEGER ,
provider_source_value VARCHAR(50) ,
specialty_source_value VARCHAR(50) ,
specialty_source_concept_id INTEGER ,
gender_source_value VARCHAR(50) ,
gender_source_value VARCHAR(50) ,
gender_source_concept_id INTEGER
)
;
@ -663,25 +624,25 @@ Standardized health economics
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE payer_plan_period
(
payer_plan_period_id BIGINT ,
person_id BIGINT ,
payer_plan_period_id BIGINT ,
person_id BIGINT ,
contract_person_id BIGINT ,
payer_plan_period_start_date TIMESTAMP ,
payer_plan_period_end_date TIMESTAMP ,
payer_plan_period_end_date TIMESTAMP ,
payer_concept_id INTEGER ,
plan_concept_id INTEGER ,
contract_concept_id INTEGER ,
sponsor_concept_id INTEGER ,
stop_reason_concept_id INTEGER ,
payer_source_value VARCHAR(50) ,
payer_source_value VARCHAR(50) ,
payer_source_concept_id INTEGER ,
plan_source_value VARCHAR(50) ,
plan_source_value VARCHAR(50) ,
plan_source_concept_id INTEGER ,
contract_source_value VARCHAR(50) ,
contract_source_concept_id INTEGER ,
sponsor_source_value VARCHAR(50) ,
sponsor_source_concept_id INTEGER ,
family_source_value VARCHAR(50) ,
family_source_value VARCHAR(50) ,
stop_reason_source_value VARCHAR(50) ,
stop_reason_source_concept_id INTEGER
)
@ -690,23 +651,22 @@ CREATE TABLE payer_plan_period
CREATE TABLE cost
(
cost_id BIGINT ,
person_id BIGINT,
cost_event_id BIGINT ,
cost_domain_id VARCHAR(20) ,
--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_type_concept_id INTEGER ,
currency_concept_id INTEGER ,
cost FLOAT ,
incurred_date TIMESTAMP ,
billed_date TIMESTAMP ,
paid_date TIMESTAMP ,
cost_id BIGINT ,
person_id BIGINT,
cost_event_id BIGINT ,
cost_event_field_concept_id INTEGER , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_concept_id INTEGER ,
cost_type_concept_id INTEGER ,
currency_concept_id INTEGER ,
cost FLOAT ,
incurred_date TIMESTAMP ,
billed_date TIMESTAMP ,
paid_date TIMESTAMP ,
revenue_code_concept_id INTEGER ,
drg_concept_id INTEGER ,
cost_source_value VARCHAR(50) ,
cost_source_concept_id INTEGER ,
revenue_code_source_value VARCHAR(50) ,
drg_concept_id INTEGER ,
cost_source_value VARCHAR(50) ,
cost_source_concept_id INTEGER ,
revenue_code_source_value VARCHAR(50) ,
drg_source_value VARCHAR(3) ,
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)
CREATE TABLE drug_era
(
drug_era_id BIGINT ,
person_id BIGINT ,
drug_concept_id INTEGER ,
drug_era_id BIGINT ,
person_id BIGINT ,
drug_concept_id INTEGER ,
drug_era_start_date TIMESTAMP ,
drug_era_end_date TIMESTAMP ,
drug_exposure_count INTEGER ,
gap_days INTEGER
gap_days INTEGER
)
;
@ -762,12 +697,12 @@ CREATE TABLE drug_era
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE dose_era
(
dose_era_id BIGINT ,
person_id BIGINT ,
drug_concept_id INTEGER ,
unit_concept_id INTEGER ,
dose_value FLOAT ,
dose_era_start_date TIMESTAMP ,
dose_era_id BIGINT ,
person_id BIGINT ,
drug_concept_id INTEGER ,
unit_concept_id INTEGER ,
dose_value FLOAT ,
dose_era_start_date TIMESTAMP ,
dose_era_end_date TIMESTAMP
)
;
@ -776,11 +711,11 @@ CREATE TABLE dose_era
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE condition_era
(
condition_era_id BIGINT ,
person_id BIGINT ,
condition_concept_id INTEGER ,
condition_era_id BIGINT ,
person_id BIGINT ,
condition_concept_id INTEGER ,
condition_era_start_date TIMESTAMP ,
condition_era_end_date TIMESTAMP ,
condition_era_end_date TIMESTAMP ,
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'
```
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
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.
@ -42,6 +43,7 @@ hadoop fs -put synpuf 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
```
* Note that these tables are in CDM v5.2.2 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 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
@ -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 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_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 ) ;
@ -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 dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;

28
Oracle/OMOP CDM oracle constraints.txt
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@ -28,7 +28,7 @@
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
@ -86,7 +86,7 @@ ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (re
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_synonym_language FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
@ -112,14 +112,6 @@ ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (n
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
ALTER TABLE attribute_definition ADD CONSTRAINT fpk_attribute_type_concept FOREIGN KEY (attribute_type_concept_id) REFERENCES concept (concept_id);
/**************************
Standardized meta-data
@ -194,9 +186,9 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (prov
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_ visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitted_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);
@ -215,7 +207,7 @@ ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitted_from_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_detail_source_concept_id) REFERENCES concept (concept_id);
@ -476,16 +468,6 @@ Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);

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 cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
/**************************
@ -127,7 +123,7 @@ ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY ( survey_occurrence_id ) ;
ALTER TABLE survey_conduct ADD CONSTRAINT xpk_survey_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_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ; --Assuming this should be added
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
@ -165,10 +161,6 @@ Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
@ -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_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_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.
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.