conceptql 0.3.0 → 0.4.0

data/schemas/omopv4_plus.yml

@@ -0,0 +1,729 @@
+---
+: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

@@ -0,0 +1,13 @@
+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