conceptql 0.4.0 → 0.5.0

data/schemas/omopv4_plus.yml

@@ -1,729 +0,0 @@
----
-:location:
-  :columns:
-    :location_id:
-      :type: Bignum
-      :primary_key: true
-    :address_1:
-      :type: String
-      :size: 50
-    :address_2:
-      :type: String
-      :size: 50
-    :city:
-      :type: String
-      :size: 50
-    :state:
-      :type: String
-      :size: 2
-      :fixed: true
-    :zip:
-      :type: String
-      :size: 9
-    :county:
-      :type: String
-      :size: 20
-    :location_source_value:
-      :type: String
-      :size: 50
-
-:organization:
-  :ignorable: true
-  :columns:
-    :organization_id:
-      :type: Bignum
-      :primary_key: true
-    :place_of_service_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :place_of_service_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :location_id:
-      :type: Bignum
-      :foreign_key: location
-    :organization_source_value:
-      :type: String
-      :size: 50
-      :null: false
-    :place_of_service_source_value:
-      :type: String
-      :size: 50
-
-:care_site:
-  :ignorable: true
-  :columns:
-    :care_site_id:
-      :type: Bignum
-      :primary_key: true
-      :null: false
-    :location_id:
-      :type: Bignum
-      :foreign_key: location
-      :null: false
-    :organization_id:
-      :type: Bignum
-      :foreign_key: organization
-      :null: false
-    :place_of_service_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :place_of_service_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :care_site_source_value:
-      :type: String
-      :size: 50
-    :place_of_service_source_value:
-      :type: String
-      :size: 50
-      :null: false
-
-:provider:
-  :columns:
-    :provider_id:
-      :type: Bignum
-      :primary_key: true
-    :npi:
-      :type: String
-      :size: 20
-      :ignorable: true
-    :dea:
-      :type: String
-      :size: 20
-      :ignorable: true
-    :specialty_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :specialty_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-      :ignorable: true
-    :care_site_id:
-      :type: Bignum
-      :foreign_key: care_site
-      :null: false
-      :ignorable: true
-    :provider_source_value:
-      :type: String
-      :size: 50
-      :null: false
-      :ignorable: true
-    :specialty_source_value:
-      :type: String
-      :size: 50
-      :ignorable: true
-
-:person:
-  :columns:
-    :person_id:
-      :type: Bignum
-      :primary_key: true
-    :gender_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :gender_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-      :ignorable: true
-    :year_of_birth:
-      :type: Integer
-      :null: false
-    :month_of_birth:
-      :type: Integer
-    :day_of_birth:
-      :type: Integer
-    :race_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :race_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-      :ignorable: true
-    :ethnicity_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :ethnicity_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-      :ignorable: true
-    :location_id:
-      :type: Bignum
-      :foreign_key: location
-    :provider_id:
-      :type: Bignum
-      :foreign_key: provider
-    :care_site_id:
-      :type: Bignum
-      :foreign_key: care_site
-      :ignorable: true
-    :person_source_value:
-      :type: String
-      :size: 50
-    :gender_source_value:
-      :type: String
-      :size: 50
-      :ignorable: true
-    :race_source_value:
-      :type: String
-      :size: 50
-      :ignorable: true
-    :ethnicity_source_value:
-      :type: String
-      :size: 50
-      :ignorable: true
-
-:death:
-  :columns:
-    :person_id:
-      :type: Bignum
-      :primary_key: true
-      :foreign_key: person
-    :death_date:
-      :type: Date
-      :null: false
-    :death_type_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :death_type_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-      :ignorable: true
-    :cause_of_death_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :ignorable: true
-    :cause_of_death_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-      :ignorable: true
-    :cause_of_death_source_value:
-      :type: String
-      :size: 50
-
-:observation_period:
-  :columns:
-    :observation_period_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :observation_period_start_date:
-      :type: Date
-      :null: false
-    :observation_period_end_date:
-      :type: Date
-      :null: false
-    :prev_ds_period_end_date:
-      :type: Date
-      :ignorable: true
-
-:payer_plan_period:
-  :columns:
-    :payer_plan_period_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :payer_plan_period_start_date:
-      :type: Date
-      :null: false
-    :payer_plan_period_end_date:
-      :type: Date
-      :null: false
-    :payer_source_value:
-      :type: String
-      :size: 50
-    :plan_source_value:
-      :type: String
-      :size: 50
-    :family_source_value:
-      :type: String
-      :size: 50
-      :ignorable: true
-    :prev_ds_period_end_date:
-      :type: Date
-      :ignorable: true
-
-:visit_occurrence:
-  :columns:
-    :visit_occurrence_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :visit_start_date:
-      :type: Date
-      :null: false
-    :visit_end_date:
-      :type: Date
-      :null: false
-    :place_of_service_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :care_site_id:
-      :type: Bignum
-      :foreign_key: care_ste
-      :ignorable: true
-    :place_of_service_source_value:
-      :type: String
-      :size: 50
-    :visit_occurrence_type_id:
-      :type: Bignum
-      :foreign_key: concept
-      :ignorable: true
-    :visit_source_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :admitting_source_value:
-      :type: String
-      :size: 50
-      :ignorable: true
-
-:condition_occurrence:
-  :columns:
-    :condition_occurrence_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :condition_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :condition_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :condition_start_date:
-      :type: Date
-      :null: false
-    :condition_end_date:
-      :type: Date
-    :condition_type_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :stop_reason:
-      :type: String
-      :size: 20
-      :ignorable: true
-    :associated_provider_id:
-      :type: Bignum
-      :foreign_key: provider
-    :visit_occurrence_id:
-      :type: Bignum
-      :foreign_key: visit_occurrence
-    :condition_source_value:
-      :type: String
-      :size: 50
-
-:drug_exposure:
-  :columns:
-    :drug_exposure_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :drug_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :drug_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :drug_exposure_start_date:
-      :type: Date
-      :null: false
-    :drug_exposure_end_date:
-      :type: Date
-    :drug_type_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :stop_reason:
-      :type: String
-      :size: 20
-      :ignorable: true
-    :refills:
-      :type: Integer
-      :ignorable: true
-    :quantity:
-      :type: Float
-    :days_supply:
-      :type: Integer
-    :sig:
-      :type: String
-      :size: 500
-      :ignorable: true
-    :prescribing_provider_id:
-      :type: Bignum
-      :foreign_key: provider
-    :visit_occurrence_id:
-      :type: Bignum
-      :foreign_key: visit_occurrence
-    :relevant_condition_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :ignorable: true
-    :drug_source_value:
-      :type: String
-      :size: 50
-
-:drug_cost:
-  :ignorable: true
-  :columns:
-    :drug_cost_id:
-      :type: Bignum
-      :primary_key: true
-    :drug_exposure_id:
-      :type: Bignum
-      :foreign_key: drug_exposure
-      :null: false
-    :paid_copay:
-      :type: Float
-      :ignorable: true
-    :paid_coinsurance:
-      :type: Float
-      :ignorable: true
-    :paid_toward_deductible:
-      :type: Float
-      :ignorable: true
-    :paid_by_payer:
-      :type: Float
-      :ignorable: true
-    :paid_by_coordination_benefits:
-      :type: Float
-      :ignorable: true
-    :total_out_of_pocket:
-      :type: Float
-      :ignorable: true
-    :total_paid:
-      :type: Float
-      :ignorable: true
-    :ingredient_cost:
-      :type: Float
-      :ignorable: true
-    :dispensing_fee:
-      :type: Float
-      :ignorable: true
-    :average_wholesale_price:
-      :type: Float
-      :ignorable: true
-    :payer_plan_period_id:
-      :type: Bignum
-      :foreign_key: payer_plan_period
-      :ignorable: true
-
-:procedure_occurrence:
-  :columns:
-    :procedure_occurrence_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :procedure_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :procedure_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :procedure_date:
-      :type: Date
-      :null: false
-    :procedure_type_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :associated_provider_id:
-      :type: Bignum
-      :foreign_key: provider
-    :visit_occurrence_id:
-      :type: Bignum
-      :foreign_key: visit_occurrence
-    :relevant_condition_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :ignorable: true
-    :procedure_source_value:
-      :type: String
-      :size: 50
-
-:procedure_cost:
-  :columns:
-    :procedure_cost_id:
-      :type: Bignum
-      :primary_key: true
-    :procedure_occurrence_id:
-      :type: Bignum
-      :foreign_key: procedure_occurrence
-      :null: false
-    :paid_copay:
-      :type: Float
-      :ignorable: true
-    :paid_coinsurance:
-      :type: Float
-      :ignorable: true
-    :paid_toward_deductible:
-      :type: Float
-      :ignorable: true
-    :paid_by_payer:
-      :type: Float
-      :ignorable: true
-    :paid_by_coordination_benefits:
-      :type: Float
-      :ignorable: true
-    :total_out_of_pocket:
-      :type: Float
-      :ignorable: true
-    :total_paid:
-      :type: Float
-      :ignorable: true
-    :disease_class_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :ignorable: true
-    :revenue_code_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :ignorable: true
-    :payer_plan_period_id:
-      :type: Bignum
-      :foreign_key: payer_plan_period
-      :ignorable: true
-    :disease_class_source_value:
-      :type: String
-      :size: 50
-    :revenue_code_source_value:
-      :type: String
-      :size: 50
-
-:observation:
-  :columns:
-    :observation_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :observation_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :observation_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :observation_date:
-      :type: Date
-      :null: false
-    :observation_time:
-      :type: Date
-      :ignorable: true
-    :value_as_number:
-      :type: Float
-    :value_as_string:
-      :type: String
-      :size: 60
-    :value_as_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :unit_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :range_low:
-      :type: Float
-    :range_high:
-      :type: Float
-    :observation_type_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :associated_provider_id:
-      :type: Bignum
-      :foreign_key: provider
-    :visit_occurrence_id:
-      :type: Bignum
-      :foreign_key: visit_occurrence
-    :relevant_condition_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :ignorable: true
-    :observation_source_value:
-      :type: String
-      :size: 50
-    :unit_source_value:
-      :type: String
-      :size: 50
-
-:concept:
-  :columns:
-    :concept_id:
-      :type: Bignum
-      :primary_key: true
-    :concept_name:
-      :type: String
-    :concept_level:
-      :type: Integer
-      :ignorable: true
-    :concept_class:
-      :type: String
-      :ignorable: true
-    :vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :concept_code:
-      :type: String
-    :valid_start_date:
-      :type: Date
-      :ignorable: true
-    :valid_end_date:
-      :type: Date
-      :ignorable: true
-    :invalid_reason:
-      :type: String
-      :ignorable: true
-
-:vocabulary:
-  :columns:
-    :vocabulary_id:
-      :type: Bignum
-      :primary_key: true
-    :vocabulary_name:
-      :type: String
-
-:source_to_concept_map:
-  :columns:
-    :source_code:
-      :type: String
-    :source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :source_code_description:
-      :type: String
-    :target_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-    :target_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :mapping_type:
-      :type: String
-    :primary_map:
-      :type: String
-    :valid_start_date:
-      :type: Date
-      :ignorable: true
-    :valid_end_date:
-      :type: Date
-      :ignorable: true
-    :invalid_reason:
-      :type: String
-      :ignorable: true
-
-:cohort:
-  :ignorable: true
-  :columns:
-    :cohort_id:
-      :type: Bignum
-      :primary_key: true
-    :cohort_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :cohort_start_date:
-      :type: Date
-      :null: false
-    :cohort_end_date:
-      :type: Date
-    :subject_id:
-      :type: Bignum
-      :null: false
-    :stop_reason:
-      :type: String
-      :size: 20
-  :indexes:
-    :coh_cohconid:
-      :columns:
-        - cohort_concept_id
-    :coh_cohid:
-      :columns:
-        - cohort_id
-    :coh_subid:
-      :columns:
-        - subject_id
-
-:condition_era:
-  :ignorable: true
-  :columns:
-    :condition_era_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :condition_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :condition_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :condition_era_start_date:
-      :type: Date
-      :null: false
-    :condition_era_end_date:
-      :type: Date
-      :null: false
-    :condition_type_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :condition_occurrence_count:
-      :type: Integer
-
-:drug_era:
-  :ignorable: true
-  :columns:
-    :drug_era_id:
-      :type: Bignum
-      :primary_key: true
-    :person_id:
-      :type: Bignum
-      :foreign_key: person
-      :null: false
-    :drug_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :drug_source_vocabulary_id:
-      :type: Bignum
-      :foreign_key: vocabulary
-    :drug_era_start_date:
-      :type: Date
-      :null: false
-    :drug_era_end_date:
-      :type: Date
-      :null: false
-    :drug_type_concept_id:
-      :type: Bignum
-      :foreign_key: concept
-      :null: false
-    :drug_exposure_count:
-      :type: Integer

data/schemas/omopv4_plus_more_ignorables.tsv

@@ -1,13 +0,0 @@
-condition_occurrence	visit_detail_id
-condition_occurrence	source
-condition_occurrence	target_concept_id
-drug_exposure	visit_detail_id
-drug_exposure	source
-drug_exposure	target_concept_id
-drug_strength	box_size
-observation	visit_detail_id
-observation	source
-observation	target_concept_id
-payer_plan_period	rx
-payer_plan_period	source
-person	source