From 8d0128d113317505742e16038b7f154963582a47 Mon Sep 17 00:00:00 2001 From: Lawrence Adams Date: Wed, 25 Sep 2024 23:13:07 +0100 Subject: [PATCH 1/9] feat: add autogenerated models from #59 --- models/omop/_models/care_site.yml | 39 ++++ models/omop/_models/cdm_source.yml | 56 ++++++ models/omop/_models/cohort.yml | 29 +++ models/omop/_models/cohort_definition.yml | 46 +++++ models/omop/_models/concept.yml | 82 ++++++++ models/omop/_models/concept_ancestor.yml | 39 ++++ models/omop/_models/concept_class.yml | 28 +++ models/omop/_models/concept_relationship.yml | 46 +++++ models/omop/_models/concept_synonym.yml | 25 +++ models/omop/_models/condition_era.yml | 47 +++++ models/omop/_models/condition_occurrence.yml | 118 ++++++++++++ models/omop/_models/cost.yml | 101 ++++++++++ models/omop/_models/death.yml | 50 +++++ models/omop/_models/device_exposure.yml | 136 +++++++++++++ models/omop/_models/domain.yml | 28 +++ models/omop/_models/dose_era.yml | 55 ++++++ models/omop/_models/drug_era.yml | 49 +++++ models/omop/_models/drug_exposure.yml | 147 +++++++++++++++ models/omop/_models/drug_strength.yml | 72 +++++++ models/omop/_models/episode.yml | 98 ++++++++++ models/omop/_models/episode_event.yml | 32 ++++ models/omop/_models/fact_relationship.yml | 44 +++++ models/omop/_models/location.yml | 48 +++++ models/omop/_models/measurement.yml | 178 ++++++++++++++++++ models/omop/_models/metadata.yml | 53 ++++++ models/omop/_models/note.yml | 107 +++++++++++ models/omop/_models/note_nlp.yml | 68 +++++++ models/omop/_models/observation.yml | 157 +++++++++++++++ models/omop/_models/observation_period.yml | 44 +++++ models/omop/_models/payer_plan_period.yml | 110 +++++++++++ models/omop/_models/person.yml | 118 ++++++++++++ models/omop/_models/procedure_occurrence.yml | 113 +++++++++++ models/omop/_models/provider.yml | 81 ++++++++ models/omop/_models/relationship.yml | 43 +++++ models/omop/_models/source_to_concept_map.yml | 64 +++++++ models/omop/_models/specimen.yml | 83 ++++++++ models/omop/_models/visit_detail.yml | 151 +++++++++++++++ models/omop/_models/visit_occurrence.yml | 133 +++++++++++++ models/omop/_models/vocabulary.yml | 32 ++++ 39 files changed, 2950 insertions(+) create mode 100644 models/omop/_models/care_site.yml create mode 100644 models/omop/_models/cdm_source.yml create mode 100644 models/omop/_models/cohort.yml create mode 100644 models/omop/_models/cohort_definition.yml create mode 100644 models/omop/_models/concept.yml create mode 100644 models/omop/_models/concept_ancestor.yml create mode 100644 models/omop/_models/concept_class.yml create mode 100644 models/omop/_models/concept_relationship.yml create mode 100644 models/omop/_models/concept_synonym.yml create mode 100644 models/omop/_models/condition_era.yml create mode 100644 models/omop/_models/condition_occurrence.yml create mode 100644 models/omop/_models/cost.yml create mode 100644 models/omop/_models/death.yml create mode 100644 models/omop/_models/device_exposure.yml create mode 100644 models/omop/_models/domain.yml create mode 100644 models/omop/_models/dose_era.yml create mode 100644 models/omop/_models/drug_era.yml create mode 100644 models/omop/_models/drug_exposure.yml create mode 100644 models/omop/_models/drug_strength.yml create mode 100644 models/omop/_models/episode.yml create mode 100644 models/omop/_models/episode_event.yml create mode 100644 models/omop/_models/fact_relationship.yml create mode 100644 models/omop/_models/location.yml create mode 100644 models/omop/_models/measurement.yml create mode 100644 models/omop/_models/metadata.yml create mode 100644 models/omop/_models/note.yml create mode 100644 models/omop/_models/note_nlp.yml create mode 100644 models/omop/_models/observation.yml create mode 100644 models/omop/_models/observation_period.yml create mode 100644 models/omop/_models/payer_plan_period.yml create mode 100644 models/omop/_models/person.yml create mode 100644 models/omop/_models/procedure_occurrence.yml create mode 100644 models/omop/_models/provider.yml create mode 100644 models/omop/_models/relationship.yml create mode 100644 models/omop/_models/source_to_concept_map.yml create mode 100644 models/omop/_models/specimen.yml create mode 100644 models/omop/_models/visit_detail.yml create mode 100644 models/omop/_models/visit_occurrence.yml create mode 100644 models/omop/_models/vocabulary.yml diff --git a/models/omop/_models/care_site.yml b/models/omop/_models/care_site.yml new file mode 100644 index 0000000..e1fa4f5 --- /dev/null +++ b/models/omop/_models/care_site.yml @@ -0,0 +1,39 @@ +models: + - name: care_site + description: The CARE_SITE table contains a list of uniquely identifiedinstitutional (physical or + organizational) units where healthcaredelivery is practiced (offices, wards, hospitals, clinics, + etc.). + columns: + - name: care_site_id + description: '' + data_type: integer + tests: + - not_null + - unique + - name: care_site_name + description: The name of the care_site as it appears in the source data + data_type: varchar(255) + - name: place_of_service_concept_id + description: This is a high-level way of characterizing a Care Site. Typically,however, Care Sites + can provide care in multiple settings (inpatient,outpatient, etc.) and this granularity should + be reflected in the visit. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: location_id + description: The location_id from the LOCATION table representing the physicallocation of the + care_site. + data_type: integer + tests: + - relationships: + to: ref('location') + field: location_id + - name: care_site_source_value + description: The identifier of the care_site as it appears in the source data. Thiscould be an + identifier separate from the name of the care_site. + data_type: varchar(50) + - name: place_of_service_source_value + description: '' + data_type: varchar(50) diff --git a/models/omop/_models/cdm_source.yml b/models/omop/_models/cdm_source.yml new file mode 100644 index 0000000..fa9ffdf --- /dev/null +++ b/models/omop/_models/cdm_source.yml @@ -0,0 +1,56 @@ +models: + - name: cdm_source + description: The CDM_SOURCE table contains detail about the source database andthe process used to + transform the data into the OMOP Common DataModel. + columns: + - name: cdm_source_name + description: The name of the CDM instance. + data_type: varchar(255) + tests: + - not_null + - name: cdm_source_abbreviation + description: The abbreviation of the CDM instance. + data_type: varchar(25) + tests: + - not_null + - name: cdm_holder + description: The holder of the CDM instance. + data_type: varchar(255) + tests: + - not_null + - name: source_description + description: The description of the CDM instance. + data_type: varchar(MAX) + - name: source_documentation_reference + description: '' + data_type: varchar(255) + - name: cdm_etl_reference + description: '' + data_type: varchar(255) + - name: source_release_date + description: The date the data was extracted from the source system. In some systemsthat is the + same as the date the ETL was run. Typically the latest evendate in the source is on the source_release_date. + data_type: date + tests: + - not_null + - name: cdm_release_date + description: The date the ETL script was completed. Typically this is after thesource_release_date. + data_type: date + tests: + - not_null + - name: cdm_version + description: Version of the OMOP CDM used as string. e.g. v5.4 + data_type: varchar(10) + - name: cdm_version_concept_id + description: The Concept Id representing the version of the CDM. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: vocabulary_version + description: Version of the OMOP standardised vocabularies loaded + data_type: varchar(20) + tests: + - not_null diff --git a/models/omop/_models/cohort.yml b/models/omop/_models/cohort.yml new file mode 100644 index 0000000..e0a5c2c --- /dev/null +++ b/models/omop/_models/cohort.yml @@ -0,0 +1,29 @@ +models: + - name: cohort + description: The subject of a cohort can have multiple, discrete records in thecohort table per cohort_definition_id, + subject_id, and non-overlappingtime periods. The definition of the cohort is contained within theCOHORT_DEFINITION + table. It is listed as part of the RESULTS schemabecause it is a table that users of the database + as well as tools suchas ATLAS need to be able to write to. The CDM and Vocabulary tables areall + read-only so it is suggested that the COHORT and COHORT_DEFINTIONtables are kept in a separate schema + to alleviate confusion. + columns: + - name: cohort_definition_id + description: '' + data_type: integer + tests: + - not_null + - name: subject_id + description: '' + data_type: integer + tests: + - not_null + - name: cohort_start_date + description: '' + data_type: date + tests: + - not_null + - name: cohort_end_date + description: '' + data_type: date + tests: + - not_null diff --git a/models/omop/_models/cohort_definition.yml b/models/omop/_models/cohort_definition.yml new file mode 100644 index 0000000..c6f3304 --- /dev/null +++ b/models/omop/_models/cohort_definition.yml @@ -0,0 +1,46 @@ +models: + - name: cohort_definition + description: The COHORT_DEFINITION table contains records defining a Cohortderived from the data through + the associated description and syntax andupon instantiation (execution of the algorithm) placed + into the COHORTtable. Cohorts are a set of subjects that satisfy a given combination ofinclusion + criteria for a duration of time. The COHORT_DEFINITION tableprovides a standardized structure for + maintaining the rules governingthe inclusion of a subject into a cohort, and can store operationalprogramming + code to instantiate the cohort within the OMOP Common DataModel. + columns: + - name: cohort_definition_id + description: This is the identifier given to the cohort, usually by the ATLASapplication + data_type: integer + tests: + - not_null + - name: cohort_definition_name + description: A short description of the cohort + data_type: varchar(255) + tests: + - not_null + - name: cohort_definition_description + description: A complete description of the cohort. + data_type: varchar(MAX) + - name: definition_type_concept_id + description: Type defining what kind of Cohort Definition the record represents andhow the syntax + may be executed. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: cohort_definition_syntax + description: Syntax or code to operationalize the Cohort Definition. + data_type: varchar(MAX) + - name: subject_concept_id + description: This field contains a Concept that represents the domain of the subjectsthat are + members of the cohort (e.g., Person, Provider, Visit). + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: cohort_initiation_date + description: A date to indicate when the Cohort was initiated in the COHORT table. + data_type: date diff --git a/models/omop/_models/concept.yml b/models/omop/_models/concept.yml new file mode 100644 index 0000000..85b8ee6 --- /dev/null +++ b/models/omop/_models/concept.yml @@ -0,0 +1,82 @@ +models: + - name: concept + description: The Standardized Vocabularies contains records, or Concepts, thatuniquely identify each + fundamental unit of meaning used to expressclinical information in all domain tables of the CDM. + Concepts arederived from vocabularies, which represent clinical information across adomain (e.g. conditions, + drugs, procedures) through the use of codes andassociated descriptions. Some Concepts are designated + Standard Concepts,meaning these Concepts can be used as normative expressions of aclinical entity + within the OMOP Common Data Model and standardizedanalytics. Each Standard Concept belongs to one + Domain, which definesthe location where the Concept would be expected to occur within thedata tables + of the CDM. Concepts can represent broad categories(‘Cardiovascular disease’), detailed clinical + elements (‘Myocardialinfarction of the anterolateral wall’), or modifying characteristics andattributes + that define Concepts at various levels of detail (severity ofa disease, associated morphology, etc.). + Records in the StandardizedVocabularies tables are derived from national or internationalvocabularies + such as SNOMED-CT, RxNorm, and LOINC, or custom OMOPConcepts defined to cover various aspects of + observational dataanalysis. + columns: + - name: concept_id + description: A unique identifier for each Concept across all domains. + data_type: integer + tests: + - not_null + - unique + - name: concept_name + description: An unambiguous, meaningful and descriptive name for the Concept. + data_type: varchar(255) + tests: + - not_null + - name: domain_id + description: A foreign key to the DOMAINtable the Concept belongs to. + data_type: varchar(20) + tests: + - not_null + - relationships: + to: ref('domain') + field: domain_id + - name: vocabulary_id + description: A foreign key to the VOCABULARYtable indicating from which source the Concept has + been adapted. + data_type: varchar(20) + tests: + - not_null + - relationships: + to: ref('vocabulary') + field: vocabulary_id + - name: concept_class_id + description: The attribute or concept class of the Concept. Examples are ‘ClinicalDrug’, ‘Ingredient’, + ‘Clinical Finding’ etc. + data_type: varchar(20) + tests: + - not_null + - relationships: + to: ref('concept_class') + field: concept_class_id + - name: standard_concept + description: This flag determines where a Concept is a Standard Concept, i.e. is usedin the data, + a Classification Concept, or a non-standard Source Concept.The allowable values are ‘S’ (Standard + Concept) and ‘C’ (ClassificationConcept), otherwise the content is NULL. + data_type: varchar(1) + - name: concept_code + description: The concept code represents the identifier of the Concept in the sourcevocabulary, + such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note thatconcept codes are not unique across + vocabularies. + data_type: varchar(50) + tests: + - not_null + - name: valid_start_date + description: The date when the Concept was first recorded. The default value is1-Jan-1970, meaning, + the Concept has no (known) date of inception. + data_type: date + tests: + - not_null + - name: valid_end_date + description: The date when the Concept became invalid because it was deleted orsuperseded (updated) + by a new concept. The default value is 31-Dec-2099,meaning, the Concept is valid until it becomes + deprecated. + data_type: date + tests: + - not_null + - name: invalid_reason + description: Reason the Concept was invalidated. Possible values are D (deleted), U(replaced with + an update) or NULL when valid_end_date has the defaultvalue. + data_type: varchar(1) diff --git a/models/omop/_models/concept_ancestor.yml b/models/omop/_models/concept_ancestor.yml new file mode 100644 index 0000000..dcabd0a --- /dev/null +++ b/models/omop/_models/concept_ancestor.yml @@ -0,0 +1,39 @@ +models: + - name: concept_ancestor + description: The CONCEPT_ANCESTOR table is designed to simplify observationalanalysis by providing + the complete hierarchical relationships betweenConcepts. Only direct parent-child relationships + between Concepts arestored in the CONCEPT_RELATIONSHIP table. To determine higher levelancestry + connections, all individual direct relationships would have tobe navigated at analysis time. The + CONCEPT_ANCESTOR table includesrecords for all parent-child relationships, as well asgrandparent-grandchild + relationships and those of any other level oflineage. Using the CONCEPT_ANCESTOR table allows for + querying for alldescendants of a hierarchical concept. For example, drug ingredients anddrug products + are all descendants of a drug class ancestor. + columns: + - name: ancestor_concept_id + description: The Concept Id for the higher-level concept that forms the ancestor inthe relationship. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: descendant_concept_id + description: The Concept Id for the lower-level concept that forms the descendant inthe relationship. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: min_levels_of_separation + description: The minimum separation in number of levels of hierarchy between ancestorand descendant + concepts. This is an attribute that is used to simplifyhierarchic analysis. + data_type: integer + tests: + - not_null + - name: max_levels_of_separation + description: The maximum separation in number of levels of hierarchy between ancestorand descendant + concepts. This is an attribute that is used to simplifyhierarchic analysis. + data_type: integer + tests: + - not_null diff --git a/models/omop/_models/concept_class.yml b/models/omop/_models/concept_class.yml new file mode 100644 index 0000000..a02af50 --- /dev/null +++ b/models/omop/_models/concept_class.yml @@ -0,0 +1,28 @@ +models: + - name: concept_class + description: The CONCEPT_CLASS table includes semantic categories that referencethe source structure + of each Vocabulary. Concept Classes representso-called horizontal (e.g. MedDRA, RxNorm) or vertical + levels(e.g. SNOMED) of the vocabulary structure. Vocabularies without anyConcept Classes, such as + HCPCS, use the vocabulary_id as the ConceptClass. This reference table is populated with a single + record for eachConcept Class, which includes a Concept Class ID and a fully specifiedConcept Class + name. + columns: + - name: concept_class_id + description: A unique key for each class. + data_type: varchar(20) + tests: + - not_null + - unique + - name: concept_class_name + description: The name describing the Concept Class, e.g. Clinical Finding,Ingredient, etc. + data_type: varchar(255) + tests: + - not_null + - name: concept_class_concept_id + description: A Concept that represents the Concept Class. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/concept_relationship.yml b/models/omop/_models/concept_relationship.yml new file mode 100644 index 0000000..1ec4933 --- /dev/null +++ b/models/omop/_models/concept_relationship.yml @@ -0,0 +1,46 @@ +models: + - name: concept_relationship + description: The CONCEPT_RELATIONSHIP table contains records that definerelationships between any + two Concepts and the nature or type of therelationship. This table captures various types of relationships,including + hierarchical, associative, and other semantic connections,enabling comprehensive analysis and interpretation + of clinical concepts.Every kind of relationship is defined in the RELATIONSHIP table. + columns: + - name: concept_id_1 + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: concept_id_2 + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: relationship_id + description: The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see theVocabularyConventions. + for more information. + data_type: varchar(20) + tests: + - not_null + - relationships: + to: ref('relationship') + field: relationship_id + - name: valid_start_date + description: The date when the relationship is first recorded. + data_type: date + tests: + - not_null + - name: valid_end_date + description: The date when the relationship is invalidated. + data_type: date + tests: + - not_null + - name: invalid_reason + description: Reason the relationship was invalidated. Possible values are ‘D’(deleted), ‘U’ (updated) + or NULL. + data_type: varchar(1) diff --git a/models/omop/_models/concept_synonym.yml b/models/omop/_models/concept_synonym.yml new file mode 100644 index 0000000..4d7d81c --- /dev/null +++ b/models/omop/_models/concept_synonym.yml @@ -0,0 +1,25 @@ +models: + - name: concept_synonym + description: The CONCEPT_SYNONYM table is used to store alternate names anddescriptions for Concepts. + columns: + - name: concept_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: concept_synonym_name + description: '' + data_type: varchar(1000) + tests: + - not_null + - name: language_concept_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/condition_era.yml b/models/omop/_models/condition_era.yml new file mode 100644 index 0000000..9bd5ded --- /dev/null +++ b/models/omop/_models/condition_era.yml @@ -0,0 +1,47 @@ +models: + - name: condition_era + description: 'A Condition Era is defined as a span of time when the Person isassumed to have a given + condition. Similar to Drug Eras, Condition Erasare chronological periods of Condition Occurrence + and every ConditionOccurrence record should be part of a Condition Era. Combiningindividual Condition + Occurrences into a single Condition Era serves twopurposes:' + columns: + - name: condition_era_id + description: '' + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: condition_concept_id + description: The Concept Id representing the Condition. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: condition_concept_id <> 0 + to_condition: domain_id = 'Condition' + - name: condition_era_start_date + description: The start date for the Condition Era constructed from the individualinstances of + Condition Occurrences. It is the start date of the veryfirst chronologically recorded instance + of the condition with at least31 days since any prior record of the same Condition. + data_type: date + tests: + - not_null + - name: condition_era_end_date + description: The end date for the Condition Era constructed from the individualinstances of Condition + Occurrences. It is the end date of the finalcontinuously recorded instance of the Condition. + data_type: date + tests: + - not_null + - name: condition_occurrence_count + description: The number of individual Condition Occurrences used to construct thecondition era. + data_type: integer diff --git a/models/omop/_models/condition_occurrence.yml b/models/omop/_models/condition_occurrence.yml new file mode 100644 index 0000000..a3a78e8 --- /dev/null +++ b/models/omop/_models/condition_occurrence.yml @@ -0,0 +1,118 @@ +models: + - name: condition_occurrence + description: This table contains records of Events of a Person suggesting thepresence of a disease + or medical condition stated as a diagnosis, asign, or a symptom, which is either observed by a Provider + or reportedby the patient. + columns: + - name: condition_occurrence_id + description: The unique key given to a condition record for a person. Refer to theETL for how + duplicate conditions during the same visit were handled. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The PERSON_ID of the PERSON for whom the condition is recorded. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: condition_concept_id + description: The CONDITION_CONCEPT_ID field is recommended for primary use inanalyses, and must + be used for network studies. This is the standardconcept mapped from the source value which + represents a condition + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: condition_concept_id <> 0 + to_condition: domain_id = 'Condition' + - name: condition_start_date + description: Use this date to determine the start date of the condition + data_type: date + tests: + - not_null + - name: condition_start_datetime + description: '' + data_type: datetime + - name: condition_end_date + description: Use this date to determine the end date of the condition + data_type: date + - name: condition_end_datetime + description: '' + data_type: datetime + - name: condition_type_concept_id + description: This field can be used to determine the provenance of the Conditionrecord, as in + whether the condition was from an EHR system, insuranceclaim, registry, or other sources. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: condition_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: condition_status_concept_id + description: This concept represents the point during the visit the diagnosis wasgiven (admitting + diagnosis, final diagnosis), whether the diagnosis wasdetermined due to laboratory findings, + if the diagnosis wasexclusionary, or if it was a preliminary diagnosis, among others. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: condition_status_concept_id <> 0 + to_condition: domain_id = 'Condition Status' + - name: stop_reason + description: The Stop Reason indicates why a Condition is no longer valid withrespect to the purpose + within the source data. Note that a Stop Reasondoes not necessarily imply that the condition + is no longer occurring. + data_type: varchar(20) + - name: provider_id + description: The provider associated with condition record, e.g. the provider whomade the diagnosis + or the provider who recorded the symptom. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: visit_occurrence_id + description: The visit during which the condition occurred. + data_type: integer + tests: + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id + - name: visit_detail_id + description: The VISIT_DETAIL record during which the condition occurred. Forexample, if the person + was in the ICU at the time of the diagnosis theVISIT_OCCURRENCE record would reflect the overall + hospital stay and theVISIT_DETAIL record would reflect the ICU stay during the hospitalvisit. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: condition_source_value + description: This field houses the verbatim value from the source data representingthe condition + that occurred. For example, this could be an ICD10 or Readcode. + data_type: varchar(50) + - name: condition_source_concept_id + description: This is the concept representing the condition source value and may notnecessarily + be standard. This field is discouraged from use in analysisbecause it is not required to contain + Standard Concepts that are usedacross the OHDSI community, and should only be used when StandardConcepts + do not adequately represent the source detail for the Conditionnecessary for a given analytic + use case. Consider usingCONDITION_CONCEPT_ID instead to enable standardized analytics that canbe + consistent across the network. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: condition_status_source_value + description: This field houses the verbatim value from the source data representingthe condition + status. + data_type: varchar(50) diff --git a/models/omop/_models/cost.yml b/models/omop/_models/cost.yml new file mode 100644 index 0000000..f991834 --- /dev/null +++ b/models/omop/_models/cost.yml @@ -0,0 +1,101 @@ +models: + - name: cost + description: The COST table captures records containing the cost of any medicalevent recorded in one + of the OMOP clinical event tables such asDRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, + VISIT_DETAIL,DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT. + columns: + - name: cost_id + description: '' + data_type: integer + tests: + - not_null + - unique + - name: cost_event_id + description: '' + data_type: integer + tests: + - not_null + - name: cost_domain_id + description: '' + data_type: varchar(20) + tests: + - not_null + - relationships: + to: ref('domain') + field: domain_id + - name: cost_type_concept_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: currency_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: total_charge + description: '' + data_type: float + - name: total_cost + description: '' + data_type: float + - name: total_paid + description: '' + data_type: float + - name: paid_by_payer + description: '' + data_type: float + - name: paid_by_patient + description: '' + data_type: float + - name: paid_patient_copay + description: '' + data_type: float + - name: paid_patient_coinsurance + description: '' + data_type: float + - name: paid_patient_deductible + description: '' + data_type: float + - name: paid_by_primary + description: '' + data_type: float + - name: paid_ingredient_cost + description: '' + data_type: float + - name: paid_dispensing_fee + description: '' + data_type: float + - name: payer_plan_period_id + description: '' + data_type: integer + - name: amount_allowed + description: '' + data_type: float + - name: revenue_code_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: revenue_code_source_value + description: Revenue codes are a method to charge for a class of procedures andconditions in the + U.S. hospital system. + data_type: varchar(50) + - name: drg_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: drg_source_value + description: Diagnosis Related Groups are US codes used to classify hospital casesinto one of + approximately 500 groups. + data_type: varchar(3) diff --git a/models/omop/_models/death.yml b/models/omop/_models/death.yml new file mode 100644 index 0000000..0c10b9b --- /dev/null +++ b/models/omop/_models/death.yml @@ -0,0 +1,50 @@ +models: + - name: death + description: 'The death domain contains the clinical event for how and when aPerson dies. A person + can have up to one record if the source systemcontains evidence about the Death, such as: Condition + in anadministrative claim, status of enrollment into a health plan, orexplicit record in EHR data.' + columns: + - name: person_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: death_date + description: The date the person was deceased. + data_type: date + tests: + - not_null + - name: death_datetime + description: '' + data_type: datetime + - name: death_type_concept_id + description: This is the provenance of the death record, i.e., where it came from. Itis possible + that an administrative claims database would source deathinformation from a government file + so do not assume the Death Type isthe same as the Visit Type, etc. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: death_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: cause_concept_id + description: This is the Standard Concept representing the Person’s cause of death,if available. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: cause_source_value + description: '' + data_type: varchar(50) + - name: cause_source_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/device_exposure.yml b/models/omop/_models/device_exposure.yml new file mode 100644 index 0000000..5bb2276 --- /dev/null +++ b/models/omop/_models/device_exposure.yml @@ -0,0 +1,136 @@ +models: + - name: device_exposure + description: The Device domain captures information about a person’s exposure to aforeign physical + object or instrument which is used for diagnostic ortherapeutic purposes through a mechanism beyond + chemical action. Devicesinclude implantable objects (e.g. pacemakers, stents, artificialjoints), + medical equipment and supplies (e.g. bandages, crutches,syringes), other instruments used in medical + procedures (e.g. sutures,defibrillators) and material used in clinical care (e.g. adhesives, bodymaterial, + dental material, surgical material). + columns: + - name: device_exposure_id + description: The unique key given to records a person’s exposure to a foreignphysical object or + instrument. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: device_concept_id + description: The DEVICE_CONCEPT_ID field is recommended for primary use in analyses,and must be + used for network studies. This is the standard conceptmapped from the source concept id which + represents a foreign object orinstrument the person was exposed to. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: device_concept_id <> 0 + to_condition: domain_id = 'Device' + - name: device_exposure_start_date + description: Use this date to determine the start date of the device record. + data_type: date + tests: + - not_null + - name: device_exposure_start_datetime + description: '' + data_type: datetime + - name: device_exposure_end_date + description: The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure endedfor the patient, + if given. + data_type: date + - name: device_exposure_end_datetime + description: '' + data_type: datetime + - name: device_type_concept_id + description: You can use the TYPE_CONCEPT_ID to denote the provenance of the record,as in whether + the record is from administrative claims or EHR. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: device_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: unique_device_id + description: This is the Unique Device Identification (UDI-DI) number for devicesregulated by + the FDA, if given. + data_type: varchar(255) + - name: production_id + description: This is the Production Identifier (UDI-PI) portion of the Unique DeviceIdentification. + data_type: varchar(255) + - name: quantity + description: '' + data_type: integer + - name: provider_id + description: The Provider associated with device record, e.g. the provider who wrotethe prescription + or the provider who implanted the device. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: visit_occurrence_id + description: The Visit during which the device was prescribed or given. + data_type: integer + tests: + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id + - name: visit_detail_id + description: The Visit Detail during which the device was prescribed or given. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: device_source_value + description: This field houses the verbatim value from the source data representingthe device + exposure that occurred. For example, this could be an NDC orGemscript code. + data_type: varchar(50) + - name: device_source_concept_id + description: This is the concept representing the device source value and may notnecessarily be + standard. This field is discouraged from use in analysisbecause it is not required to contain + Standard Concepts that are usedacross the OHDSI community, and should only be used when StandardConcepts + do not adequately represent the source detail for the Devicenecessary for a given analytic use + case. Consider usingDEVICE_CONCEPT_ID instead to enable standardized analytics that can beconsistent + across the network. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: unit_concept_id + description: UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unitdomain that + best represents the unit as given in the source data. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: unit_concept_id <> 0 + to_condition: domain_id = 'Unit' + - name: unit_source_value + description: This field houses the verbatim value from the source data representingthe unit of + the Device. For example, blood transfusions are considereddevices and can be given in mL quantities. + data_type: varchar(50) + - name: unit_source_concept_id + description: This is the concept representing the UNIT_SOURCE_VALUE and may notnecessarily be + standard. This field is discouraged from use in analysisbecause it is not required to contain + Standard Concepts that are usedacross the OHDSI community, and should only be used when StandardConcepts + do not adequately represent the source detail for the Unitnecessary for a given analytic use + case. Consider using UNIT_CONCEPT_IDinstead to enable standardized analytics that can be consistent + acrossthe network. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/domain.yml b/models/omop/_models/domain.yml new file mode 100644 index 0000000..ce5429b --- /dev/null +++ b/models/omop/_models/domain.yml @@ -0,0 +1,28 @@ +models: + - name: domain + description: The DOMAIN table includes a list of OMOP-defined Domains to which theConcepts of the + Standardized Vocabularies can belong. A Domainrepresents a clinical definition whereby we assign + matching Concepts forthe standardized fields in the CDM tables. For example, the ConditionDomain + contains Concepts that describe a patient condition, and theseConcepts can only be used in the condition_concept_id + field of theCONDITION_OCCURRENCE and CONDITION_ERA tables. This reference table ispopulated with + a single record for each Domain, including a Domain IDand a descriptive name for every Domain. + columns: + - name: domain_id + description: A unique key for each domain. + data_type: varchar(20) + tests: + - not_null + - unique + - name: domain_name + description: The name describing the Domain, e.g. Condition, Procedure, Measurementetc. + data_type: varchar(255) + tests: + - not_null + - name: domain_concept_id + description: A Concept representing the Domain Concept the DOMAIN record belongs to. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/dose_era.yml b/models/omop/_models/dose_era.yml new file mode 100644 index 0000000..82d39a2 --- /dev/null +++ b/models/omop/_models/dose_era.yml @@ -0,0 +1,55 @@ +models: + - name: dose_era + description: A Dose Era is defined as a span of time when the Person is assumed tobe exposed to a + constant dose of a specific active ingredient. + columns: + - name: dose_era_id + description: '' + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: drug_concept_id + description: The Concept Id representing the specific drug ingredient. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: drug_concept_id <> 0 + to_condition: domain_id = 'Drug' + - name: unit_concept_id + description: The Concept Id representing the unit of the specific drug ingredient. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: unit_concept_id <> 0 + to_condition: domain_id = 'Unit' + - name: dose_value + description: The numeric value of the dosage of the drug_ingredient. + data_type: float + tests: + - not_null + - name: dose_era_start_date + description: The date the Person started on the specific dosage, with at least 31days since any + prior exposure. + data_type: date + tests: + - not_null + - name: dose_era_end_date + description: '' + data_type: date + tests: + - not_null diff --git a/models/omop/_models/drug_era.yml b/models/omop/_models/drug_era.yml new file mode 100644 index 0000000..64f7c33 --- /dev/null +++ b/models/omop/_models/drug_era.yml @@ -0,0 +1,49 @@ +models: + - name: drug_era + description: 'A Drug Era is defined as a span of time when the Person is assumed tobe exposed to a + particular active ingredient. A Drug Era is not the sameas a Drug Exposure: Exposures are individual + records corresponding tothe source when Drug was delivered to the Person, while successiveperiods + of Drug Exposures are combined under certain rules to producecontinuous Drug Eras. Every record + in the DRUG_EXPOSURE table should bepart of a drug era based on the dates of exposure.' + columns: + - name: drug_era_id + description: '' + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: drug_concept_id + description: The drug_concept_id should conform to the concept class ‘ingredient’ asthe drug_era + is an era of time where a person is exposed to a particulardrug ingredient. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: drug_concept_id <> 0 + to_condition: domain_id = 'Drug' + - name: drug_era_start_date + description: '' + data_type: date + tests: + - not_null + - name: drug_era_end_date + description: '' + data_type: date + tests: + - not_null + - name: drug_exposure_count + description: The count of grouped DRUG_EXPOSURE records that were included in theDRUG_ERA row + data_type: integer + - name: gap_days + description: '' + data_type: integer diff --git a/models/omop/_models/drug_exposure.yml b/models/omop/_models/drug_exposure.yml new file mode 100644 index 0000000..dd31fca --- /dev/null +++ b/models/omop/_models/drug_exposure.yml @@ -0,0 +1,147 @@ +models: + - name: drug_exposure + description: This table captures records about the exposure to a Drug ingested orotherwise introduced + into the body. A Drug is a biochemical substanceformulated in such a way that when administered + to a Person it willexert a certain biochemical effect on the metabolism. Drugs includeprescription + and over-the-counter medicines, vaccines, andlarge-molecule biologic therapies. Radiological devices + ingested orapplied locally do not count as Drugs. + columns: + - name: drug_exposure_id + description: The unique key given to records of drug dispensings or administrationsfor a person. + Refer to the ETL for how duplicate drugs during the samevisit were handled. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The PERSON_ID of the PERSON for whom the drug dispensing oradministration is recorded. + This may be a system generated code. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: drug_concept_id + description: The DRUG_CONCEPT_ID field is recommended for primary use in analyses,and must be + used for network studies. This is the standard conceptmapped from the source concept id which + represents a drug product ormolecule otherwise introduced to the body. The drug concepts can + have avarying degree of information about drug strength and dose. Thisinformation is relevant + in the context of quantity and administrationinformation in the subsequent fields plus strength + information from theDRUG_STRENGTH table, provided as part of the standard vocabularydownload. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: drug_concept_id <> 0 + to_condition: domain_id = 'Drug' + - name: drug_exposure_start_date + description: Use this date to determine the start date of the drug record. + data_type: date + tests: + - not_null + - name: drug_exposure_start_datetime + description: '' + data_type: datetime + - name: drug_exposure_end_date + description: The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended forthe patient. + data_type: date + tests: + - not_null + - name: drug_exposure_end_datetime + description: '' + data_type: datetime + - name: verbatim_end_date + description: This is the end date of the drug exposure as it appears in the sourcedata, if it + is given + data_type: date + - name: drug_type_concept_id + description: You can use the TYPE_CONCEPT_ID to delineate between prescriptionswritten vs. prescriptions + dispensed vs. medication historyvs. patient-reported exposure, etc. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: drug_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: stop_reason + description: The reason a person stopped a medication as it is represented in thesource. Reasons + include regimen completed, changed, removed, etc. Thisfield will be retired in v6.0. + data_type: varchar(20) + - name: refills + description: This is only filled in when the record is coming from a prescriptionwritten this + field is meant to represent intended refills at time of theprescription. + data_type: integer + - name: quantity + description: '' + data_type: float + - name: days_supply + description: '' + data_type: integer + - name: sig + description: This is the verbatim instruction for the drug as written by theprovider. + data_type: varchar(MAX) + - name: route_concept_id + description: '' + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: route_concept_id <> 0 + to_condition: domain_id = 'Route' + - name: lot_number + description: '' + data_type: varchar(50) + - name: provider_id + description: The Provider associated with drug record, e.g. the provider who wrotethe prescription + or the provider who administered the drug. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: visit_occurrence_id + description: The Visit during which the drug was prescribed, administered ordispensed. + data_type: integer + tests: + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id + - name: visit_detail_id + description: The VISIT_DETAIL record during which the drug exposure occurred. Forexample, if the + person was in the ICU at the time of the drugadministration the VISIT_OCCURRENCE record would + reflect the overallhospital stay and the VISIT_DETAIL record would reflect the ICU stayduring + the hospital visit. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: drug_source_value + description: This field houses the verbatim value from the source data representingthe drug exposure + that occurred. For example, this could be an NDC orGemscript code. + data_type: varchar(50) + - name: drug_source_concept_id + description: This is the concept representing the drug source value and may notnecessarily be + standard. This field is discouraged from use in analysisbecause it is not required to contain + Standard Concepts that are usedacross the OHDSI community, and should only be used when StandardConcepts + do not adequately represent the source detail for the Drugnecessary for a given analytic use + case. Consider using DRUG_CONCEPT_IDinstead to enable standardized analytics that can be consistent + acrossthe network. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: route_source_value + description: This field houses the verbatim value from the source data representingthe drug route. + data_type: varchar(50) + - name: dose_unit_source_value + description: This field houses the verbatim value from the source data representingthe dose unit + of the drug given. + data_type: varchar(50) diff --git a/models/omop/_models/drug_strength.yml b/models/omop/_models/drug_strength.yml new file mode 100644 index 0000000..869d53f --- /dev/null +++ b/models/omop/_models/drug_strength.yml @@ -0,0 +1,72 @@ +models: + - name: drug_strength + description: The DRUG_STRENGTH table contains structured content about the amountor concentration + and associated units of a specific ingredient containedwithin a particular drug product. This table + is supplemental informationto support standardized analysis of drug utilization. + columns: + - name: drug_concept_id + description: The Concept representing the Branded Drug or Clinical Drug Product. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: ingredient_concept_id + description: The Concept representing the active ingredient contained within the drugproduct. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: amount_value + description: The numeric value or the amount of active ingredient contained withinthe drug product. + data_type: float + - name: amount_unit_concept_id + description: The Concept representing the Unit of measure for the amount of activeingredient contained + within the drug product. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: numerator_value + description: The concentration of the active ingredient contained within the drugproduct. + data_type: float + - name: numerator_unit_concept_id + description: The Concept representing the Unit of measure for the concentration ofactive ingredient. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: denominator_value + description: The amount of total liquid (or other divisible product, such asointment, gel, spray, + etc.). + data_type: float + - name: denominator_unit_concept_id + description: The Concept representing the denominator unit for the concentration ofactive ingredient. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: box_size + description: The number of units of Clinical Branded Drug or Quantified Clinical orBranded Drug + contained in a box as dispensed to the patient. + data_type: integer + - name: valid_start_date + description: The date when the Concept was first recorded. The default value is1-Jan-1970. + data_type: date + tests: + - not_null + - name: valid_end_date + description: The date when then Concept became invalid. + data_type: date + tests: + - not_null + - name: invalid_reason + description: Reason the concept was invalidated. Possible values are D (deleted), U(replaced with + an update) or NULL when valid_end_date has the defaultvalue. + data_type: varchar(1) diff --git a/models/omop/_models/episode.yml b/models/omop/_models/episode.yml new file mode 100644 index 0000000..9a439c3 --- /dev/null +++ b/models/omop/_models/episode.yml @@ -0,0 +1,98 @@ +models: + - name: episode + description: + The EPISODE table aggregates lower-level clinical events(VISIT_OCCURRENCE, DRUG_EXPOSURE, + PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE)into a higher-level abstraction representing clinically and + analyticallyrelevant disease phases,outcomes and treatments. The EPISODE_EVENT tableconnects qualifying + clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE,PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate + EPISODE entry.For example cancers including their development over time, theirtreatment, and final + resolution. + columns: + - name: episode_id + description: A unique identifier for each Episode. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The PERSON_ID of the PERSON for whom the episode is recorded. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: episode_concept_id + description: + The EPISODE_CONCEPT_ID represents the kind abstraction related to thedisease phase, + outcome or treatment. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: episode_concept_id <> 0 + to_condition: domain_id = 'Episode' + - name: episode_start_date + description: The date when the Episode beings. + data_type: date + tests: + - not_null + - name: episode_start_datetime + description: The date and time when the Episode begins. + data_type: datetime + - name: episode_end_date + description: The date when the instance of the Episode is considered to have ended. + data_type: date + - name: episode_end_datetime + description: The date when the instance of the Episode is considered to have ended. + data_type: datetime + - name: episode_parent_id + description: + Use this field to find the Episode that subsumes the given Episoderecord. This is + used in the case that an Episode are nested into eachother. + data_type: integer + - name: episode_number + description: + For sequences of episodes, this is used to indicate the order theepisodes occurred. + For example, lines of treatment could be indicatedhere. + data_type: integer + - name: episode_object_concept_id + description: + A Standard Concept representing the disease phase, outcome, or otherabstraction of + which the episode consists. For example, if theEPISODE_CONCEPT_ID is treatmentregimen then the + EPISODE_OBJECT_CONCEPT_ID should contain thechemotherapy regimen concept, like Afatinibmonotherapy. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: episode_object_concept_id <> 0 + to_condition: domain_id = 'Procedure, Regimen' + - name: episode_type_concept_id + description: + This field can be used to determine the provenance of the Episoderecord, as in whether + the episode was from an EHR system, insuranceclaim, registry, or other sources. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: episode_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: episode_source_value + description: + The source code for the Episode as it appears in the source data. Thiscode is mapped + to a Standard Condition Concept in the StandardizedVocabularies and the original code is stored + here for reference. + data_type: varchar(50) + - name: episode_source_concept_id + description: A foreign key to a Episode Concept that refers to the code used in thesource. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/episode_event.yml b/models/omop/_models/episode_event.yml new file mode 100644 index 0000000..81b8335 --- /dev/null +++ b/models/omop/_models/episode_event.yml @@ -0,0 +1,32 @@ +models: + - name: episode_event + description: The EPISODE_EVENT table connects qualifying clinical events (such asCONDITION_OCCURRENCE, + DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT)to the appropriate EPISODE entry. For example, + linking the preciselocation of the metastasis (cancer modifier in MEASUREMENT) to thedisease episode. + columns: + - name: episode_id + description: Use this field to link the EPISODE_EVENT record to its EPISODE. + data_type: integer + tests: + - not_null + - relationships: + to: ref('episode') + field: episode_id + - name: event_id + description: This field is the primary key of the linked record in the database. Forexample, if + the Episode Event is a Condition Occurrence, then theCONDITION_OCCURRENCE_ID of the linked record + goes in this field. + data_type: integer + tests: + - not_null + - name: episode_event_field_concept_id + description: This field is the CONCEPT_ID that identifies which table the primary keyof the linked + record came from. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: episode_event_field_concept_id <> 0 + to_condition: domain_id = 'Metadata' diff --git a/models/omop/_models/fact_relationship.yml b/models/omop/_models/fact_relationship.yml new file mode 100644 index 0000000..d0f1ed2 --- /dev/null +++ b/models/omop/_models/fact_relationship.yml @@ -0,0 +1,44 @@ +models: + - name: fact_relationship + description: 'The FACT_RELATIONSHIP table contains records about the relationshipsbetween facts stored + as records in any table of the CDM. Relationshipscan be defined between facts from the same domain, + or different domains.Examples of Fact Relationships include: Personrelationships (parent-child), + care site relationships (hierarchicalorganizational structure of facilities within a health system),indication + relationship (between drug exposures and associatedconditions), usage relationships (of devices + during the course of anassociated procedure), or facts derived from one another (measurementsderived + from an associated specimen).' + columns: + - name: domain_concept_id_1 + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: fact_id_1 + description: '' + data_type: integer + tests: + - not_null + - name: domain_concept_id_2 + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: fact_id_2 + description: '' + data_type: integer + tests: + - not_null + - name: relationship_concept_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/location.yml b/models/omop/_models/location.yml new file mode 100644 index 0000000..50ed15d --- /dev/null +++ b/models/omop/_models/location.yml @@ -0,0 +1,48 @@ +models: + - name: location + description: The LOCATION table represents a generic way to capture physicallocation or address information + of Persons and Care Sites. + columns: + - name: location_id + description: The unique key given to a unique Location. + data_type: integer + tests: + - not_null + - unique + - name: address_1 + description: This is the first line of the address. + data_type: varchar(50) + - name: address_2 + description: This is the second line of the address + data_type: varchar(50) + - name: city + description: '' + data_type: varchar(50) + - name: state + description: '' + data_type: varchar(2) + - name: zip + description: '' + data_type: varchar(9) + - name: county + description: '' + data_type: varchar(20) + - name: location_source_value + description: '' + data_type: varchar(50) + - name: country_concept_id + description: The Concept Id representing the country. Values should conform to the Geographydomain. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: country_source_value + description: The name of the country. + data_type: varchar(80) + - name: latitude + description: '' + data_type: float + - name: longitude + description: '' + data_type: float diff --git a/models/omop/_models/measurement.yml b/models/omop/_models/measurement.yml new file mode 100644 index 0000000..adb0b48 --- /dev/null +++ b/models/omop/_models/measurement.yml @@ -0,0 +1,178 @@ +models: + - name: measurement + description: The MEASUREMENT table contains records of Measurements,i.e. structured values (numerical + or categorical) obtained throughsystematic and standardized examination or testing of a Person orPerson’s + sample. The MEASUREMENT table contains both orders and resultsof such Measurements as laboratory + tests, vital signs, quantitativefindings from pathology reports, etc. Measurements are stored asattribute + value pairs, with the attribute as the Measurement Concept andthe value representing the result. + The value can be a Concept (stored inVALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with + a Unit(UNIT_CONCEPT_ID). The Procedure for obtaining the sample is housed inthe PROCEDURE_OCCURRENCE + table, though it is unnecessary to create aPROCEDURE_OCCURRENCE record for each measurement if one + does not existin the source data. Measurements differ from Observations in that theyrequire a standardized + test or some other activity to generate aquantitative or qualitative result. If there is no result, + it is assumedthat the lab test was conducted but the result was not captured. + columns: + - name: measurement_id + description: The unique key given to a Measurement record for a Person. Refer to theETL for how + duplicate Measurements during the same Visit were handled. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The PERSON_ID of the Person for whom the Measurement is recorded. Thismay be a system + generated code. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: measurement_concept_id + description: The MEASUREMENT_CONCEPT_ID field is recommended for primary use inanalyses, and must + be used for network studies. This is the standardconcept mapped from the source value which + represents a measurement. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: measurement_concept_id <> 0 + to_condition: domain_id = 'Measurement' + - name: measurement_date + description: Use this date to determine the date of the measurement. + data_type: date + tests: + - not_null + - name: measurement_datetime + description: '' + data_type: datetime + - name: measurement_time + description: '' + data_type: varchar(10) + - name: measurement_type_concept_id + description: This field can be used to determine the provenance of the Measurementrecord, as in + whether the measurement was from an EHR system, insuranceclaim, registry, or other sources. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: measurement_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: operator_concept_id + description: The meaning of Concept 4172703for ‘=’ is identical to omission of a OPERATOR_CONCEPT_ID + value. Sincethe use of this field is rare, it’s important when devising analyses tonot to forget + testing for the content of this field for values differentfrom =. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: value_as_number + description: This is the numerical value of the Result of the Measurement, ifavailable. Note that + measurements such as blood pressures will be splitinto their component parts i.e. one record + for systolic, one record fordiastolic. + data_type: float + - name: value_as_concept_id + description: If the raw data gives a categorial result for measurements those valuesare captured + and mapped to standard concepts in the ‘Meas Value’ domain. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: unit_concept_id + description: At present, there isn’t a prescribed unit for individual measurements,such as Hemoglobin + A1C, meaning it’s not obligatory to express thesemeasurements as a percentage. UNIT_SOURCE_VALUES + should be linked to aStandard Concept within the Unit domain that most accurately reflectsthe + unit provided in the source data. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: unit_concept_id <> 0 + to_condition: domain_id = 'Unit' + - name: range_low + description: Ranges have the same unit as the VALUE_AS_NUMBER. These ranges areprovided by the + source and should remain NULL if not given. + data_type: float + - name: range_high + description: Ranges have the same unit as the VALUE_AS_NUMBER. These ranges areprovided by the + source and should remain NULL if not given. + data_type: float + - name: provider_id + description: The provider associated with measurement record, e.g. the provider whoordered the + test or the provider who recorded the result. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: visit_occurrence_id + description: The visit during which the Measurement occurred. + data_type: integer + tests: + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id + - name: visit_detail_id + description: The VISIT_DETAIL record during which the Measurement occurred. Forexample, if the + Person was in the ICU at the time the VISIT_OCCURRENCErecord would reflect the overall hospital + stay and the VISIT_DETAILrecord would reflect the ICU stay during the hospital visit. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: measurement_source_value + description: This field contains the exact value from the source data that representsthe measurement + that occurred. + data_type: varchar(50) + - name: measurement_source_concept_id + description: This is the concept representing the MEASUREMENT_SOURCE_VALUE and maynot necessarily + be standard. This field is discouraged from use inanalysis because it is not required to contain + Standard Concepts thatare used across the OHDSI community, and should only be used whenStandard + Concepts do not adequately represent the source detail for theMeasurement necessary for a given + analytic use case. Consider usingMEASUREMENT_CONCEPT_ID instead to enable standardized analytics + that canbe consistent across the network. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: unit_source_value + description: This field contains the exact value from the source data that representsthe unit + of measurement used. + data_type: varchar(50) + - name: unit_source_concept_id + description: “This is the concept representing the UNIT_SOURCE_VALUE and may notnecessarily be + standard. This field is discouraged from use in analysisbecause it is not required to contain + Standard Concepts that are usedacross the OHDSI community, and should only be used when StandardConcepts + do not adequately represent the source detail for theMeasurement necessary for a given analytic + use case. Consider usingUNIT_CONCEPT_ID instead to enable standardized analytics that can beconsistent + across the network.” + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: value_source_value + description: This field houses the verbatim result value of the Measurement from thesource data + . + data_type: varchar(50) + - name: measurement_event_id + description: If the Measurement record is related to another record in the database,this field + is the primary key of the linked record. + data_type: integer + - name: meas_event_field_concept_id + description: If the Measurement record is related to another record in the database,this field + is the CONCEPT_ID that identifies which table the primary keyof the linked record came from. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/metadata.yml b/models/omop/_models/metadata.yml new file mode 100644 index 0000000..05f489e --- /dev/null +++ b/models/omop/_models/metadata.yml @@ -0,0 +1,53 @@ +models: + - name: metadata + description: The METADATA table contains metadata information about a dataset thathas been transformed + to the OMOP Common Data Model. + columns: + - name: metadata_id + description: The unique key given to a Metadata record. + data_type: integer + tests: + - not_null + - unique + - name: metadata_concept_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: metadata_type_concept_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: name + description: '' + data_type: varchar(250) + tests: + - not_null + - name: value_as_string + description: '' + data_type: varchar(250) + - name: value_as_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: value_as_number + description: This is the numerical value of the result of the Metadata, if applicableand available. + It is not expected that all Metadata will have numericresults, rather, this field is here to + house values should they exist. + data_type: float + - name: metadata_date + description: '' + data_type: date + - name: metadata_datetime + description: '' + data_type: datetime diff --git a/models/omop/_models/note.yml b/models/omop/_models/note.yml new file mode 100644 index 0000000..eb75148 --- /dev/null +++ b/models/omop/_models/note.yml @@ -0,0 +1,107 @@ +models: + - name: note + description: The NOTE table captures unstructured information that was recorded bya provider about + a patient in free text (in ASCII, or preferably in UTF8format) notes on a given date. The type of + note_text is CLOB orvarchar(MAX) depending on RDBMS. + columns: + - name: note_id + description: A unique identifier for each note. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: note_date + description: The date the note was recorded. + data_type: date + tests: + - not_null + - name: note_datetime + description: '' + data_type: datetime + - name: note_type_concept_id + description: The provenance of the note. Most likely this will be EHR. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: note_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: note_class_concept_id + description: A Standard Concept Id representing the HL7 LOINC Document TypeVocabulary classification + of the note. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: note_title + description: The title of the note. + data_type: varchar(250) + - name: note_text + description: The content of the note. + data_type: varchar(MAX) + tests: + - not_null + - name: encoding_concept_id + description: This is the Concept representing the character encoding type. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: language_concept_id + description: The language of the note. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: provider_id + description: The Provider who wrote the note. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: visit_occurrence_id + description: The Visit during which the note was written. + data_type: integer + tests: + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id + - name: visit_detail_id + description: The Visit Detail during which the note was written. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: note_source_value + description: '' + data_type: varchar(50) + - name: note_event_id + description: If the Note record is related to another record in the database, thisfield is the + primary key of the linked record. + data_type: integer + - name: note_event_field_concept_id + description: If the Note record is related to another record in the database, thisfield is the + CONCEPT_ID that identifies which table the primary key ofthe linked record came from. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/note_nlp.yml b/models/omop/_models/note_nlp.yml new file mode 100644 index 0000000..41a0cd4 --- /dev/null +++ b/models/omop/_models/note_nlp.yml @@ -0,0 +1,68 @@ +models: + - name: note_nlp + description: The NOTE_NLP table encodes all output of NLP on clinical notes. Eachrow represents a + single extracted term from a note. + columns: + - name: note_nlp_id + description: A unique identifier for the NLP record. + data_type: integer + tests: + - not_null + - unique + - name: note_id + description: This is the NOTE_ID for the NOTE record the NLP record is associated to. + data_type: integer + tests: + - not_null + - name: section_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: snippet + description: A small window of text surrounding the term + data_type: varchar(250) + - name: “offset” + description: Character offset of the extracted term in the input note + data_type: varchar(50) + - name: lexical_variant + description: Raw text extracted from the NLP tool. + data_type: varchar(250) + tests: + - not_null + - name: note_nlp_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: note_nlp_source_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: nlp_system + description: '' + data_type: varchar(250) + - name: nlp_date + description: The date of the note processing. + data_type: date + tests: + - not_null + - name: nlp_datetime + description: The date and time of the note processing. + data_type: datetime + - name: term_exists + description: '' + data_type: varchar(1) + - name: term_temporal + description: '' + data_type: varchar(50) + - name: term_modifiers + description: '' + data_type: varchar(2000) diff --git a/models/omop/_models/observation.yml b/models/omop/_models/observation.yml new file mode 100644 index 0000000..51be4fa --- /dev/null +++ b/models/omop/_models/observation.yml @@ -0,0 +1,157 @@ +models: + - name: observation + description: The OBSERVATION table captures clinical facts about a Person obtainedin the context of + examination, questioning or a procedure. Any data thatcannot be represented by any other domains, + such as social and lifestylefacts, medical history, family history, etc. are recorded here. + columns: + - name: observation_id + description: The unique key given to an Observation record for a Person. Refer to theETL for how + duplicate Observations during the same Visit were handled. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The PERSON_ID of the Person for whom the Observation is recorded. Thismay be a system + generated code. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: observation_concept_id + description: The OBSERVATION_CONCEPT_ID field is recommended for primary use inanalyses, and must + be used for network studies. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: observation_date + description: The date of when the Observation was obtained. Depending on what theObservation represents + this could be the date of a lab test, the date ofa survey, or the date a patient’s family history + was taken. + data_type: date + tests: + - not_null + - name: observation_datetime + description: '' + data_type: datetime + - name: observation_type_concept_id + description: This field can be used to determine the provenance of the Observationrecord, as in + whether the measurement was from an EHR system, insuranceclaim, registry, or other sources. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: observation_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: value_as_number + description: This is the numerical value of the Result of the Observation, ifapplicable and available. + It is not expected that all Observations willhave numeric results, rather, this field is here + to house values shouldthey exist. + data_type: float + - name: value_as_string + description: This is the categorical value of the Result of the Observation, ifapplicable and + available. + data_type: varchar(60) + - name: value_as_concept_id + description: It is possible that some records destined for the Observation table havetwo clinical + ideas represented in one source code. This is common withICD10 codes that describe a family + history of some Condition, forexample. In OMOP the Vocabulary breaks these two clinical ideas + into twocodes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes theVALUE_AS_CONCEPT_ID. + It is important when using the Observation table tokeep this possibility in mind and to examine + the VALUE_AS_CONCEPT_IDfield for relevant information. + data_type: Integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: qualifier_concept_id + description: This field contains all attributes specifying the clinical fact further,such as as + degrees, severities, drug-drug interaction alerts etc. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: unit_concept_id + description: There is currently no recommended unit for individual observationconcepts. UNIT_SOURCE_VALUES + should be mapped to a Standard Concept inthe Unit domain that best represents the unit as given + in the sourcedata. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: unit_concept_id <> 0 + to_condition: domain_id = 'Unit' + - name: provider_id + description: The provider associated with the observation record, e.g. the providerwho ordered + the test or the provider who recorded the result. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: visit_occurrence_id + description: The visit during which the Observation occurred. + data_type: integer + tests: + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id + - name: visit_detail_id + description: The VISIT_DETAIL record during which the Observation occurred. Forexample, if the + Person was in the ICU at the time the VISIT_OCCURRENCErecord would reflect the overall hospital + stay and the VISIT_DETAILrecord would reflect the ICU stay during the hospital visit. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: observation_source_value + description: This field houses the verbatim value from the source data representingthe Observation + that occurred. For example, this could be an ICD10 orRead code. + data_type: varchar(50) + - name: observation_source_concept_id + description: This is the concept representing the OBSERVATION_SOURCE_VALUE and maynot necessarily + be standard. This field is discouraged from use inanalysis because it is not required to contain + Standard Concepts thatare used across the OHDSI community, and should only be used whenStandard + Concepts do not adequately represent the source detail for theObservation necessary for a given + analytic use case. Consider usingOBSERVATION_CONCEPT_ID instead to enable standardized analytics + that canbe consistent across the network. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: unit_source_value + description: This field houses the verbatim value from the source data representingthe unit of + the Observation that occurred. + data_type: varchar(50) + - name: qualifier_source_value + description: This field houses the verbatim value from the source data representingthe qualifier + of the Observation that occurred. + data_type: varchar(50) + - name: value_source_value + description: This field houses the verbatim result value of the Observation from thesource data. + Do not get confused with the Observation_source_value whichcaptures source value of the observation + mapped toobservation_concept_id. This field is the observation result value fromthe source. + data_type: varchar(50) + - name: observation_event_id + description: If the Observation record is related to another record in the database,this field + is the primary key of the linked record. + data_type: integer + - name: obs_event_field_concept_id + description: If the Observation record is related to another record in the database,this field + is the CONCEPT_ID that identifies which table the primary keyof the linked record came from. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/observation_period.yml b/models/omop/_models/observation_period.yml new file mode 100644 index 0000000..e48d0ef --- /dev/null +++ b/models/omop/_models/observation_period.yml @@ -0,0 +1,44 @@ +models: + - name: observation_period + description: 'This table contains records which define spans of time during whichtwo conditions are + expected to hold: (i) Clinical Events that happenedto the Person are recorded in the Event tables, + and (ii) absence ofrecords indicate such Events did not occur during this span of time.' + columns: + - name: observation_period_id + description: A Person can have multiple discrete Observation Periods which areidentified by the + Observation_Period_Id. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The Person ID of the PERSON record for which the Observation Period isrecorded. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: observation_period_start_date + description: Use this date to determine the start date of the Observation Period. + data_type: date + tests: + - not_null + - name: observation_period_end_date + description: Use this date to determine the end date of the period for which we canassume that + all events for a Person are recorded. + data_type: date + tests: + - not_null + - name: period_type_concept_id + description: This field can be used to determine the provenance of the ObservationPeriod as in + whether the period was determined from an insuranceenrollment file, EHR healthcare encounters, + or other sources. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: period_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' diff --git a/models/omop/_models/payer_plan_period.yml b/models/omop/_models/payer_plan_period.yml new file mode 100644 index 0000000..6eaf0b9 --- /dev/null +++ b/models/omop/_models/payer_plan_period.yml @@ -0,0 +1,110 @@ +models: + - name: payer_plan_period + description: The PAYER_PLAN_PERIOD table captures details of the period of timethat a Person is continuously + enrolled under a specific health Planbenefit structure from a given Payer. Each Person receiving + healthcareis typically covered by a health benefit plan, which pays for (fully orpartially), or + directly provides, the care. These benefit plans areprovided by payers, such as health insurances + or state or governmentagencies. In each plan the details of the health benefits are definedfor the + Person or her family, and the health benefit Plan might changeover time typically with increasing + utilization (reaching certain costthresholds such as deductibles), plan availability and purchasingchoices + of the Person. The unique combinations of Payer organizations,health benefit Plans and time periods + in which they are valid for aPerson are recorded in this table. + columns: + - name: payer_plan_period_id + description: A unique identifier for each unique combination of a Person, Payer,Plan, and Period + of time. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The Person covered by the Plan. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: payer_plan_period_start_date + description: Start date of Plan coverage. + data_type: date + tests: + - not_null + - name: payer_plan_period_end_date + description: End date of Plan coverage. + data_type: date + tests: + - not_null + - name: payer_concept_id + description: This field represents the organization who reimburses the provider whichadministers + care to the Person. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: payer_source_value + description: This is the Payer as it appears in the source data. + data_type: varchar(50) + - name: payer_source_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: plan_concept_id + description: This field represents the specific health benefit Plan the Person isenrolled in. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: plan_source_value + description: This is the health benefit Plan of the Person as it appears in thesource data. + data_type: varchar(50) + - name: plan_source_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: sponsor_concept_id + description: This field represents the sponsor of the Plan who finances the Plan.This includes + self-insured, small group health plan and large grouphealth plan. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: sponsor_source_value + description: The Plan sponsor as it appears in the source data. + data_type: varchar(50) + - name: sponsor_source_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: family_source_value + description: The common identifier for all people (often a family) that covered bythe same policy. + data_type: varchar(50) + - name: stop_reason_concept_id + description: This field represents the reason the Person left the Plan, if known. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: stop_reason_source_value + description: The Plan stop reason as it appears in the source data. + data_type: varchar(50) + - name: stop_reason_source_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/person.yml b/models/omop/_models/person.yml new file mode 100644 index 0000000..93b734a --- /dev/null +++ b/models/omop/_models/person.yml @@ -0,0 +1,118 @@ +models: + - name: person + description: This table serves as the central identity management for all Personsin the database. + It contains records that uniquely identify each personor patient, and some demographic information. + columns: + - name: person_id + description: It is assumed that every person with a different unique identifier is infact a different + person and should be treated independently. + data_type: integer + tests: + - not_null + - unique + - name: gender_concept_id + description: This field is meant to capture the biological sex at birth of thePerson. This field + should not be used to study gender identity issues. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: gender_concept_id <> 0 + to_condition: domain_id = 'Gender' + - name: year_of_birth + description: Compute age using year_of_birth. + data_type: integer + tests: + - not_null + - name: month_of_birth + description: '' + data_type: integer + - name: day_of_birth + description: '' + data_type: integer + - name: birth_datetime + description: '' + data_type: datetime + - name: race_concept_id + description: This field captures race or ethnic background of the person. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: race_concept_id <> 0 + to_condition: domain_id = 'Race' + - name: ethnicity_concept_id + description: 'This field captures Ethnicity as defined by the Office of Management andBudget (OMB) + of the US Government: it distinguishes only between“Hispanic” and “Not Hispanic”. Races and + ethnic backgrounds are notstored here.' + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: ethnicity_concept_id <> 0 + to_condition: domain_id = 'Ethnicity' + - name: location_id + description: The location refers to the physical address of the person. This fieldshould capture + the last known location of the person. + data_type: integer + tests: + - relationships: + to: ref('location') + field: location_id + - name: provider_id + description: The Provider refers to the last known primary care provider (GeneralPractitioner). + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: care_site_id + description: The Care Site refers to where the Provider typically provides theprimary care. + data_type: integer + tests: + - relationships: + to: ref('care_site') + field: care_site_id + - name: person_source_value + description: Use this field to link back to persons in the source data. This istypically used + for error checking of ETL logic. + data_type: varchar(50) + - name: gender_source_value + description: This field is used to store the biological sex of the person from thesource data. + It is not intended for use in standard analytics but forreference only. + data_type: varchar(50) + - name: gender_source_concept_id + description: Due to the small number of options, this tends to be zero. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: race_source_value + description: This field is used to store the race of the person from the source data.It is not + intended for use in standard analytics but for reference only. + data_type: varchar(50) + - name: race_source_concept_id + description: Due to the small number of options, this tends to be zero. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: ethnicity_source_value + description: This field is used to store the ethnicity of the person from the sourcedata. It is + not intended for use in standard analytics but for referenceonly. + data_type: varchar(50) + - name: ethnicity_source_concept_id + description: Due to the small number of options, this tends to be zero. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/procedure_occurrence.yml b/models/omop/_models/procedure_occurrence.yml new file mode 100644 index 0000000..4d50ae4 --- /dev/null +++ b/models/omop/_models/procedure_occurrence.yml @@ -0,0 +1,113 @@ +models: + - name: procedure_occurrence + description: This table contains records of activities or processes ordered by, orcarried out by, + a healthcare provider on the patient with a diagnosticor therapeutic purpose. + columns: + - name: procedure_occurrence_id + description: The unique key given to a procedure record for a person. Refer to theETL for how + duplicate procedures during the same visit were handled. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The PERSON_ID of the PERSON for whom the procedure is recorded. This maybe a system + generated code. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: procedure_concept_id + description: The PROCEDURE_CONCEPT_ID field is recommended for primary use inanalyses, and must + be used for network studies. This is the standardconcept mapped from the source value which + represents a procedure + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: procedure_concept_id <> 0 + to_condition: domain_id = 'Procedure' + - name: procedure_date + description: Use this date to determine the date the procedure started. + data_type: date + tests: + - not_null + - name: procedure_datetime + description: '' + data_type: datetime + - name: procedure_end_date + description: Use this field to house the date that the procedure ended. + data_type: date + - name: procedure_end_datetime + description: Use this field to house the datetime that the procedure ended. + data_type: datetime + - name: procedure_type_concept_id + description: This field can be used to determine the provenance of the Procedurerecord, as in + whether the procedure was from an EHR system, insuranceclaim, registry, or other sources. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: procedure_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: modifier_concept_id + description: The modifiers are intended to give additional information about theprocedure but + as of now the vocabulary is under review. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: quantity + description: If the quantity value is omitted, a single procedure is assumed. + data_type: integer + - name: provider_id + description: The provider associated with the procedure record, e.g. the provider whoperformed + the Procedure. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: visit_occurrence_id + description: The visit during which the procedure occurred. + data_type: integer + tests: + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id + - name: visit_detail_id + description: The VISIT_DETAIL record during which the Procedure occurred. Forexample, if the Person + was in the ICU at the time of the Procedure theVISIT_OCCURRENCE record would reflect the overall + hospital stay and theVISIT_DETAIL record would reflect the ICU stay during the hospitalvisit. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: procedure_source_value + description: This field houses the verbatim value from the source data representingthe procedure + that occurred. For example, this could be an CPT4 or OPCS4code. + data_type: varchar(50) + - name: procedure_source_concept_id + description: This is the concept representing the procedure source value and may notnecessarily + be standard. This field is discouraged from use in analysisbecause it is not required to contain + Standard Concepts that are usedacross the OHDSI community, and should only be used when StandardConcepts + do not adequately represent the source detail for the Procedurenecessary for a given analytic + use case. Consider usingPROCEDURE_CONCEPT_ID instead to enable standardized analytics that canbe + consistent across the network. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: modifier_source_value + description: This field houses the verbatim value from the source data representingthe modifier + code for the procedure that occurred. + data_type: varchar(50) diff --git a/models/omop/_models/provider.yml b/models/omop/_models/provider.yml new file mode 100644 index 0000000..4246d5e --- /dev/null +++ b/models/omop/_models/provider.yml @@ -0,0 +1,81 @@ +models: + - name: provider + description: The PROVIDER table contains a list of uniquely identified healthcareproviders; duplication + is not allowed. These are individuals providinghands-on healthcare to patients, such as physicians, + nurses, midwives,physical therapists etc. + columns: + - name: provider_id + description: It is assumed that every provider with a different unique identifier isin fact a + different person and should be treated independently. + data_type: integer + tests: + - not_null + - unique + - name: provider_name + description: This field contains information that describes a healthcare provider. + data_type: varchar(255) + - name: npi + description: This is the National Provider Number issued to health care providers inthe US by + the Centers for Medicare and Medicaid Services (CMS). + data_type: varchar(20) + - name: dea + description: This is the identifier issued by the DEA, a US federal agency, thatallows a provider + to write prescriptions for controlled substances. + data_type: varchar(20) + - name: specialty_concept_id + description: This field either represents the most common specialty that occurs inthe data or + the most specific concept that represents all specialtieslisted, should the provider have more + than one. This includes physicianspecialties such as internal medicine, emergency medicine, + etc. andallied health professionals such as nurses, midwives, and pharmacists. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: care_site_id + description: This is the CARE_SITE_ID for the location that the provider primarilypractices in. + data_type: integer + tests: + - relationships: + to: ref('care_site') + field: care_site_id + - name: year_of_birth + description: '' + data_type: integer + - name: gender_concept_id + description: This field represents the recorded gender of the provider in the sourcedata. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: gender_concept_id <> 0 + to_condition: domain_id = 'Gender' + - name: provider_source_value + description: Use this field to link back to providers in the source data. This istypically used + for error checking of ETL logic. + data_type: varchar(50) + - name: specialty_source_value + description: This refers to the specific type of healthcare provider or field ofexpertise listed + in the source data, encompassing physician specialtieslike internal medicine, emergency medicine, + etc., as well as alliedhealth professionals such as nurses, midwives, and pharmacists. Itcovers + medical specialties like surgery, internal medicine, andradiology, while other services like + prosthetics, acupuncture, andphysical therapy fall under the domain of “Service.” + data_type: varchar(50) + - name: specialty_source_concept_id + description: This is often zero as many sites use proprietary codes to storephysician speciality. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: gender_source_value + description: This is provider’s gender as it appears in the source data. + data_type: varchar(50) + - name: gender_source_concept_id + description: This is often zero as many sites use proprietary codes to store providergender. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/relationship.yml b/models/omop/_models/relationship.yml new file mode 100644 index 0000000..bad246d --- /dev/null +++ b/models/omop/_models/relationship.yml @@ -0,0 +1,43 @@ +models: + - name: relationship + description: The RELATIONSHIP table provides a reference list of all types ofrelationships that can + be used to associate any two concepts in theCONCEPT_RELATIONSHP table. + columns: + - name: relationship_id + description: The type of relationship captured by the relationship record. + data_type: varchar(20) + tests: + - not_null + - unique + - name: relationship_name + description: '' + data_type: varchar(255) + tests: + - not_null + - name: is_hierarchical + description: Defines whether a relationship defines concepts into classes orhierarchies. Values + are 1 for hierarchical relationship or 0 if not. + data_type: varchar(1) + tests: + - not_null + - name: defines_ancestry + description: Defines whether a hierarchical relationship contributes to theconcept_ancestor table. + These are subsets of the hierarchicalrelationships. Valid values are 1 or 0. + data_type: varchar(1) + tests: + - not_null + - name: reverse_relationship_id + description: The identifier for the relationship used to define the reverserelationship between + two concepts. + data_type: varchar(20) + tests: + - not_null + - name: relationship_concept_id + description: A foreign key that refers to an identifier in the CONCEPTtable for the unique relationship + concept. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id diff --git a/models/omop/_models/source_to_concept_map.yml b/models/omop/_models/source_to_concept_map.yml new file mode 100644 index 0000000..5beb900 --- /dev/null +++ b/models/omop/_models/source_to_concept_map.yml @@ -0,0 +1,64 @@ +models: + - name: source_to_concept_map + description: The source to concept map table is recommended for use in ETLprocesses to maintain local + source codes which are not available asConcepts in the Standardized Vocabularies, and to establish + mappings foreach source code into a Standard Concept as target_concept_ids that canbe used to populate + the Common Data Model tables. TheSOURCE_TO_CONCEPT_MAP table is no longer populated with content + withinthe Standardized Vocabularies published to the OMOP community.There are OHDSI tools to help + you populate this table; Usagi and Perseus. You can read moreabout OMOP vocabulary mapping in TheBook + of OHDSI Chapter 6.3. + columns: + - name: source_code + description: The source code being translated into a Standard Concept. + data_type: varchar(50) + tests: + - not_null + - name: source_concept_id + description: A foreign key to the Source Concept that is being translated into aStandard Concept. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: source_vocabulary_id + description: A foreign key to the VOCABULARY table defining the vocabulary of thesource code that + is being translated to a Standard Concept. + data_type: varchar(20) + tests: + - not_null + - name: source_code_description + description: An optional description for the source code. This is included as aconvenience to + compare the description of the source code to the name ofthe concept. + data_type: varchar(255) + - name: target_concept_id + description: The target Concept to which the source code is being mapped. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: target_vocabulary_id + description: The Vocabulary of the target Concept. + data_type: varchar(20) + tests: + - not_null + - relationships: + to: ref('vocabulary') + field: vocabulary_id + - name: valid_start_date + description: The date when the mapping instance was first recorded. + data_type: date + tests: + - not_null + - name: valid_end_date + description: The date when the mapping instance became invalid because it was deletedor superseded + (updated) by a new relationship. Default value is31-Dec-2099. + data_type: date + tests: + - not_null + - name: invalid_reason + description: Reason the mapping instance was invalidated. Possible values are D(deleted), U (replaced + with an update) or NULL when valid_end_date hasthe default value. + data_type: varchar(1) diff --git a/models/omop/_models/specimen.yml b/models/omop/_models/specimen.yml new file mode 100644 index 0000000..f59cde3 --- /dev/null +++ b/models/omop/_models/specimen.yml @@ -0,0 +1,83 @@ +models: + - name: specimen + description: The specimen domain contains the records identifying biologicalsamples from a person. + columns: + - name: specimen_id + description: Unique identifier for each specimen. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: The person from whom the specimen is collected. + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: specimen_concept_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id + - name: specimen_type_concept_id + description: '' + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: specimen_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: specimen_date + description: The date the specimen was collected. + data_type: date + tests: + - not_null + - name: specimen_datetime + description: '' + data_type: datetime + - name: quantity + description: The amount of specimen collected from the person. + data_type: float + - name: unit_concept_id + description: The unit for the quantity of the specimen. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: anatomic_site_concept_id + description: This is the site on the body where the specimen is from. + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: disease_status_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: specimen_source_id + description: This is the identifier for the specimen from the source system. + data_type: varchar(50) + - name: specimen_source_value + description: '' + data_type: varchar(50) + - name: unit_source_value + description: '' + data_type: varchar(50) + - name: anatomic_site_source_value + description: '' + data_type: varchar(50) + - name: disease_status_source_value + description: '' + data_type: varchar(50) diff --git a/models/omop/_models/visit_detail.yml b/models/omop/_models/visit_detail.yml new file mode 100644 index 0000000..0a2d4e4 --- /dev/null +++ b/models/omop/_models/visit_detail.yml @@ -0,0 +1,151 @@ +models: + - name: visit_detail + description: The VISIT_DETAIL table is an optional table used to representsdetails of each record + in the parent VISIT_OCCURRENCE table. A goodexample of this would be the movement between units + in a hospital duringan inpatient stay or claim lines associated with a one insurance claim.For every + record in the VISIT_OCCURRENCE table there may be 0 or morerecords in the VISIT_DETAIL table with + a 1:n relationship where n may be0. The VISIT_DETAIL table is structurally very similar toVISIT_OCCURRENCE + table and belongs to the visit domain. + columns: + - name: visit_detail_id + description: Use this to identify unique interactions between a person and the healthcare system. + This identifier links across the other CDM event tables toassociate events with a visit detail. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: visit_detail_concept_id + description: This field contains a concept id representing the kind of visit detail,like inpatient + or outpatient. All concepts in this field should bestandard and belong to the Visit domain. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: visit_detail_concept_id <> 0 + to_condition: domain_id = 'Visit' + - name: visit_detail_start_date + description: This is the date of the start of the encounter. This may or may not beequal to the + date of the Visit the Visit Detail is associated with. + data_type: date + tests: + - not_null + - name: visit_detail_start_datetime + description: '' + data_type: datetime + - name: visit_detail_end_date + description: This the end date of the patient-provider interaction. If a Person isstill an inpatient + in the hospital at the time of the data extract anddoes not have a visit_end_date, then set + the visit_end_date to the dateof the data pull. + data_type: date + tests: + - not_null + - name: visit_detail_end_datetime + description: If a Person is still an inpatient in the hospital at the time of thedata extract + and does not have a visit_end_datetime, then set thevisit_end_datetime to the datetime of the + data pull. + data_type: datetime + - name: visit_detail_type_concept_id + description: Use this field to understand the provenance of the visit detail record,or where the + record comes from. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: visit_detail_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: provider_id + description: There will only be one provider per visit record andthe ETL document should clearly + state how they were chosen (attending,admitting, etc.). This is a typical reason for leveraging + theVISIT_DETAIL table as even though each VISIT_DETAIL record can only haveone provider, there + is no limit to the number of VISIT_DETAIL recordsthat can be associated to a VISIT_OCCURRENCE + record. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: care_site_id + description: This field provides information about the Care Site where the VisitDetail took place. + data_type: integer + tests: + - relationships: + to: ref('care_site') + field: care_site_id + - name: visit_detail_source_value + description: This field houses the verbatim value from the source data representingthe kind of + visit detail that took place (inpatient, outpatient,emergency, etc.) + data_type: varchar(50) + - name: visit_detail_source_concept_id + description: '' + data_type: Integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: admitted_from_concept_id + description: Use this field to determine where the patient was admitted from. Thisconcept is part + of the visit domain and can indicate if a patient wasadmitted to the hospital from a long-term + care facility, for example. + data_type: Integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: admitted_from_concept_id <> 0 + to_condition: domain_id = 'Visit' + - name: admitted_from_source_value + description: '' + data_type: varchar(50) + - name: discharged_to_source_value + description: '' + data_type: varchar(50) + - name: discharged_to_concept_id + description: Use this field to determine where the patient was discharged to after avisit. This + concept is part of the visit domain and can indicate if apatient was transferred to another + hospital or sent to a long-term carefacility, for example. It is assumed that a person is discharged + to hometherefore there is not a standard concept id for “home”. Use concept id= 0 when a person + is discharged to home. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: discharged_to_concept_id <> 0 + to_condition: domain_id = 'Visit' + - name: preceding_visit_detail_id + description: Use this field to find the visit detail that occurred for the personprior to the + given visit detail record. There could be a few days or afew years in between. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: parent_visit_detail_id + description: Use this field to find the visit detail that subsumes the given visitdetail record. + This is used in the case that a visit detail record needsto be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL + relationship. + data_type: integer + tests: + - relationships: + to: ref('visit_detail') + field: visit_detail_id + - name: visit_occurrence_id + description: Use this field to link the VISIT_DETAIL record to its VISIT_OCCURRENCE. + data_type: integer + tests: + - not_null + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id diff --git a/models/omop/_models/visit_occurrence.yml b/models/omop/_models/visit_occurrence.yml new file mode 100644 index 0000000..13b95ba --- /dev/null +++ b/models/omop/_models/visit_occurrence.yml @@ -0,0 +1,133 @@ +models: + - name: visit_occurrence + description: This table contains Events where Persons engage with the healthcaresystem for a duration + of time. They are often also called “Encounters”.Visits are defined by a configuration of circumstances + under which theyoccur, such as (i) whether the patient comes to a healthcareinstitution, the other + way around, or the interaction is remote, (ii)whether and what kind of trained medical staff is + delivering the serviceduring the Visit, and (iii) whether the Visit is transient or for alonger + period involving a stay in bed. + columns: + - name: visit_occurrence_id + description: Use this to identify unique interactions between a person and the healthcare system. + This identifier links across the other CDM event tables toassociate events with a visit. + data_type: integer + tests: + - not_null + - unique + - name: person_id + description: '' + data_type: integer + tests: + - not_null + - relationships: + to: ref('person') + field: person_id + - name: visit_concept_id + description: This field contains a concept id representing the kind of visit, likeinpatient or + outpatient. All concepts in this field should be standardand belong to the Visit domain. + data_type: integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: visit_concept_id <> 0 + to_condition: domain_id = 'Visit' + - name: visit_start_date + description: For inpatient visits, the start date is typically the admission date.For outpatient + visits the start date and end date will be the same. + data_type: date + tests: + - not_null + - name: visit_start_datetime + description: '' + data_type: datetime + - name: visit_end_date + description: For inpatient visits the end date is typically the discharge date. If aPerson is + still an inpatient in the hospital at the time of the dataextract and does not have a visit_end_date, + then set the visit_end_dateto the date of the data pull. + data_type: date + tests: + - not_null + - name: visit_end_datetime + description: If a Person is still an inpatient in the hospital at the time of thedata extract + and does not have a visit_end_datetime, then set thevisit_end_datetime to the datetime of the + data pull. + data_type: datetime + - name: visit_type_concept_id + description: Use this field to understand the provenance of the visit record, orwhere the record + comes from. + data_type: Integer + tests: + - not_null + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: visit_type_concept_id <> 0 + to_condition: domain_id = 'Type Concept' + - name: provider_id + description: There will only be one provider per visit record and the ETL documentshould clearly + state how they were chosen (attending, admitting, etc.).If there are multiple providers associated + with a visit in the source,this can be reflected in the event tables (CONDITION_OCCURRENCE,PROCEDURE_OCCURRENCE, + etc.) or in the VISIT_DETAIL table. + data_type: integer + tests: + - relationships: + to: ref('provider') + field: provider_id + - name: care_site_id + description: This field provides information about the Care Site where the Visit tookplace. + data_type: integer + tests: + - relationships: + to: ref('care_site') + field: care_site_id + - name: visit_source_value + description: This field houses the verbatim value from the source data representingthe kind of + visit that took place (inpatient, outpatient, emergency,etc.) + data_type: varchar(50) + - name: visit_source_concept_id + description: '' + data_type: integer + tests: + - relationships: + to: ref('concept') + field: concept_id + - name: admitted_from_concept_id + description: Use this field to determine where the patient was admitted from. Thisconcept is part + of the visit domain and can indicate if a patient wasadmitted to the hospital from a long-term + care facility, for example. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: admitted_from_concept_id <> 0 + to_condition: domain_id = 'Visit' + - name: admitted_from_source_value + description: '' + data_type: varchar(50) + - name: discharged_to_concept_id + description: Use this field to determine where the patient was discharged to after avisit. This + concept is part of the visit domain and can indicate if apatient was transferred to another + hospital or sent to a long-term carefacility, for example. It is assumed that a person is discharged + to hometherefore there is not a standard concept id for “home”. Use concept id= 0 when a person + is discharged to home. + data_type: integer + tests: + - dbt_utils.relationships_where: + to: ref('concept') + field: concept_id + from_condition: discharged_to_concept_id <> 0 + to_condition: domain_id = 'Visit' + - name: discharged_to_source_value + description: '' + data_type: varchar(50) + - name: preceding_visit_occurrence_id + description: Use this field to find the visit that occurred for the person prior tothe given visit. + There could be a few days or a few years in between. + data_type: integer + tests: + - relationships: + to: ref('visit_occurrence') + field: visit_occurrence_id diff --git a/models/omop/_models/vocabulary.yml b/models/omop/_models/vocabulary.yml new file mode 100644 index 0000000..54c0224 --- /dev/null +++ b/models/omop/_models/vocabulary.yml @@ -0,0 +1,32 @@ +models: + - name: vocabulary + description: The VOCABULARY table includes a list of the Vocabularies integratedfrom various sources + or created de novo in OMOP CDM. This referencetable contains a single record for each Vocabulary + and includes adescriptive name and other associated attributes for the Vocabulary. + columns: + - name: vocabulary_id + description: A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. + data_type: varchar(20) + tests: + - not_null + - unique + - name: vocabulary_name + description: The name describing the vocabulary, for example, InternationalClassification of Diseases, + Ninth Revision, Clinical Modification,Volume 1 and 2 (NCHS) etc. + data_type: varchar(255) + tests: + - not_null + - name: vocabulary_reference + description: External reference to documentation or available download of the aboutthe vocabulary. + data_type: varchar(255) + - name: vocabulary_version + description: Version of the Vocabulary as indicated in the source. + data_type: varchar(255) + - name: vocabulary_concept_id + description: A Concept that represents the Vocabulary the VOCABULARY record belongsto. + data_type: integer + tests: + - not_null + - relationships: + to: ref('concept') + field: concept_id From 8f3564d64c2b30b0a5d5452f45fa6a769cbf33d0 Mon Sep 17 00:00:00 2001 From: Lawrence Adams Date: Thu, 26 Sep 2024 07:55:28 +0100 Subject: [PATCH 2/9] fix: add missing concepts causing failing tests - now at minimum required vocab for all OMOP tests to pass --- seeds/vocabulary/concept.csv | 1229 ++++++++++++++++++++++++++++++++++ 1 file changed, 1229 insertions(+) diff --git a/seeds/vocabulary/concept.csv b/seeds/vocabulary/concept.csv index 0bc0d45..ec71723 100644 --- a/seeds/vocabulary/concept.csv +++ b/seeds/vocabulary/concept.csv @@ -31975,3 +31975,1232 @@ concept_id,concept_name,domain_id,vocabulary_id,concept_class_id,standard_concep 1751615,"IBUPROFEN - ibuprofen tablet, film coated",Drug,SPL,Prescription Drug,C,84f1cc9a-6560-4de0-e053-2a91aa0a1636,2021-02-17,2099-12-31, 36159540,HAILEY FE 1.5/30 - norethindrone acetate and ethinyl estradiol and ferrous fumarate kit,Drug,SPL,Prescription Drug,C,84f6d573-3022-4982-aaa4-ac69393210a2,2023-02-21,2099-12-31, 45791972,"CONGESTION RELIEF - ibuprofen, phenylephrine hcl tablet, film coated",Drug,SPL,OTC Drug,C,84f932b6-0aee-4cf9-b4b9-213560c42c1d,2019-12-05,2099-12-31, +798878,"OMOP CDM Version 5.4.1",Metadata,CDM,CDM,S,CDM v5.4.1,2023-02-08,2099-12-31, +45754678,Laboratory Class,Metadata,Concept Class,Concept Class,,1,1970-01-01,2099-12-31, +45754679,Clinical Class,Metadata,Concept Class,Concept Class,,2,1970-01-01,2099-12-31, +45754680,Claims Attachments,Metadata,Concept Class,Concept Class,,3,1970-01-01,2099-12-31, +33070,Language,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32967,Variable,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32958,Procedure Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32536,MEDRT Extension,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46277305,Non-human drug class Animal Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32484,LOINC Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32486,OMOP CDM Table,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32487,OMOP CDM Table Field,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754875,5-digit billing V code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754874,4-digit billing V code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754872,5-digit billing E code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754869,4-digit billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754873,3-digit billing V code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754868,3-digit billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754870,5-digit billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754861,Human drug class Cellular Therapy,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754860,Human drug class Non-Standardized Allergenic,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754876,3-digit non-billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754881,2-digit non-billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754857,Human drug class Human Prescription Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754871,4-digit billing E code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754862,Quantified Clinical Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754856,Human drug class Standardized Allergenic,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754863,Quantified Branded Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819027,Device Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819028,Semantic Clinical Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819029,Observable Entity,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819030,Race,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819034,Condition Cohort,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819035,Ethnicity,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819037,System Organ Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819038,Enrollment Basis,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819039,Visit Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819040,Drug Product,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819042,Indication or Contra-Indication,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819043,Organism,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819044,Undefined,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819046,Special Concept,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819047,Biological Function,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819048,Condition,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819049,Currency,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819050,Substance,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819052,Physical Force,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819054,Anatomical Therapeutic Chemical Classification,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819055,Specimen,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819057,Namespace Concept,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819058,Model Component,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819059,Measurement Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819060,Standardized MedDRA Query,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819061,Note Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819063,Semantic Branded Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819064,Semantic Clinical Drug Component,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819065,Brand Name,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819066,Dose Form,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819067,Physiologic Effect,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819068,Chemical Structure,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819069,Drug Interaction,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819070,Attribute,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819071,Measurement,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819072,Unit,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819073,Standard Unit,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819074,Custom Unit,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819075,Revenue Code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819076,Observation Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819079,Patient Status,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819080,Procedure,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819081,Lowest Level Term,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819082,Enhanced Therapeutic Classification,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819083,Discharge Status,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819084,Encounter Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819085,Hispanic,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819086,Gender,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819087,1st level - Anatomical Main Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2016-12-15,D +44819088,2nd level - Therapeutic Subgroup,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2016-12-15,D +44819089,3rd level - Pharmacological Subgroup,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2016-12-15,D +44819091,5th level - Chemical Substance,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2016-12-15,D +44819092,Quality Metric,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819093,Observation,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819094,Device,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819095,Procedure Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819169,Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819170,"Endocrine, nutritional and metabolic diseases",Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819172,Diseases of the nervous system,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819173,Diseases of the eye and adnexa,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819174,Diseases of the ear and mastoid process,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819175,Diseases of the circulatory system,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754799,Disease Related Group Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754800,Diagnosis Code Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754801,Diagnosis Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754802,Procedure Code Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754803,Vital Source,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754804,Blood Pressure Position,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754795,Navigational Concept,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754796,Inactive Concept,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754797,Linkage Concept,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754798,Link Assertion,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754822,Linkage Assertion,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818995,Therapeutic Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818996,Body Structure,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819187,Factors influencing health status and contact with health services,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819188,Certain infectious and parasitic diseases,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819236,Codes for special purposes,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819243,11-digit NDC code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819244,9-digit NDC code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819245,Ambulatory Patient Classification,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819246,Cohort,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819247,OMOP Concept Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819248,OMOP Condition Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819250,Disease-related Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819251,Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819252,Drug Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819253,Gemscript,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819254,GCN_SEQNO,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819255,Generic Product Identifier,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819256,Healthcare Common Procedure Coding System,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819257,HES Specialty,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819258,ICD10 code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819259,ICD9CM code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2015-01-03,D +44819260,ICD9CM E code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2015-01-03,D +44819261,ICD9CM V code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2015-01-03,D +44819262,Indication,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819263,Logical Observation Identifiers Names and Code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819264,LOINC Hierarchy,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819265,Major Diagnostic Category,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819266,Medical Dictionary for Regulatory Activities,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819267,Multilex,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819268,Multum,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819271,Oxford Medical Information System,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819272,OMOP Procedure Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819273,Read,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819274,OMOP Relationship,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819276,SPL,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819277,VA Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819279,OMOP Vocabulary,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819282,Canonical Unit,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819283,ATC 2nd Level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819284,ATC 5th Level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818997,Clinical Finding,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818999,Record Artifact,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819000,Death Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819001,Measurement Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819002,Admitting Source,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819003,Discharge Disposition,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819004,Semantic Branded Drug Component,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819005,Mechanism of Action,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819006,Pharmacologic Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819007,Pharmaceutical / Biologic Product,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819008,Morphologic Abnormality,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819009,Physical Object,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819012,Condition Occurrence Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819013,Procedure Occurrence Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819014,Health Care Provider Specialty,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819016,Specialty,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819017,Preferred Term,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819018,High Level Term,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819019,Biobank Flag,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819020,Semantic Clinical Drug Form,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819021,Qualifier Value,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819022,Social Context,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819023,OMOP Visit,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819024,Drug Cohort,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819025,Domain,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754906,ICD10 Hierarchy,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754686,CPT4 Hierarchy,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818981,Ingredient,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818982,Semantic Branded Pack,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818984,Pharmacokinetics,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818985,Place Of Service,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818986,Administrative Concept,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818990,High Level Group Term,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818991,Chart Availability,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818992,Semantic Clinical Pack,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754823,ICD9CM non-billable code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2015-01-03,D +45754824,ICD9Proc non-billable code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754877,4-digit non-billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754879,3-digit non-billing E code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754880,4-digit non-billing E code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754687,HCPCS Modifier,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754688,HCPCS Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819176,Diseases of the respiratory system,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819177,Diseases of the digestive system,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819178,Diseases of the skin and subcutaneous tissue,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819179,Diseases of the musculoskeletal system and connective tissue,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819181,"Pregnancy, childbirth and the puerperium",Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819182,Certain conditions originating in the perinatal period,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819184,Symptom,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905711,Test,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905714,Anatomy,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905715,Question,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905716,LabSet,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905718,ConvSet,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905721,Symptom/Finding,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905722,Misc Order,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905723,Workflow,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905724,State,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905725,Program,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905726,Aggregate Measurement,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905727,Indicator,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905728,Health Care Monitoring Topics,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905729,Radiology/Imaging Procedure,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905730,Frequency,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905734,Drug form,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905735,Medical supply,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32524,Disease Extent,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32525,Treatment,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32526,Episode of Care,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233638,Main Heading or Descriptor,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233639,Supplementary Concept,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233658,3-character non-billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233659,4-character non-billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233660,5-character non-billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233661,6-character non-billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233662,7-character non-billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233663,3-character billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233664,4-character billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233665,5-character billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233666,6-character billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233667,7-character billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46233669,3-digit billing E code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46274138,Non-human drug class Supplement,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46274139,Non-human drug class Cosmetic,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +200,Quantified Branded Drug Box,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +202,Branded Drug Box,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +240,Non-human drug class Disinfectant,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +241,Non-human drug class Imaging Material,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +244,"Supplier: Manufacturer, Wholesaler",Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +253,New Form Code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +259,ICD-10-PCS Hierarchical Code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5002,Actual Medicinal Product,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5003,Actual Medicinal Product Pack,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5004,Virtual Medicinal Product,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5005,Virtual Medicinal Product Pack,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5006,dm+d Dose Form,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5007,Virtual Therapeutic Moiety,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5023,Dose Form Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5024,Semantic Clinical Dose Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5025,Semantic Branded Dose Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5022,Precise Ingredient,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32543,Episode Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32550,Animal life circumstance,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32717,LOINC System,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32718,LOINC Component,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32722,LOINC Property,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32737,Procedure Hierarchy,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5030,Cost Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5043,Clinical Pack Box,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5044,Branded Pack Box,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5035,AU Qualifier (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5036,Medicinal Product Unit of Use (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5037,Medicinal Product Pack (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5038,Medicinal Product (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5039,Trade Product Pack (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5040,Trade Product (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5041,Trade Product Unit of Use (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5042,Containered Trade Product Pack (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32794,Regimen Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32888,OMOP Condition Status,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32674,Metadata,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5048,Kind of Note Attribute,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5050,Point of Care Setting of Note Attribute,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5051,Note Subject Matter Domain Attribute,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5052,Provider Role of Note Attribute,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581377,OMOP Specimen Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32689,BioCondition,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32690,Modality,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32636,Regimen type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32638,Route,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32639,Regimen,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32640,Component Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32641,Context,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581401,CVX vaccine,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581407,Topic,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32694,KCD7 code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581440,CDT,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581444,ISBT Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581446,ISBT Attrib value,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581447,ISBT Attrib group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581448,ISBT Attrib cat,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581449,ISBT Category,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581433,ICDO Topography,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581434,ICDO Histology,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581435,ICDO Condition,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581453,Type Concept,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581455,Detail,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32038,Frequency code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32039,Full,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32040,Typ bill 3 digits,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32041,UB04 Point of Origin,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32042,UB04 Pri Typ of Adm,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32043,UB04 Pt dis status,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32575,OMOP Provider,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32576,OMOP Physician Specialty,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32559,10th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32562,12th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32565,6th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32566,2nd administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32567,11th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32568,4th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819053,Canonical,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32571,United States Census Bureau Region,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32572,United States Census Bureau Division,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32449,LOINC Document Subject Matter Domain,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32450,LOINC Document Type of Service,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32451,LOINC Document Role,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32464,SUS,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32651,NAACCR Procedure Schema,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32480,Sponsor - institution or individual financing healthcare transactions,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32481,Plan Stop Reason - Reason for termination of the Health Plan,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32483,Metal level: ratio of split of the healthcare transaction costs between Health Plan and patient,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32741,ICD10 Histology,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32743,ICD10 SubChapter,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32745,6-dig billing code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32746,ICD9Proc Chapter,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32773,CAP Variable,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32774,CAP Header,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32775,CAP Protocol,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32926,Variant,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32927,Protein Variant,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32930,Cancer topography and anatomical site,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32932,Lymph node metastases,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32933,Official Grade or Stage System,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32934,Local cancer growth and invasion into adjacent tissue and organs,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32935,Tumor size and dimension,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32936,Histological patterns of cancer tissue,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32937,Distant metastases,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32938,Disease Dynamic,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32950,AJCC Chapter,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32924,DNA Variant,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32923,RNA Variant,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32969,Precoordinated (Question-Answer/Variable-Value) pair,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33094,Vaccine Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33106,"Variant at the DNA level not attributable to a single gene, including a karyotype",Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33107,Variant at the protein level for a gene,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33108,Variant of unspecified modality at the gene level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33109,Variant at the DNA level attributable to a gene,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33110,Variant at the transcript (RNA) level for a gene,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33099,Disorder,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754681,Surveys,Metadata,Concept Class,Concept Class,,4,1970-01-01,2099-12-31, +32968,Value,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32966,Category,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32538,Disposition,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754858,Human drug class Human OTC Drug,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754859,Human drug class Plasma Derivative,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819051,Situation with explicit context,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819062,Observation Period Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819077,Diagnostic Category,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819090,4th level - Chemical Subgroup,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2016-12-15,D +44819168,Neoplasms,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819171,"Mental, Behavioral and Neurodevelopmental disorders",Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45756722,4-digit non-billing V code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819249,Current Procedural Terminology version 4,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819269,National Uniform Claim Committee Specialty,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754677,LOINC Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819010,Staging and Scales,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819011,Environment or Geographical Location,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819026,Concept Relationship,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754685,CPT4 Modifier,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754878,3-digit non-billing V code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819183,"Congenital malformations, deformations and chromosomal abnormalities",Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819186,External causes of morbidity,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905712,Diagnosis,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905713,Finding,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905717,MedSet,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905719,Misc,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45905732,Units of Measure,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +250,Marketed Product,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5000,Encrypted Gemscript for the THIN database,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32719,LOINC Scale,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32720,LOINC Time,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5034,AU Substance (AMT),Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +5049,Service or activity resulting in Note Attribute,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32637,Component,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581409,PPI Modifier,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581439,CDT Hierarchy,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581445,ISBT Modifier,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32560,3rd administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32561,8th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32563,9th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32564,5th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32569,7th administrative level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32452,LOINC Document Kind,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32453,LOINC Document Setting,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32653,NAACCR Value,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32482,Benefit - healthcare items or services covered under a Health Plan,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32742,ICD10 Chapter,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32805,Question source,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32772,CAP Value,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32931,Tumor resection margins and involvement by cancer cells,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32925,Genetic Variation,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754855,Human drug class Vaccine,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819056,Event,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819281,ATC 1st Level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819285,ATC 4th Level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45754682,Answers,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +45757047,Medicare Severity Disease-related Group,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818983,Pharmaceutical Preparations,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +46274137,Non-human drug class Food,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +260,ICD-10-PCS Code,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581372,LOINC Document Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581454,Summary,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32652,NAACCR Procedure,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32654,NAACCR Schema,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32655,NAACCR Variable,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32663,Permissible Range,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32951,AJCC Category,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33001,Multiple Ingredients,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819078,Drug Exposure Type,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819280,ATC 3rd Level,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819180,Diseases of the genitourinary system,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819185,"Injury, poisoning and certain other consequences of external causes",Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +201,Quantified Clinical Drug Box,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581408,Module,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +581443,ISBT Product,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32479,Payer - institution administering healthcare transactions,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32522,CDM,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +203,Clinical Drug Box,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +32721,LOINC Method,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819041,Semantic Branded Drug Form,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44819278,VA Product,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +44818993,Drug Class,Metadata,Concept Class,Concept Class,,OMOP generated,1970-01-01,2099-12-31, +33100,Process acts on (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33101,Affected by process (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33102,Before (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33103,After (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33104,Towards (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33105,Subject of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33067,Status of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33066,Has status,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33065,Target population of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33064,Has target population (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33063,Is sterile of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33062,Is sterile (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33060,Has surface texture (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33059,Ingredient qualitative strength of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33058,Has ingredient qualitative strength (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33057,Process extends from (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33056,Process extends to (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33055,Absorbability of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33054,Has absorbability (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33053,Coating material of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33031,Has immunotherapy - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33027,Has endocrine therapy - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33025,Has endocrine therapy (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33024,Cytotoxic chemotherapy of - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33023,Has cytotoxic chemotherapy - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33022,Cytotoxic chemotherapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33021,Has cytotoxic chemotherapy (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33020,FDA labeling of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33019,Has FDA labeling (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33017,Has antibody-drug conjugate - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33016,Antibody-drug conjugate of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33015,Has antibody-drug conjugate (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +46233679,Contained in panel,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33012,ICDO broader to OncoTree,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33011,OncoTree to ICDO broader,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33010,ICDO to OncoTree equivalent,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33009,OncoTree to ICDO equivalent,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32977,Has biosimilar,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32975,Category of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32974,Has Category,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32973,Value of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32972,Has Value,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32970,Has precoordinated (Question-Answer/Variable-Value) pair,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754867,RxNorm to SPL (NLM),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754866,SPL to RxNorm (NLM),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818903,SNOMED to MedDRA equivalent (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818902,SNOMED to CPT-4 equivalent (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818901,SNOMED category to CPT-4 (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818900,SNOMED to ICD-9-Procedure equivalent (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818899,Finding informer of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818898,Finding method of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818897,Route of administration of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818896,Has clinical course of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818895,Access device used by (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818894,Substance used by (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818893,Energy used by (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818892,Device used by (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818891,Surgical approach of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818890,Finding associated with (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818889,Temporal context of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818888,Procedure context of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818887,Finding context of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818884,Indirect procedure site of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818883,Direct procedure site of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818882,Associated procedure of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818881,Occurs before (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818880,Dose form of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818879,Subject relationship context of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818878,Due to of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818877,Specimen substance of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818876,Specimen source topography of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818875,Specimen source morphology of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818873,Specimen procedure of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818871,Scale type of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818870,Property of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818869,Measurement method of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818868,Associated finding of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818867,Associated morphology of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818865,Component of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818864,Direct device of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818863,Direct morphology of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818862,Direct substance of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818835,Active metabolite of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818834,May be prevented by (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818833,Contraindicated by (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818832,May be treated by (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818831,Pharmacokinetics of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818830,Contraindicating mechanism of action of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818829,Mechanism of action of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818827,Ingredient of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818826,Contraindicating physiological effect induced by (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818825,Physiological effect induced by (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818824,Diagnosed through (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818823,Induced by (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818861,Episodicity of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818860,Finding site of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818859,Active ingredient of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818858,Definitional manifestation of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818856,Intent of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818855,Interpretation of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818854,Specimen of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33047,Has targeted therapy - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33046,Targeted therapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33043,Has radiotherapy - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33042,Radiotherapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33041,Has radiotherapy (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33038,Radioconjugate of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33037,Has radioconjugate (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33034,Peptide-drug conjugate of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33033,Has peptide-drug conjugate (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818853,Indirect device of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818852,Indirect morphology of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818851,Interprets of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818850,Laterality of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818848,Occurrence of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818847,Access of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818846,Revision status of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818845,Severity of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818844,Part of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818843,Pathological process of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818842,Priority of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818841,Procedure site of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818840,Recipient category of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818838,Chemical structure of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818837,Inhibits effect (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818822,Dose form of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818820,Reformulated in (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818819,Is contained in (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818817,Ingredient of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818816,Form of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818815,Dose form of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818814,Tradename of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818813,Precise ingredient of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818812,Concept replaces (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818811,SMQ consists of MedDRA (MedDRA),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818810,ATC to RxNorm,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818809,ETC to RxNorm (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818808,Has drug contra-indication (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818807,Has off-label drug indication (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818806,Has FDA-approved drug indication (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818805,MedDRA to SNOMED equivalent (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818804,CPT-4 to SNOMED equivalent (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818803,CPT-4 to SNOMED category (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818802,ICD-9-Procedure to SNOMED equivalent (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818801,Using finding informer (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818800,Using finding method (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818797,Using access device (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818796,Using substance (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818795,Using energy (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818794,Using device (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818793,Has surgical approach (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818792,Associated with finding (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818791,Has temporal context (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818790,Has procedure context (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818789,Has finding context (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818787,Has procedure device (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818786,Has indirect procedure site (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818785,Has direct procedure site (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818784,Has associated procedure (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818782,Has dose form (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818781,Has subject relationship context (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818780,Has due to (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818779,Has specimen substance (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818778,Has specimen source topography (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818777,Has specimen source morphology (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818775,Has specimen procedure (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818771,Has measurement method (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754816,Has Extent (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754817,Extent of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754820,Has Approach (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754821,Approach of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754683,Has Answer,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754684,Answer of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754836,ATC to VA Class equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754837,NDFRT to ATC equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754827,Has quantified form (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754828,Quantified form of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754829,Is a (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754835,VA Class to ATC equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754838,ATC to NDFRT equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754839,VA Class to NDFRT equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754840,NDFRT to VA Class equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754841,Chemical Structure to Pharmaceutical Preparation equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754842,Pharmaceutical Preparation to Chemical Structure equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754844,RxNorm to SNOMED equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754845,SNOMED to NDF-RT equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754846,NDF-RT to SNOMED equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754847,SNOMED to VA Class equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754848,VA Class to SNOMED equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754849,SNOMED to ATC equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754850,ATC to SNOMED equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754851,Has product component (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754852,Product component of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819241,Unit concept to non-standard map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819240,Type concept to non-standard map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819239,Non-standard to value_as_concept map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819238,Non-standard to unit concept map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819237,Non-standard to type concept map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818979,Concept replaces (UCUM),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818977,Mapping relationship to Standard Concept (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818976,Mapping relationship from Standard Concept (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818975,Non-standard to Standard include child (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818974,Non-standard to Standard exclude child (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818973,Standard to Non-standard include child (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818971,Concept replaced by (ICD-9-Procedure),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818970,Standard to Non-standard exclude child (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818969,Is a domain (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818968,Domain subsumes (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818967,HCPCS is a SNOMED measurement (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818966,SNOMED measurement subsumes HCPCS (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818964,Inactive was_a active (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818963,Active possibly_equivalent_to inactive (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818962,Inactive possibly_equivalent_to active (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818961,Active alternative_to inactive (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818960,Inactive alternative_to active (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818959,Active same_as inactive (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818958,Inactive same_as active (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818957,Concept replaces,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818953,Drug Source to RxNorm equivalent (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818952,RxNorm to Drug Source equivalent (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818951,Ingredient of (Multilex),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818950,Has ingredient (Multilex),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818947,Concept replaces (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818946,Concept replaced by (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818945,RxNorm to VA Product equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818944,VA Product to RxNorm equivalent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818942,VA Product to NDF-RT (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818941,Place of Service to Visit category (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818940,Visit category to Place of Service (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818939,MDC category to DRG (CMS),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818938,DRG to MDC category (CMS),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818937,MS-DRG to DRG equivalent (CMS),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818936,DRG to MS-DRG equivalent (CMS),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818935,CMS Specialty to NUCC (CMS),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818932,HOI contains MedDRA (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818931,RxNorm contained in DOI (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818930,DOI contains RxNorm (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818929,SNOMED contained in HOI (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818928,HOI contains SNOMED (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818925,RxNorm to ETC equivalent by concept_name (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818924,ETC to RxNorm equivalent by concept_name (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818923,NDF-RT to RxNorm equivalent by concept_name (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818922,RxNorm to NDF-RT equivalent by concept_name (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818920,SNOMED procedure subsumes HCPCS (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818919,Has inferred drug class (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818918,Inferred drug class of (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818916,Has pharmaceutical preparation (NDF),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33048,RxNorm targeted therapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33044,RxNorm radiotherapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33040,RxNorm radioconjugate of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33036,RxNorm peptide-drug conjugate of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33032,RxNorm immunotherapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33028,RxNorm endocrine therapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33018,RxNorm antibody-drug conjugate of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818914,Drug-drug interaction for (NDF),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818913,Therapeutic class of (NDF),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818912,Has therapeutic class (NDF),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818911,SNOMED to Indication/Contra-indication,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818910,Indication/Contra-indication to SNOMED,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818909,MedDRA contained in SMQ (MedDRA),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818908,RxNorm to ATC,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818906,Is contra-indication of (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818905,Is off-label indication of (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818904,Is FDA-approved indication of (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754806,Has Morphology (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754807,Morphology of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754808,Has Measured Component (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754809,Measured Component of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754810,Caused by (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754811,Causes (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754812,Has Etiology (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754813,Etiology of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754814,Has Stage (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754883,Non-standard to operator concept map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754884,Operator concept to non-standard map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754886,Value_as_number to non-standard map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818769,Has associated morphology (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818768,Has causative agent (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818766,Has direct device (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818765,Has direct morphology (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818764,Has direct substance (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818763,Has episodicity (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818762,Has finding site (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818760,Has definitional manifestation (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818758,Has intent (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818757,Has interpretation (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818756,Has specimen (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818755,Has indirect device (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818753,Has interprets (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818752,Has laterality (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818750,Has occurrence (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818749,Has access (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818748,Has revision status (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818746,Has part of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818745,Has pathological process (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818744,Has priority (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818743,Has procedure site (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818742,Has recipient category (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818741,NDF-RT to RxNorm equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818740,Has chemical structure (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818739,Effect may be inhibited by (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818738,Has site of metabolism (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818736,May prevent (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818735,Contraindication to (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818732,Has contraindicating mechanism of action (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818731,Has mechanism of action (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818730,Has contraindicating chemical class (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818729,Has ingredient (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818728,Has contraindicating physiological effect (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818727,Has physiological effect (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818726,May diagnose (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818725,Induces (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818723,Subsumes,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818722,Reformulation of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818721,Contains (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818719,Has ingredient (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818718,Has form (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818717,Has dose form (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818716,Has tradename (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818715,Has precise ingredient (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818714,Concept replaced by (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819287,MedDRA to ICD-9-CM (MSSO),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819289,FDB Indication/Contraindication to ICD-9-CM (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819286,ICD-9-CM to MedDRA (MSSO),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819288,ICD-9-CM to FDB Indication/Contraindication (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905737,Has specific active ingredient (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905790,Excipient of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905791,Has excipient (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905792,Follows (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905738,Has basis of strength substance (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905736,Has dispensed dose form (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905741,Has licensed route (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905742,Has unit relating to the size (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905744,Has route (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905746,Is pack of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905747,Has trade family group (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905748,Dispensed dose form of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905749,Specific active ingredient of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905750,Basis of strength substance of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905751,Virtual Medicinal Product of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905752,Incipient of (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905753,Licensed route of (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905754,Unit relating to the size of (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905755,Unit relating to the entity that can be handled of (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905756,Route of (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905758,Has pack (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905759,Trade family group of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905794,Has VMP non-availability indicator (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905795,VMP non-availability indicator of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905796,Has ARP (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905799,VRP of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905802,Has flavor (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905803,Flavor of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905804,Has discontinued indicator (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905805,Discontinued indicator of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905806,VRP has prescribing status (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905810,VMP has prescribing status (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905811,VMP prescribing status of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905812,Has legal category (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45956695,LOINC Hierarchy to SNOMED equivalent (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45956696,SNOMED to LOINC Hierarchy equivalent (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45956697,LOINC to CPT4 equivalent (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45956699,OPCS4 to SNOMED equivalent or categorical (NHS),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818751,Has method,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818849,Method of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818774,Has time aspect,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818767,Has component,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +233,Drug class of drug (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +234,Drug has drug class (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +221,Has brand name (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +223,Is available in a prepackaged box (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +224,Prepackaged box of (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +225,Is standard ingredient of ingredient (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +226,Has standard ingredient (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +227,Is standard Brand Name of (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +228,Has standard Brand Name (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +229,Is standard Dose Form of (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +230,Has standard Dose Form (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32540,Role played by,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +246,Has marketed form (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +247,Marketed form of (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +248,Has supplier or manufacturer (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +249,Supplier or manufacturer of (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5026,Dose form group of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5027,Has dose form group (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32551,Has physiologic state (SNOMED Vet),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32552,Physiologic state of (SNOMED Vet),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32554,Sub-specimen of (SNOMED Vet),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32555,Has life circumstance (SNOMED Vet),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32556,Life circumstance (SNOMED Vet),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32711,Has end date,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32712,End date of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32714,Start date of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32715,Has system,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32716,System of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32782,CAP to Nebraska Lexicon category,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32783,Nebraska Lexicon to CAP category,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32784,CAP to Nebraska Lexicon equivalent,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32785,Nebraska Lexicon to CAP equivalent,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32469,Has PPI parent code,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32470,PPI parent code of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32786,Has accepted use (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32787,Accepted use of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32788,Has FDA indication (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32789,FDA indication of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32790,Is currently used in (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32791,Currently treated by (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32792,Is historically used in (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32793,Historically treated by (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32670,Has unit,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32671,Unit of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32672,Has type,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32673,Type of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5065,Has precondition (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5067,Has inherent location (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5068,Inherent location of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5069,Has technique (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5070,Technique of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5071,Has relative part (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5072,Relative part of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5073,Has process output (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5074,Process output of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5075,Has property type,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5076,Property type of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5077,Inheres in (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5079,Has direct site (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5080,Direct site of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5082,Is characterized by (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32679,Has controlled drug category (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32680,Controlled drug cathehory of (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32681,Has ontological dose form presentation (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32683,Has combination product indicator (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32685,Has dose form continuity indicator (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32686,Dose form continuity indicator (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32691,Has modality (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32692,Modality of (Hemonc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32609,Has vaccine group (CVX),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32612,CVX to CPT4 equivalent (CVX),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32614,Has antineoplastic - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32617,Antineoplastic of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32618,Has context (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32622,Has immunosuppressor (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32623,Immunosuppressor of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32624,Has local therapy - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32625,RxNorm local therapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32626,Has local therapy (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32627,Local therapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32629,Regimen type of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32630,Has supportive medication - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32631,RxNorm Supportive medication of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32632,Has supportive medication (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32633,Supportive medication of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32635,May be route of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581402,RxNorm - CVX (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581403,CVX - RxNorm (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581405,Module of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581406,Has Module,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32409,Has unit of administration (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32410,Unit of administration of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581416,Has presentation strength denominator unit (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581417,Presentation strength denominator unit of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581419,Presentation strength denominator value of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581420,Has presentation strength numerator unit (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581421,Presentation strength numerator unit of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581423,Presentation strength numerator value of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581424,During (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581425,Has complication (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581414,Topic of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581427,Has Histology ICDO,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581428,Histology of ICDO,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581429,Has Topography ICDO,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581430,Topography of ICDO,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581431,ICDO - SNOMED,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581432,SNOMED - ICDO,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32403,Typ bill Full to Frequency code (UB04),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32404,Frequency code to Typ bill Full (UB04),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32406,Typ bill 3 digits to Typ bill Full (UB04),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581460,Basic dose form of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581461,Has disposition (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581463,Has dose form administration method (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581466,Dose form intended site of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581468,Dose form release characteristic of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581469,Has dose form transformation (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581473,Temporally related to (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581474,Has temporal finding (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32427,Has precise active ingredient (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32428,Precise active ingredient of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32429,Has unit of presentation (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32430,Unit of presentation of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32431,Has concentration strength numerator value (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32432,Concentration strength numerator value of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32433,Has concentration strength denominator value (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32434,Concentration strength denominator value of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32435,Has concentration strength denominator unit (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32436,Concentration strength denominator unit of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32437,Has concentration strength numerator unit (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32438,Concentration strength numerator unit of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32440,Has modification of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32443,Answer of (PPI),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32444,Has answer (PPI),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32454,Has subject matter domain (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32455,Subject matter domain of (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32456,Has type of service (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32457,Type of service of (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32458,Has role (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32460,Has kind (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32461,Kind of (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32462,Has setting (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32643,Procedure Schema to ICDO Condition (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32644,ICDO Condition to Procedure Schema (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32645,Schema to ICDO Condition (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32647,Schema to Value (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32648,Value to Schema (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32649,Schema to Variable (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32650,Variable to Schema (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32657,Parent item of (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32659,Date of variable (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32664,Has permissible range,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32665,Permissible range of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32520,OMOP CDM Version contains table/field (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32521,Table/field contained in OMOP CDM Version (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32747,Has NHS dm+d (dictionary of medicines and devices) additional monitoring indicator,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32748,NHS dm+d (dictionary of medicines and devices) additional monitoring indicator of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32749,Has NHS dm+d (dictionary of medicines and devices) AMP (actual medicinal product) availability restriction indicator,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32751,Has NHS dm+d parallel import indicator,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32752,NHS dm+d parallel import indicator of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32753,Has NHS dm+d freeness indicator,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32754,NHS dm+d freenes indicator of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32755,Process duration,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32756,Process duration of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32796,RxNorm/Extension to ATC pr lateral (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32797,ATC to RxNorm/Extension secondary lateral (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32798,RxNorm/Extension to ATC secondary lateral (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32799,ATC to RxNorm/Extension primary upwards (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32800,RxNorm/Extension to ATC primary upwards (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32801,ATC to RxNorm/Extension secondary upwards (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32802,RxNorm/Extension to ATC secondary upwards (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32803,Has question source,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32804,Question source of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32776,CAP value of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32777,Has CAP value,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32778,Has CAP parent item,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32780,Has CAP protocol,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32781,CAP protocol of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32919,Genomic DNA transcribes to mRNA,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32921,mRNA Translates to protein,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32920,mRNA is transcribed from genomic DNA,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32952,Category in Chapter,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32953,Chapter has Category,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32955,ICDO to Chapter,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32979,Relative to (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32980,Relative to of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32982,Is count of active ingredients in (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32983,Has product characteristic (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32985,Has surface characteristic (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32986,Surface characteristic of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32987,Has device intended site (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32988,Device intended site of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32989,Has compositional material (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32990,Compositional material of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32991,Has filling (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32992,Filling material of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32998,Variant refer to concept,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32997,Reference to variant,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33073,Has steroid therapy (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33074,Steroid therapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33075,Has steroid therapy - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33076,RxNorm steroid therapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33077,Is current in adult (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33078,Current adult indication for (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33080,Current pediatric indication for (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33081,Is historical in adult (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33082,Historical adult indication for (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33086,Investigational use for (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33087,Has PDC - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33088,RxNorm PDC of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33089,Is historical in pediatric (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33090,Historical pediatric indication for (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33061,Surface texture of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33052,Has coating material (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33029,Has immunotherapy (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33026,Endocrine therapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32978,Biosimilar of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32971,Precoordinated (Question-Answer/Variable-Value) pair of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818886,Procedure morphology of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818885,Procedure device of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818866,Causative agent of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818857,Focus of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33035,Has peptide-drug conjugate - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818821,Is a,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818818,Consists of (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818799,Has route of administration (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818788,Has procedure morphology (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818772,Has property,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754830,Inverse is a (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754843,SNOMED to RxNorm equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44819242,Value_as_concept to non-standard map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818978,Concept replaced by (UCUM),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818972,Concept replaces (ICD-9-Procedure),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818965,Active was_a inactive (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818943,NDF-RT to VA Product (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818934,NUCC to CMS Specialty (CMS),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818927,RxNorm to ATC equivalent by concept_name (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818926,ATC to RxNorm equivalent by concept_name (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818921,HCPCS is a SNOMED procedure (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818915,Is involved in drug-drug interaction (NDF),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818907,RxNorm to ETC (FDB),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754815,Stage of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45754885,Non-standard to value_as_number map (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818759,Has focus (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818754,Has indirect morphology (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818747,Has severity (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818737,Has active metabolites (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818734,May treat (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818724,Has dose form (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905740,Has incipient (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905743,Has unit relating to the entity that can be handled (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905745,Has Actual Medicinal Product (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905793,Followed by (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905798,Has VRP (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905807,VRP prescribing status of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905813,Legal category of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45956700,SNOMED to OPCS4 equivalent or categorical (NHS),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818872,Time aspect of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +222,Brand name of (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32553,Includes sub-specimen (SNOMED Vet),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5066,Precondition of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5078,Has inherent (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32684,Combination product indicator of (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32615,RxNorm antineoplastic of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32616,Has antineoplastic (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32620,Has immunosuppressor - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32621,RxNorm immunosuppressor of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32628,Has regimen type (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32611,CPT4 to CVX equivalent (CVX),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581422,Has presentation strength numerator value (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581415,Has Topic,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581459,Has basic dose form (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581464,Dose form administration method of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581465,Has dose form intended site (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581467,Has dose form release characteristic (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581470,Dose form transformation of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581471,Has state of matter (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581472,State of matter of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32439,Is modification of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32441,Has count of base of active ingredient (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32459,Role of (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32463,Setting of (LOINC),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32646,ICDO Condition to Schema (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32656,Has parent item (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32658,Variable has date (NAACCR),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32750,NHS dm+d (dictionary of medicines and devices) AMP (actual medicinal product) availability restriction indicator of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32795,ATC to RxNorm/Extension primary lateral (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32954,Chapter to ICDO,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32981,Count of active ingredients (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32984,Product characteristic of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33079,Is current in pediatric (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33083,Had accepted use (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +46233678,Panel contains,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818836,Site of metabolism of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33039,Has radioconjugate - RxNorm (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818839,RxNorm to NDF-RT equivalent (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818798,Has clinical course (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818783,Occurs after (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818773,Has scale type,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818933,MedDRA contained in HOI (OMOP),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818917,Pharmaceutical preparation contained in (NDF),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818770,Has associated finding (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818761,Has active ingredient (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818720,Constitutes (RxNorm),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905739,Has Virtual Medicinal Product (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905757,Actual Medicinal Product of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32539,Plays role,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32713,Has start date,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32682,Ontological dose form presentation of (DM+D),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32610,Vaccine group of (CVX),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32634,May have route (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581462,Disposition of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32442,Count of base of active ingredient of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32779,CAP parent item of,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32922,Protein is translated from mRNA,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33085,Has investigational use (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33030,Immunotherapy of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818828,Contraindicating chemical class of (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818776,Has specimen source identity (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818733,Has pharmacokinetics (NDF-RT),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32619,Context of (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +581418,Has presentation strength denominator value (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33084,Had accepted for (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +33045,Has targeted therapy (HemOnc),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +5081,Characterizes (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818956,Concept replaced by,Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45905797,ARP of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +32405,Typ bill Full to Typ bill 3 digits (UB04),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +44818874,Specimen source identity of (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45956698,CPT4 to LOINC equivalent (SNOMED),Metadata,Relationship,Relationship,,OMOP generated,1970-01-01,2099-12-31, +45756746,Provider Specialty (American Board of Medical Specialties),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819135,OMOP Death Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819137,National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819138,Medicare Specialty,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819140,Structured Product Labeling (FDA),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819126,OMOP Drug Exposure Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819127,OMOP Condition Occurrence Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819128,OMOP Procedure Occurrence Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819129,OMOP Observation Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819133,UB04/CMS1450 Revenue Codes (CMS),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819134,OMOP Ethnicity,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819150,OMOP Visit Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819151,OMOP Device Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819152,OMOP Measurement Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819153,International Currency Symbol (ISO 4217),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819233,OMOP Concept Class,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819232,OMOP Vocabulary,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819235,OMOP Relationship,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819234,OMOP Cohort Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819096,OMOP Standardized Vocabularies,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819097,Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819098,"International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)",Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819099,"International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS)",Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819117,WHO Anatomic Therapeutic Chemical Classification,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32485,OMOP Common DataModel,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819100,Current Procedural Terminology version 4 (AMA),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819101,Healthcare Common Procedure Coding System (CMS),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819105,National Drug Code (FDA and manufacturers),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819108,OMOP Gender,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819109,Race and Ethnicity Code Set (USBC),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819110,CMS Place of Service,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819146,OMOP Note Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819147,OMOP Domain,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819149,OMOP Observation Period Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32046,UB04 Claim Inpatient Admission Type Code (CMS),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32047,UB04 Patient Discharge Status Code (CMS),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32473,SOPT,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32523,OMOP Episode,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +5046,"International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)",Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32808,OMOP Type Concept,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32887,OMOP Condition Status,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +581457,OMOP Cost,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32044,UB04 Type of Bill - Institutional (USHIK),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32045,UB04 Claim Source Inpatient Admission Code (CMS),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32758,OMOP Extension (OHDSI),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32570,Census regions of the United States (USCB),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32472,OMOP Sponsor,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +252,OMOP RxNorm Extension,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32471,OMOP Health Plan,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32474,OMOP Plan Stop Reason,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32541,OpenStreetMap (OSMF),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32675,OMOP Metadata,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +33069,OMOP Language,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +32724,Korean Revenue Code (KNHIS),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819104,RxNorm (NLM),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819102,Logical Observation Identifiers Names and Codes (Regenstrief Institute),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819107,Unified Code for Units of Measure (Regenstrief Institute),Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +5029,OMOP Cost Type,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +44819119,OMOP Visit,Metadata,Vocabulary,Vocabulary,,OMOP generated,1970-01-01,2099-12-31, +33068,Language,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +2,Gender,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +3,Race,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +4,Ethnicity,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +7,Metadata,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +8,Visit,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +10,Procedure,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +12,Modifier,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +13,Drug,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +15,Route,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +16,Unit,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +17,Device,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +19,Condition,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +21,Measurement,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +23,Measurement value operator,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +24,Measurement value,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +27,Observation,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +31,Relationship,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32,Place of Service,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +33,Provider,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +34,Currency,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +35,Revenue code,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +36,Specimen,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +38,Specimen anatomic site,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +39,Specimen disease status,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +41,Device/Procedure,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +42,Observation/Procedure,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +43,Measurement/Procedure,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +44,Measurement/Observation,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +45,Device/Observation,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +47,Condition/Measurement,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +49,Condition/Procedure,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +50,Device/Drug,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +51,Drug/Measurement,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +52,Drug/Observation,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +54,Drug/Procedure,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32527,Episode,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +58,Type Concept,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +235,Condition/Device,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32889,OMOP Condition Status,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +5085,Note,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32687,Treatment Regimen,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +581456,Cost,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32558,Geographical object,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32475,"Health Plan - contract to administer healthcare transactions by the payer, facilitated by the sponsor",Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32476,Sponsor - institution or individual financing healthcare transactions,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32477,Payer - institution administering healthcare transactions,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +32478,Plan Stop Reason - Reason for termination of the Health Plan,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +48,Condition/Observation,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, +53,Condition/Drug,Metadata,Domain,Domain,,OMOP generated,1970-01-01,2099-12-31, From 2f3638aa5bbf5e2b081ec43b6d5dd7afb69a5027 Mon Sep 17 00:00:00 2001 From: Lawrence Adams Date: Sat, 28 Sep 2024 03:33:52 +0100 Subject: [PATCH 3/9] refactor: Update table descriptions to fix typos and improve clarity --- models/omop/_models/care_site.yml | 4 +-- models/omop/_models/cdm_source.yml | 4 +-- models/omop/_models/concept.yml | 26 ++++++++-------- models/omop/_models/concept_ancestor.yml | 14 ++++----- models/omop/_models/concept_class.yml | 10 +++--- models/omop/_models/concept_relationship.yml | 9 +++--- models/omop/_models/concept_synonym.yml | 2 +- models/omop/_models/condition_era.yml | 8 ++--- models/omop/_models/condition_occurrence.yml | 6 ++-- models/omop/_models/cost.yml | 6 ++-- models/omop/_models/death.yml | 6 ++-- models/omop/_models/device_exposure.yml | 12 +++---- models/omop/_models/domain.yml | 13 ++++---- models/omop/_models/dose_era.yml | 2 +- models/omop/_models/drug_era.yml | 10 +++--- models/omop/_models/drug_exposure.yml | 10 +++--- models/omop/_models/drug_strength.yml | 6 ++-- models/omop/_models/episode.yml | 31 +++++++------------ models/omop/_models/episode_event.yml | 6 ++-- models/omop/_models/fact_relationship.yml | 14 ++++----- models/omop/_models/location.yml | 2 +- models/omop/_models/measurement.yml | 23 +++++++------- models/omop/_models/metadata.yml | 2 +- models/omop/_models/note.yml | 6 ++-- models/omop/_models/note_nlp.yml | 2 +- models/omop/_models/observation.yml | 6 ++-- models/omop/_models/observation_period.yml | 6 ++-- models/omop/_models/payer_plan_period.yml | 18 +++++------ models/omop/_models/person.yml | 4 +-- models/omop/_models/procedure_occurrence.yml | 4 +-- models/omop/_models/provider.yml | 6 ++-- models/omop/_models/relationship.yml | 4 +-- models/omop/_models/source_to_concept_map.yml | 14 ++++----- models/omop/_models/specimen.yml | 2 +- models/omop/_models/visit_detail.yml | 12 +++---- models/omop/_models/visit_occurrence.yml | 10 +++--- models/omop/_models/vocabulary.yml | 6 ++-- 37 files changed, 161 insertions(+), 165 deletions(-) diff --git a/models/omop/_models/care_site.yml b/models/omop/_models/care_site.yml index e1fa4f5..5c36e6f 100644 --- a/models/omop/_models/care_site.yml +++ b/models/omop/_models/care_site.yml @@ -1,7 +1,7 @@ models: - name: care_site - description: The CARE_SITE table contains a list of uniquely identifiedinstitutional (physical or - organizational) units where healthcaredelivery is practiced (offices, wards, hospitals, clinics, + description: The CARE_SITE table contains a list of uniquely identified institutional (physical or + organizational) units where healthcare delivery is practiced (offices, wards, hospitals, clinics, etc.). columns: - name: care_site_id diff --git a/models/omop/_models/cdm_source.yml b/models/omop/_models/cdm_source.yml index fa9ffdf..a997153 100644 --- a/models/omop/_models/cdm_source.yml +++ b/models/omop/_models/cdm_source.yml @@ -1,7 +1,7 @@ models: - name: cdm_source - description: The CDM_SOURCE table contains detail about the source database andthe process used to - transform the data into the OMOP Common DataModel. + description: The CDM_SOURCE table contains detail about the source database and the process used to + transform the data into the OMOP Common Data Model. columns: - name: cdm_source_name description: The name of the CDM instance. diff --git a/models/omop/_models/concept.yml b/models/omop/_models/concept.yml index 85b8ee6..bdaf0e6 100644 --- a/models/omop/_models/concept.yml +++ b/models/omop/_models/concept.yml @@ -1,18 +1,18 @@ models: - name: concept - description: The Standardized Vocabularies contains records, or Concepts, thatuniquely identify each - fundamental unit of meaning used to expressclinical information in all domain tables of the CDM. - Concepts arederived from vocabularies, which represent clinical information across adomain (e.g. conditions, - drugs, procedures) through the use of codes andassociated descriptions. Some Concepts are designated - Standard Concepts,meaning these Concepts can be used as normative expressions of aclinical entity - within the OMOP Common Data Model and standardizedanalytics. Each Standard Concept belongs to one - Domain, which definesthe location where the Concept would be expected to occur within thedata tables - of the CDM. Concepts can represent broad categories(‘Cardiovascular disease’), detailed clinical - elements (‘Myocardialinfarction of the anterolateral wall’), or modifying characteristics andattributes - that define Concepts at various levels of detail (severity ofa disease, associated morphology, etc.). - Records in the StandardizedVocabularies tables are derived from national or internationalvocabularies - such as SNOMED-CT, RxNorm, and LOINC, or custom OMOPConcepts defined to cover various aspects of - observational dataanalysis. + description: The Standardized Vocabularies contains records, or Concepts, that uniquely identify each + fundamental unit of meaning used to express clinical information in all domain tables of the CDM. + Concepts are derived from vocabularies, which represent clinical information across a domain (e.g. conditions, + drugs, procedures) through the use of codes and associated descriptions. Some Concepts are designated + Standard Concepts, meaning these Concepts can be used as normative expressions of a clinical entity + within the OMOP Common Data Model and standardized analytics. Each Standard Concept belongs to one + Domain, which defines the location where the Concept would be expected to occur within the data + tables of the CDM. Concepts can represent broad categories (‘Cardiovascular disease’), detailed + clinical elements (‘Myocardial infarction of the anterolateral wall’), or modifying characteristics + and attributes that define Concepts at various levels of detail (severity of a disease, associated + morphology, etc.). Records in the Standardized Vocabularies tables are derived from national or + international vocabularies such as SNOMED-CT, RxNorm, and LOINC, or custom OMOP Concepts defined + to cover various aspects of observational data analysis. columns: - name: concept_id description: A unique identifier for each Concept across all domains. diff --git a/models/omop/_models/concept_ancestor.yml b/models/omop/_models/concept_ancestor.yml index dcabd0a..86153e6 100644 --- a/models/omop/_models/concept_ancestor.yml +++ b/models/omop/_models/concept_ancestor.yml @@ -1,12 +1,12 @@ models: - name: concept_ancestor - description: The CONCEPT_ANCESTOR table is designed to simplify observationalanalysis by providing - the complete hierarchical relationships betweenConcepts. Only direct parent-child relationships - between Concepts arestored in the CONCEPT_RELATIONSHIP table. To determine higher levelancestry - connections, all individual direct relationships would have tobe navigated at analysis time. The - CONCEPT_ANCESTOR table includesrecords for all parent-child relationships, as well asgrandparent-grandchild - relationships and those of any other level oflineage. Using the CONCEPT_ANCESTOR table allows for - querying for alldescendants of a hierarchical concept. For example, drug ingredients anddrug products + description: The CONCEPT_ANCESTOR table is designed to simplify observational analysis by providing + the complete hierarchical relationships between Concepts. Only direct parent-child relationships + between Concepts are stored in the CONCEPT_RELATIONSHIP table. To determine higher level ancestry + connections, all individual direct relationships would have to be navigated at analysis time. The + CONCEPT_ANCESTOR table includes records for all parent-child relationships, as well as grandparent-grandchild + relationships and those of any other level of lineage. Using the CONCEPT_ANCESTOR table allows for + querying for all descendants of a hierarchical concept. For example, drug ingredients and drug products are all descendants of a drug class ancestor. columns: - name: ancestor_concept_id diff --git a/models/omop/_models/concept_class.yml b/models/omop/_models/concept_class.yml index a02af50..782a44f 100644 --- a/models/omop/_models/concept_class.yml +++ b/models/omop/_models/concept_class.yml @@ -1,10 +1,10 @@ models: - name: concept_class - description: The CONCEPT_CLASS table includes semantic categories that referencethe source structure - of each Vocabulary. Concept Classes representso-called horizontal (e.g. MedDRA, RxNorm) or vertical - levels(e.g. SNOMED) of the vocabulary structure. Vocabularies without anyConcept Classes, such as - HCPCS, use the vocabulary_id as the ConceptClass. This reference table is populated with a single - record for eachConcept Class, which includes a Concept Class ID and a fully specifiedConcept Class + description: The CONCEPT_CLASS table includes semantic categories that reference the source structure + of each Vocabulary. Concept Classes represent so-called horizontal (e.g. MedDRA, RxNorm) or vertical + levels (e.g. SNOMED) of the vocabulary structure. Vocabularies without any Concept Classes, such + as HCPCS, use the vocabulary_id as the Concept Class. This reference table is populated with a single + record for each Concept Class, which includes a Concept Class ID and a fully specified Concept Class name. columns: - name: concept_class_id diff --git a/models/omop/_models/concept_relationship.yml b/models/omop/_models/concept_relationship.yml index 1ec4933..4545d0b 100644 --- a/models/omop/_models/concept_relationship.yml +++ b/models/omop/_models/concept_relationship.yml @@ -1,9 +1,10 @@ models: - name: concept_relationship - description: The CONCEPT_RELATIONSHIP table contains records that definerelationships between any - two Concepts and the nature or type of therelationship. This table captures various types of relationships,including - hierarchical, associative, and other semantic connections,enabling comprehensive analysis and interpretation - of clinical concepts.Every kind of relationship is defined in the RELATIONSHIP table. + description: The CONCEPT_RELATIONSHIP table contains records that define relationships between any + two Concepts and the nature or type of the relationship. This table captures various types of relationships, + including hierarchical, associative, and other semantic connections, enabling comprehensive analysis + and interpretation of clinical concepts. Every kind of relationship is defined in the RELATIONSHIP + table. columns: - name: concept_id_1 description: '' diff --git a/models/omop/_models/concept_synonym.yml b/models/omop/_models/concept_synonym.yml index 4d7d81c..c6596e2 100644 --- a/models/omop/_models/concept_synonym.yml +++ b/models/omop/_models/concept_synonym.yml @@ -1,6 +1,6 @@ models: - name: concept_synonym - description: The CONCEPT_SYNONYM table is used to store alternate names anddescriptions for Concepts. + description: The CONCEPT_SYNONYM table is used to store alternate names and descriptions for Concepts. columns: - name: concept_id description: '' diff --git a/models/omop/_models/condition_era.yml b/models/omop/_models/condition_era.yml index 9bd5ded..967d45d 100644 --- a/models/omop/_models/condition_era.yml +++ b/models/omop/_models/condition_era.yml @@ -1,9 +1,9 @@ models: - name: condition_era - description: 'A Condition Era is defined as a span of time when the Person isassumed to have a given - condition. Similar to Drug Eras, Condition Erasare chronological periods of Condition Occurrence - and every ConditionOccurrence record should be part of a Condition Era. Combiningindividual Condition - Occurrences into a single Condition Era serves twopurposes:' + description: 'A Condition Era is defined as a span of time when the Person is assumed to have a given + condition. Similar to Drug Eras, Condition Eras are chronological periods of Condition Occurrence + and every Condition Occurrence record should be part of a Condition Era. Combining individual Condition + Occurrences into a single Condition Era serves two purposes:' columns: - name: condition_era_id description: '' diff --git a/models/omop/_models/condition_occurrence.yml b/models/omop/_models/condition_occurrence.yml index a3a78e8..13c8631 100644 --- a/models/omop/_models/condition_occurrence.yml +++ b/models/omop/_models/condition_occurrence.yml @@ -1,8 +1,8 @@ models: - name: condition_occurrence - description: This table contains records of Events of a Person suggesting thepresence of a disease - or medical condition stated as a diagnosis, asign, or a symptom, which is either observed by a Provider - or reportedby the patient. + description: This table contains records of Events of a Person suggesting the presence of a disease + or medical condition stated as a diagnosis, a sign, or a symptom, which is either observed by a + Provider or reported by the patient. columns: - name: condition_occurrence_id description: The unique key given to a condition record for a person. Refer to theETL for how diff --git a/models/omop/_models/cost.yml b/models/omop/_models/cost.yml index f991834..dabc30c 100644 --- a/models/omop/_models/cost.yml +++ b/models/omop/_models/cost.yml @@ -1,8 +1,8 @@ models: - name: cost - description: The COST table captures records containing the cost of any medicalevent recorded in one - of the OMOP clinical event tables such asDRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, - VISIT_DETAIL,DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT. + description: The COST table captures records containing the cost of any medical event recorded in + one of the OMOP clinical event tables such as DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, + VISIT_DETAIL, DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT. columns: - name: cost_id description: '' diff --git a/models/omop/_models/death.yml b/models/omop/_models/death.yml index 0c10b9b..034b72c 100644 --- a/models/omop/_models/death.yml +++ b/models/omop/_models/death.yml @@ -1,8 +1,8 @@ models: - name: death - description: 'The death domain contains the clinical event for how and when aPerson dies. A person - can have up to one record if the source systemcontains evidence about the Death, such as: Condition - in anadministrative claim, status of enrollment into a health plan, orexplicit record in EHR data.' + description: 'The death domain contains the clinical event for how and when a Person dies. A person + can have up to one record if the source system contains evidence about the Death, such as: Condition + in an administrative claim, status of enrollment into a health plan, or explicit record in EHR data.' columns: - name: person_id description: '' diff --git a/models/omop/_models/device_exposure.yml b/models/omop/_models/device_exposure.yml index 5bb2276..cf78823 100644 --- a/models/omop/_models/device_exposure.yml +++ b/models/omop/_models/device_exposure.yml @@ -1,11 +1,11 @@ models: - name: device_exposure - description: The Device domain captures information about a person’s exposure to aforeign physical - object or instrument which is used for diagnostic ortherapeutic purposes through a mechanism beyond - chemical action. Devicesinclude implantable objects (e.g. pacemakers, stents, artificialjoints), - medical equipment and supplies (e.g. bandages, crutches,syringes), other instruments used in medical - procedures (e.g. sutures,defibrillators) and material used in clinical care (e.g. adhesives, bodymaterial, - dental material, surgical material). + description: The Device domain captures information about a person’s exposure to a foreign physical + object or instrument which is used for diagnostic or therapeutic purposes through a mechanism beyond + chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), + medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical + procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body + material, dental material, surgical material). columns: - name: device_exposure_id description: The unique key given to records a person’s exposure to a foreignphysical object or diff --git a/models/omop/_models/domain.yml b/models/omop/_models/domain.yml index ce5429b..09d8e1d 100644 --- a/models/omop/_models/domain.yml +++ b/models/omop/_models/domain.yml @@ -1,11 +1,12 @@ models: - name: domain - description: The DOMAIN table includes a list of OMOP-defined Domains to which theConcepts of the - Standardized Vocabularies can belong. A Domainrepresents a clinical definition whereby we assign - matching Concepts forthe standardized fields in the CDM tables. For example, the ConditionDomain - contains Concepts that describe a patient condition, and theseConcepts can only be used in the condition_concept_id - field of theCONDITION_OCCURRENCE and CONDITION_ERA tables. This reference table ispopulated with - a single record for each Domain, including a Domain IDand a descriptive name for every Domain. + description: The DOMAIN table includes a list of OMOP-defined Domains to which the Concepts of the + Standardized Vocabularies can belong. A Domain represents a clinical definition whereby we assign + matching Concepts for the standardized fields in the CDM tables. For example, the Condition Domain + contains Concepts that describe a patient condition, and these Concepts can only be used in the + condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA tables. This reference + table is populated with a single record for each Domain, including a Domain ID and a descriptive + name for every Domain. columns: - name: domain_id description: A unique key for each domain. diff --git a/models/omop/_models/dose_era.yml b/models/omop/_models/dose_era.yml index 82d39a2..23a4125 100644 --- a/models/omop/_models/dose_era.yml +++ b/models/omop/_models/dose_era.yml @@ -1,6 +1,6 @@ models: - name: dose_era - description: A Dose Era is defined as a span of time when the Person is assumed tobe exposed to a + description: A Dose Era is defined as a span of time when the Person is assumed to be exposed to a constant dose of a specific active ingredient. columns: - name: dose_era_id diff --git a/models/omop/_models/drug_era.yml b/models/omop/_models/drug_era.yml index 64f7c33..2b218b5 100644 --- a/models/omop/_models/drug_era.yml +++ b/models/omop/_models/drug_era.yml @@ -1,10 +1,10 @@ models: - name: drug_era - description: 'A Drug Era is defined as a span of time when the Person is assumed tobe exposed to a - particular active ingredient. A Drug Era is not the sameas a Drug Exposure: Exposures are individual - records corresponding tothe source when Drug was delivered to the Person, while successiveperiods - of Drug Exposures are combined under certain rules to producecontinuous Drug Eras. Every record - in the DRUG_EXPOSURE table should bepart of a drug era based on the dates of exposure.' + description: 'A Drug Era is defined as a span of time when the Person is assumed to be exposed to + a particular active ingredient. A Drug Era is not the same as a Drug Exposure: Exposures are individual + records corresponding to the source when Drug was delivered to the Person, while successive periods + of Drug Exposures are combined under certain rules to produce continuous Drug Eras. Every record + in the DRUG_EXPOSURE table should be part of a drug era based on the dates of exposure.' columns: - name: drug_era_id description: '' diff --git a/models/omop/_models/drug_exposure.yml b/models/omop/_models/drug_exposure.yml index dd31fca..72ca581 100644 --- a/models/omop/_models/drug_exposure.yml +++ b/models/omop/_models/drug_exposure.yml @@ -1,10 +1,10 @@ models: - name: drug_exposure - description: This table captures records about the exposure to a Drug ingested orotherwise introduced - into the body. A Drug is a biochemical substanceformulated in such a way that when administered - to a Person it willexert a certain biochemical effect on the metabolism. Drugs includeprescription - and over-the-counter medicines, vaccines, andlarge-molecule biologic therapies. Radiological devices - ingested orapplied locally do not count as Drugs. + description: This table captures records about the exposure to a Drug ingested or otherwise introduced + into the body. A Drug is a biochemical substance formulated in such a way that when administered + to a Person it will exert a certain biochemical effect on the metabolism. Drugs include prescription + and over-the-counter medicines, vaccines, and large-molecule biologic therapies. Radiological devices + ingested or applied locally do not count as Drugs. columns: - name: drug_exposure_id description: The unique key given to records of drug dispensings or administrationsfor a person. diff --git a/models/omop/_models/drug_strength.yml b/models/omop/_models/drug_strength.yml index 869d53f..1ccdf97 100644 --- a/models/omop/_models/drug_strength.yml +++ b/models/omop/_models/drug_strength.yml @@ -1,8 +1,8 @@ models: - name: drug_strength - description: The DRUG_STRENGTH table contains structured content about the amountor concentration - and associated units of a specific ingredient containedwithin a particular drug product. This table - is supplemental informationto support standardized analysis of drug utilization. + description: The DRUG_STRENGTH table contains structured content about the amount or concentration + and associated units of a specific ingredient contained within a particular drug product. This table + is supplemental information to support standardized analysis of drug utilization. columns: - name: drug_concept_id description: The Concept representing the Branded Drug or Clinical Drug Product. diff --git a/models/omop/_models/episode.yml b/models/omop/_models/episode.yml index 9a439c3..bcabec5 100644 --- a/models/omop/_models/episode.yml +++ b/models/omop/_models/episode.yml @@ -1,12 +1,11 @@ models: - name: episode - description: - The EPISODE table aggregates lower-level clinical events(VISIT_OCCURRENCE, DRUG_EXPOSURE, - PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE)into a higher-level abstraction representing clinically and - analyticallyrelevant disease phases,outcomes and treatments. The EPISODE_EVENT tableconnects qualifying - clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE,PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate - EPISODE entry.For example cancers including their development over time, theirtreatment, and final - resolution. + description: The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, + PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and + analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying + clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the + appropriate EPISODE entry. For example cancers including their development over time, their treatment, + and final resolution. columns: - name: episode_id description: A unique identifier for each Episode. @@ -23,8 +22,7 @@ models: to: ref('person') field: person_id - name: episode_concept_id - description: - The EPISODE_CONCEPT_ID represents the kind abstraction related to thedisease phase, + description: The EPISODE_CONCEPT_ID represents the kind abstraction related to thedisease phase, outcome or treatment. data_type: integer tests: @@ -49,18 +47,15 @@ models: description: The date when the instance of the Episode is considered to have ended. data_type: datetime - name: episode_parent_id - description: - Use this field to find the Episode that subsumes the given Episoderecord. This is + description: Use this field to find the Episode that subsumes the given Episoderecord. This is used in the case that an Episode are nested into eachother. data_type: integer - name: episode_number - description: - For sequences of episodes, this is used to indicate the order theepisodes occurred. + description: For sequences of episodes, this is used to indicate the order theepisodes occurred. For example, lines of treatment could be indicatedhere. data_type: integer - name: episode_object_concept_id - description: - A Standard Concept representing the disease phase, outcome, or otherabstraction of + description: A Standard Concept representing the disease phase, outcome, or otherabstraction of which the episode consists. For example, if theEPISODE_CONCEPT_ID is treatmentregimen then the EPISODE_OBJECT_CONCEPT_ID should contain thechemotherapy regimen concept, like Afatinibmonotherapy. data_type: integer @@ -72,8 +67,7 @@ models: from_condition: episode_object_concept_id <> 0 to_condition: domain_id = 'Procedure, Regimen' - name: episode_type_concept_id - description: - This field can be used to determine the provenance of the Episoderecord, as in whether + description: This field can be used to determine the provenance of the Episoderecord, as in whether the episode was from an EHR system, insuranceclaim, registry, or other sources. data_type: integer tests: @@ -84,8 +78,7 @@ models: from_condition: episode_type_concept_id <> 0 to_condition: domain_id = 'Type Concept' - name: episode_source_value - description: - The source code for the Episode as it appears in the source data. Thiscode is mapped + description: The source code for the Episode as it appears in the source data. Thiscode is mapped to a Standard Condition Concept in the StandardizedVocabularies and the original code is stored here for reference. data_type: varchar(50) diff --git a/models/omop/_models/episode_event.yml b/models/omop/_models/episode_event.yml index 81b8335..df09eee 100644 --- a/models/omop/_models/episode_event.yml +++ b/models/omop/_models/episode_event.yml @@ -1,8 +1,8 @@ models: - name: episode_event - description: The EPISODE_EVENT table connects qualifying clinical events (such asCONDITION_OCCURRENCE, - DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT)to the appropriate EPISODE entry. For example, - linking the preciselocation of the metastasis (cancer modifier in MEASUREMENT) to thedisease episode. + description: The EPISODE_EVENT table connects qualifying clinical events (such as CONDITION_OCCURRENCE, + DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT) to the appropriate EPISODE entry. For example, + linking the precise location of the metastasis (cancer modifier in MEASUREMENT) to the disease episode. columns: - name: episode_id description: Use this field to link the EPISODE_EVENT record to its EPISODE. diff --git a/models/omop/_models/fact_relationship.yml b/models/omop/_models/fact_relationship.yml index d0f1ed2..c02f415 100644 --- a/models/omop/_models/fact_relationship.yml +++ b/models/omop/_models/fact_relationship.yml @@ -1,12 +1,12 @@ models: - name: fact_relationship - description: 'The FACT_RELATIONSHIP table contains records about the relationshipsbetween facts stored - as records in any table of the CDM. Relationshipscan be defined between facts from the same domain, - or different domains.Examples of Fact Relationships include: Personrelationships (parent-child), - care site relationships (hierarchicalorganizational structure of facilities within a health system),indication - relationship (between drug exposures and associatedconditions), usage relationships (of devices - during the course of anassociated procedure), or facts derived from one another (measurementsderived - from an associated specimen).' + description: 'The FACT_RELATIONSHIP table contains records about the relationships between facts stored + as records in any table of the CDM. Relationships can be defined between facts from the same domain, + or different domains. Examples of Fact Relationships include: Person relationships (parent-child), + care site relationships (hierarchical organizational structure of facilities within a health system), + indication relationship (between drug exposures and associated conditions), usage relationships + (of devices during the course of an associated procedure), or facts derived from one another (measurements + derived from an associated specimen).' columns: - name: domain_concept_id_1 description: '' diff --git a/models/omop/_models/location.yml b/models/omop/_models/location.yml index 50ed15d..dbe3578 100644 --- a/models/omop/_models/location.yml +++ b/models/omop/_models/location.yml @@ -1,6 +1,6 @@ models: - name: location - description: The LOCATION table represents a generic way to capture physicallocation or address information + description: The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites. columns: - name: location_id diff --git a/models/omop/_models/measurement.yml b/models/omop/_models/measurement.yml index adb0b48..f39420c 100644 --- a/models/omop/_models/measurement.yml +++ b/models/omop/_models/measurement.yml @@ -1,16 +1,17 @@ models: - name: measurement - description: The MEASUREMENT table contains records of Measurements,i.e. structured values (numerical - or categorical) obtained throughsystematic and standardized examination or testing of a Person orPerson’s - sample. The MEASUREMENT table contains both orders and resultsof such Measurements as laboratory - tests, vital signs, quantitativefindings from pathology reports, etc. Measurements are stored asattribute - value pairs, with the attribute as the Measurement Concept andthe value representing the result. - The value can be a Concept (stored inVALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with - a Unit(UNIT_CONCEPT_ID). The Procedure for obtaining the sample is housed inthe PROCEDURE_OCCURRENCE - table, though it is unnecessary to create aPROCEDURE_OCCURRENCE record for each measurement if one - does not existin the source data. Measurements differ from Observations in that theyrequire a standardized - test or some other activity to generate aquantitative or qualitative result. If there is no result, - it is assumedthat the lab test was conducted but the result was not captured. + description: The MEASUREMENT table contains records of Measurements, i.e. structured values (numerical + or categorical) obtained through systematic and standardized examination or testing of a Person + or Person’s sample. The MEASUREMENT table contains both orders and results of such Measurements + as laboratory tests, vital signs, quantitative findings from pathology reports, etc. Measurements + are stored as attribute value pairs, with the attribute as the Measurement Concept and the value + representing the result. The value can be a Concept (stored in VALUE_AS_CONCEPT), or a numerical + value (VALUE_AS_NUMBER) with a Unit (UNIT_CONCEPT_ID). The Procedure for obtaining the sample is + housed in the PROCEDURE_OCCURRENCE table, though it is unnecessary to create a PROCEDURE_OCCURRENCE + record for each measurement if one does not exist in the source data. Measurements differ from Observations + in that they require a standardized test or some other activity to generate a quantitative or qualitative + result. If there is no result, it is assumed that the lab test was conducted but the result was + not captured. columns: - name: measurement_id description: The unique key given to a Measurement record for a Person. Refer to theETL for how diff --git a/models/omop/_models/metadata.yml b/models/omop/_models/metadata.yml index 05f489e..62d46c4 100644 --- a/models/omop/_models/metadata.yml +++ b/models/omop/_models/metadata.yml @@ -1,6 +1,6 @@ models: - name: metadata - description: The METADATA table contains metadata information about a dataset thathas been transformed + description: The METADATA table contains metadata information about a dataset that has been transformed to the OMOP Common Data Model. columns: - name: metadata_id diff --git a/models/omop/_models/note.yml b/models/omop/_models/note.yml index eb75148..a2b394b 100644 --- a/models/omop/_models/note.yml +++ b/models/omop/_models/note.yml @@ -1,8 +1,8 @@ models: - name: note - description: The NOTE table captures unstructured information that was recorded bya provider about - a patient in free text (in ASCII, or preferably in UTF8format) notes on a given date. The type of - note_text is CLOB orvarchar(MAX) depending on RDBMS. + description: The NOTE table captures unstructured information that was recorded by a provider about + a patient in free text (in ASCII, or preferably in UTF8 format) notes on a given date. The type + of note_text is CLOB or varchar(MAX) depending on RDBMS. columns: - name: note_id description: A unique identifier for each note. diff --git a/models/omop/_models/note_nlp.yml b/models/omop/_models/note_nlp.yml index 41a0cd4..2c6f065 100644 --- a/models/omop/_models/note_nlp.yml +++ b/models/omop/_models/note_nlp.yml @@ -1,6 +1,6 @@ models: - name: note_nlp - description: The NOTE_NLP table encodes all output of NLP on clinical notes. Eachrow represents a + description: The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note. columns: - name: note_nlp_id diff --git a/models/omop/_models/observation.yml b/models/omop/_models/observation.yml index 51be4fa..65a15a4 100644 --- a/models/omop/_models/observation.yml +++ b/models/omop/_models/observation.yml @@ -1,8 +1,8 @@ models: - name: observation - description: The OBSERVATION table captures clinical facts about a Person obtainedin the context of - examination, questioning or a procedure. Any data thatcannot be represented by any other domains, - such as social and lifestylefacts, medical history, family history, etc. are recorded here. + description: The OBSERVATION table captures clinical facts about a Person obtained in the context + of examination, questioning or a procedure. Any data that cannot be represented by any other domains, + such as social and lifestyle facts, medical history, family history, etc. are recorded here. columns: - name: observation_id description: The unique key given to an Observation record for a Person. Refer to theETL for how diff --git a/models/omop/_models/observation_period.yml b/models/omop/_models/observation_period.yml index e48d0ef..0f991db 100644 --- a/models/omop/_models/observation_period.yml +++ b/models/omop/_models/observation_period.yml @@ -1,8 +1,8 @@ models: - name: observation_period - description: 'This table contains records which define spans of time during whichtwo conditions are - expected to hold: (i) Clinical Events that happenedto the Person are recorded in the Event tables, - and (ii) absence ofrecords indicate such Events did not occur during this span of time.' + description: 'This table contains records which define spans of time during which two conditions are + expected to hold: (i) Clinical Events that happened to the Person are recorded in the Event tables, + and (ii) absence of records indicate such Events did not occur during this span of time.' columns: - name: observation_period_id description: A Person can have multiple discrete Observation Periods which areidentified by the diff --git a/models/omop/_models/payer_plan_period.yml b/models/omop/_models/payer_plan_period.yml index 6eaf0b9..944dcff 100644 --- a/models/omop/_models/payer_plan_period.yml +++ b/models/omop/_models/payer_plan_period.yml @@ -1,14 +1,14 @@ models: - name: payer_plan_period - description: The PAYER_PLAN_PERIOD table captures details of the period of timethat a Person is continuously - enrolled under a specific health Planbenefit structure from a given Payer. Each Person receiving - healthcareis typically covered by a health benefit plan, which pays for (fully orpartially), or - directly provides, the care. These benefit plans areprovided by payers, such as health insurances - or state or governmentagencies. In each plan the details of the health benefits are definedfor the - Person or her family, and the health benefit Plan might changeover time typically with increasing - utilization (reaching certain costthresholds such as deductibles), plan availability and purchasingchoices - of the Person. The unique combinations of Payer organizations,health benefit Plans and time periods - in which they are valid for aPerson are recorded in this table. + description: The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously + enrolled under a specific health Plan benefit structure from a given Payer. Each Person receiving + healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or + directly provides, the care. These benefit plans are provided by payers, such as health insurances + or state or government agencies. In each plan the details of the health benefits are defined for + the Person or her family, and the health benefit Plan might change over time typically with increasing + utilization (reaching certain cost thresholds such as deductibles), plan availability and purchasing + choices of the Person. The unique combinations of Payer organizations, health benefit Plans and + time periods in which they are valid for a Person are recorded in this table. columns: - name: payer_plan_period_id description: A unique identifier for each unique combination of a Person, Payer,Plan, and Period diff --git a/models/omop/_models/person.yml b/models/omop/_models/person.yml index 93b734a..45370c9 100644 --- a/models/omop/_models/person.yml +++ b/models/omop/_models/person.yml @@ -1,7 +1,7 @@ models: - name: person - description: This table serves as the central identity management for all Personsin the database. - It contains records that uniquely identify each personor patient, and some demographic information. + description: This table serves as the central identity management for all Persons in the database. + It contains records that uniquely identify each person or patient, and some demographic information. columns: - name: person_id description: It is assumed that every person with a different unique identifier is infact a different diff --git a/models/omop/_models/procedure_occurrence.yml b/models/omop/_models/procedure_occurrence.yml index 4d50ae4..af8a49a 100644 --- a/models/omop/_models/procedure_occurrence.yml +++ b/models/omop/_models/procedure_occurrence.yml @@ -1,7 +1,7 @@ models: - name: procedure_occurrence - description: This table contains records of activities or processes ordered by, orcarried out by, - a healthcare provider on the patient with a diagnosticor therapeutic purpose. + description: This table contains records of activities or processes ordered by, or carried out by, + a healthcare provider on the patient with a diagnostic or therapeutic purpose. columns: - name: procedure_occurrence_id description: The unique key given to a procedure record for a person. Refer to theETL for how diff --git a/models/omop/_models/provider.yml b/models/omop/_models/provider.yml index 4246d5e..a9c9ec3 100644 --- a/models/omop/_models/provider.yml +++ b/models/omop/_models/provider.yml @@ -1,8 +1,8 @@ models: - name: provider - description: The PROVIDER table contains a list of uniquely identified healthcareproviders; duplication - is not allowed. These are individuals providinghands-on healthcare to patients, such as physicians, - nurses, midwives,physical therapists etc. + description: The PROVIDER table contains a list of uniquely identified healthcare providers; duplication + is not allowed. These are individuals providing hands-on healthcare to patients, such as physicians, + nurses, midwives, physical therapists etc. columns: - name: provider_id description: It is assumed that every provider with a different unique identifier isin fact a diff --git a/models/omop/_models/relationship.yml b/models/omop/_models/relationship.yml index bad246d..41f2cac 100644 --- a/models/omop/_models/relationship.yml +++ b/models/omop/_models/relationship.yml @@ -1,7 +1,7 @@ models: - name: relationship - description: The RELATIONSHIP table provides a reference list of all types ofrelationships that can - be used to associate any two concepts in theCONCEPT_RELATIONSHP table. + description: The RELATIONSHIP table provides a reference list of all types of relationships that can + be used to associate any two concepts in the CONCEPT_RELATIONSHP table. columns: - name: relationship_id description: The type of relationship captured by the relationship record. diff --git a/models/omop/_models/source_to_concept_map.yml b/models/omop/_models/source_to_concept_map.yml index 5beb900..3ed069c 100644 --- a/models/omop/_models/source_to_concept_map.yml +++ b/models/omop/_models/source_to_concept_map.yml @@ -1,12 +1,12 @@ models: - name: source_to_concept_map - description: The source to concept map table is recommended for use in ETLprocesses to maintain local - source codes which are not available asConcepts in the Standardized Vocabularies, and to establish - mappings foreach source code into a Standard Concept as target_concept_ids that canbe used to populate - the Common Data Model tables. TheSOURCE_TO_CONCEPT_MAP table is no longer populated with content - withinthe Standardized Vocabularies published to the OMOP community.There are OHDSI tools to help - you populate this table; Usagi and Perseus. You can read moreabout OMOP vocabulary mapping in TheBook - of OHDSI Chapter 6.3. + description: The source to concept map table is recommended for use in ETL processes to maintain local + source codes which are not available as Concepts in the Standardized Vocabularies, and to establish + mappings for each source code into a Standard Concept as target_concept_ids that can be used to + populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with + content within the Standardized Vocabularies published to the OMOP community. There are OHDSI tools + to help you populate this table; Usagi and Perseus. You can read more about OMOP vocabulary mapping + in The Book of OHDSI Chapter 6.3. columns: - name: source_code description: The source code being translated into a Standard Concept. diff --git a/models/omop/_models/specimen.yml b/models/omop/_models/specimen.yml index f59cde3..a40f5a1 100644 --- a/models/omop/_models/specimen.yml +++ b/models/omop/_models/specimen.yml @@ -1,6 +1,6 @@ models: - name: specimen - description: The specimen domain contains the records identifying biologicalsamples from a person. + description: The specimen domain contains the records identifying biological samples from a person. columns: - name: specimen_id description: Unique identifier for each specimen. diff --git a/models/omop/_models/visit_detail.yml b/models/omop/_models/visit_detail.yml index 0a2d4e4..b8e5e86 100644 --- a/models/omop/_models/visit_detail.yml +++ b/models/omop/_models/visit_detail.yml @@ -1,11 +1,11 @@ models: - name: visit_detail - description: The VISIT_DETAIL table is an optional table used to representsdetails of each record - in the parent VISIT_OCCURRENCE table. A goodexample of this would be the movement between units - in a hospital duringan inpatient stay or claim lines associated with a one insurance claim.For every - record in the VISIT_OCCURRENCE table there may be 0 or morerecords in the VISIT_DETAIL table with - a 1:n relationship where n may be0. The VISIT_DETAIL table is structurally very similar toVISIT_OCCURRENCE - table and belongs to the visit domain. + description: The VISIT_DETAIL table is an optional table used to represents details of each record + in the parent VISIT_OCCURRENCE table. A good example of this would be the movement between units + in a hospital during an inpatient stay or claim lines associated with a one insurance claim. For + every record in the VISIT_OCCURRENCE table there may be 0 or more records in the VISIT_DETAIL table + with a 1:n relationship where n may be 0. The VISIT_DETAIL table is structurally very similar to + VISIT_OCCURRENCE table and belongs to the visit domain. columns: - name: visit_detail_id description: Use this to identify unique interactions between a person and the healthcare system. diff --git a/models/omop/_models/visit_occurrence.yml b/models/omop/_models/visit_occurrence.yml index 13b95ba..5e36644 100644 --- a/models/omop/_models/visit_occurrence.yml +++ b/models/omop/_models/visit_occurrence.yml @@ -1,10 +1,10 @@ models: - name: visit_occurrence - description: This table contains Events where Persons engage with the healthcaresystem for a duration - of time. They are often also called “Encounters”.Visits are defined by a configuration of circumstances - under which theyoccur, such as (i) whether the patient comes to a healthcareinstitution, the other - way around, or the interaction is remote, (ii)whether and what kind of trained medical staff is - delivering the serviceduring the Visit, and (iii) whether the Visit is transient or for alonger + description: This table contains Events where Persons engage with the healthcare system for a duration + of time. They are often also called “Encounters”. Visits are defined by a configuration of circumstances + under which they occur, such as (i) whether the patient comes to a healthcare institution, the other + way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is + delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. columns: - name: visit_occurrence_id diff --git a/models/omop/_models/vocabulary.yml b/models/omop/_models/vocabulary.yml index 54c0224..9c4e084 100644 --- a/models/omop/_models/vocabulary.yml +++ b/models/omop/_models/vocabulary.yml @@ -1,8 +1,8 @@ models: - name: vocabulary - description: The VOCABULARY table includes a list of the Vocabularies integratedfrom various sources - or created de novo in OMOP CDM. This referencetable contains a single record for each Vocabulary - and includes adescriptive name and other associated attributes for the Vocabulary. + description: The VOCABULARY table includes a list of the Vocabularies integrated from various sources + or created de novo in OMOP CDM. This reference table contains a single record for each Vocabulary + and includes a descriptive name and other associated attributes for the Vocabulary. columns: - name: vocabulary_id description: A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. From 97f078b50dd56450941f435ef797af1948cb9387 Mon Sep 17 00:00:00 2001 From: Lawrence Adams Date: Sat, 28 Sep 2024 04:23:24 +0100 Subject: [PATCH 4/9] Delete models/omop/_models/cohort.yml --- models/omop/_models/cohort.yml | 29 ----------------------------- 1 file changed, 29 deletions(-) delete mode 100644 models/omop/_models/cohort.yml diff --git a/models/omop/_models/cohort.yml b/models/omop/_models/cohort.yml deleted file mode 100644 index e0a5c2c..0000000 --- a/models/omop/_models/cohort.yml +++ /dev/null @@ -1,29 +0,0 @@ -models: - - name: cohort - description: The subject of a cohort can have multiple, discrete records in thecohort table per cohort_definition_id, - subject_id, and non-overlappingtime periods. The definition of the cohort is contained within theCOHORT_DEFINITION - table. It is listed as part of the RESULTS schemabecause it is a table that users of the database - as well as tools suchas ATLAS need to be able to write to. The CDM and Vocabulary tables areall - read-only so it is suggested that the COHORT and COHORT_DEFINTIONtables are kept in a separate schema - to alleviate confusion. - columns: - - name: cohort_definition_id - description: '' - data_type: integer - tests: - - not_null - - name: subject_id - description: '' - data_type: integer - tests: - - not_null - - name: cohort_start_date - description: '' - data_type: date - tests: - - not_null - - name: cohort_end_date - description: '' - data_type: date - tests: - - not_null From 37e8ee8320cfee93bd2265fde6718a6efef09f89 Mon Sep 17 00:00:00 2001 From: Lawrence Adams Date: Sat, 28 Sep 2024 04:23:42 +0100 Subject: [PATCH 5/9] Delete models/omop/_models/cohort_definition.yml --- models/omop/_models/cohort_definition.yml | 46 ----------------------- 1 file changed, 46 deletions(-) delete mode 100644 models/omop/_models/cohort_definition.yml diff --git a/models/omop/_models/cohort_definition.yml b/models/omop/_models/cohort_definition.yml deleted file mode 100644 index c6f3304..0000000 --- a/models/omop/_models/cohort_definition.yml +++ /dev/null @@ -1,46 +0,0 @@ -models: - - name: cohort_definition - description: The COHORT_DEFINITION table contains records defining a Cohortderived from the data through - the associated description and syntax andupon instantiation (execution of the algorithm) placed - into the COHORTtable. Cohorts are a set of subjects that satisfy a given combination ofinclusion - criteria for a duration of time. The COHORT_DEFINITION tableprovides a standardized structure for - maintaining the rules governingthe inclusion of a subject into a cohort, and can store operationalprogramming - code to instantiate the cohort within the OMOP Common DataModel. - columns: - - name: cohort_definition_id - description: This is the identifier given to the cohort, usually by the ATLASapplication - data_type: integer - tests: - - not_null - - name: cohort_definition_name - description: A short description of the cohort - data_type: varchar(255) - tests: - - not_null - - name: cohort_definition_description - description: A complete description of the cohort. - data_type: varchar(MAX) - - name: definition_type_concept_id - description: Type defining what kind of Cohort Definition the record represents andhow the syntax - may be executed. - data_type: integer - tests: - - not_null - - relationships: - to: ref('concept') - field: concept_id - - name: cohort_definition_syntax - description: Syntax or code to operationalize the Cohort Definition. - data_type: varchar(MAX) - - name: subject_concept_id - description: This field contains a Concept that represents the domain of the subjectsthat are - members of the cohort (e.g., Person, Provider, Visit). - data_type: integer - tests: - - not_null - - relationships: - to: ref('concept') - field: concept_id - - name: cohort_initiation_date - description: A date to indicate when the Cohort was initiated in the COHORT table. - data_type: date From 51b4a269ee39727e488170ca203a27075dcaa432 Mon Sep 17 00:00:00 2001 From: Lawrence Adams Date: Sat, 28 Sep 2024 04:25:05 +0100 Subject: [PATCH 6/9] Delete models/omop/_omop__models.yml Superseded by _models yml files --- models/omop/_omop__models.yml | 786 ---------------------------------- 1 file changed, 786 deletions(-) delete mode 100644 models/omop/_omop__models.yml diff --git a/models/omop/_omop__models.yml b/models/omop/_omop__models.yml deleted file mode 100644 index a596a74..0000000 --- a/models/omop/_omop__models.yml +++ /dev/null @@ -1,786 +0,0 @@ -version: 2 - -models: - - name: person - columns: - - name: person_id - description: "A unique identifier for each person." - tests: - - unique - - not_null - - name: gender_concept_id - tests: - - not_null - - name: year_of_birth - description: "The year of birth of the person." - tests: - - not_null - - name: month_of_birth - description: "The month of birth of the person." - - name: day_of_birth - description: "The day of birth of the person." - - name: birth_datetime - description: "The date and time of birth of the person." - - name: race_concept_id - tests: - - not_null - - name: ethnicity_concept_id - tests: - - not_null - - name: location_id - description: "A foreign key to the location table." - - name: provider_id - description: "A foreign key to the provider table." - - name: care_site_id - description: "A foreign key to the care site table." - - name: person_source_value - - name: gender_source_value - - name: gender_source_concept_id - - name: race_source_value - - name: race_source_concept_id - - name: ethnicity_source_value - - name: ethnicity_source_concept_id - - - name: care_site - columns: - - name: care_site_id - type: integer - tests: - - unique - - not_null - - name: care_site_name - type: varchar - - name: care_site_source_value - type: varchar - - name: location_id - type: integer - - name: place_of_service_concept_id - type: integer - - name: place_of_service_source_value - type: varchar - - - name: cdm_source - columns: - - name: cdm_etl_reference - type: string - - name: cdm_holder - type: string - tests: - - not_null - - name: cdm_release_date - type: date - tests: - - not_null - - name: cdm_source_abbreviation - type: string - tests: - - not_null - - name: cdm_source_name - type: string - tests: - - not_null - - name: cdm_version - type: string - - name: cdm_version_concept_id - type: integer - tests: - - not_null - - name: source_description - type: string - - name: source_documentation_reference - type: string - - name: source_release_date - type: date - tests: - - not_null - - name: vocabulary_version - type: string - tests: - - not_null - - - name: condition_era - columns: - - name: condition_era_id - type: integer - tests: - - unique - - not_null - - name: condition_concept_id - type: integer - tests: - - not_null - - name: condition_era_start_date - type: datetime - tests: - - not_null - - name: condition_era_end_date - type: datetime - tests: - - not_null - - name: condition_occurrence_count - type: integer - - name: person_id - type: integer - tests: - - not_null - - - name: condition_occurrence - columns: - - name: condition_occurrence_id - type: integer - tests: - - unique - - not_null - - name: condition_concept_id - type: integer - tests: - - not_null - - name: condition_start_date - type: date - tests: - - not_null - - name: condition_start_datetime - type: datetime - - name: condition_end_date - type: date - - name: condition_end_datetime - type: datetime - - name: condition_type_concept_id - type: integer - tests: - - not_null - - name: condition_status_concept_id - type: integer - - name: condition_source_value - type: string - - name: condition_source_concept_id - type: integer - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: stop_reason - type: string - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: cost - columns: - - name: cost_id - type: integer - tests: - - unique - - not_null - - name: amount_allowed - type: float - - name: cost_domain_id - type: string - tests: - - not_null - - name: cost_event_id - type: integer - tests: - - not_null - - name: cost_type_concept_id - type: integer - tests: - - not_null - - name: currency_concept_id - type: integer - - name: drg_concept_id - type: integer - - name: drg_source_value - type: string - - name: paid_by_patient - type: float - - name: paid_by_payer - type: float - - name: paid_by_primary - type: float - - name: paid_dispensing_fee - type: float - - name: paid_ingredient_cost - type: float - - name: paid_patient_coinsurance - type: float - - name: paid_patient_copay - type: float - - name: paid_patient_deductible - type: float - - name: payer_plan_period_id - type: integer - - name: revenue_code_concept_id - type: integer - - name: revenue_code_source_value - type: string - - name: total_charge - type: float - - name: total_cost - type: float - - name: total_paid - type: float - - - name: death - columns: - - name: person_id - type: integer - tests: - - not_null - - name: cause_concept_id - type: integer - - name: cause_source_concept_id - type: integer - - name: cause_source_value - type: string - - name: death_date - type: date - tests: - - not_null - - name: death_datetime - type: datetime - - name: death_type_concept_id - type: integer - - - name: device_exposure - columns: - - name: device_exposure_id - type: integer - tests: - - unique - - not_null - - name: device_concept_id - type: integer - tests: - - not_null - - name: device_exposure_start_date - type: date - tests: - - not_null - - name: device_exposure_start_datetime - type: datetime - - name: device_exposure_end_date - type: date - - name: device_exposure_end_datetime - type: datetime - - name: device_type_concept_id - type: integer - tests: - - not_null - - name: device_source_concept_id - type: integer - - name: device_source_value - type: string - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: quantity - type: integer - - name: unique_device_id - type: string - - name: unit_concept_id - type: integer - - name: unit_source_concept_id - type: integer - - name: unit_source_value - type: string - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: drug_era - columns: - - name: drug_era_id - type: integer - tests: - - unique - - not_null - - name: drug_concept_id - type: integer - tests: - - not_null - - name: drug_era_start_date - type: datetime - tests: - - not_null - - name: drug_era_end_date - type: datetime - tests: - - not_null - - name: drug_exposure_count - type: integer - - name: gap_days - type: integer - - name: person_id - type: integer - tests: - - not_null - - - name: drug_exposure - columns: - - name: drug_exposure_id - type: integer - tests: - - unique - - not_null - - name: drug_concept_id - type: integer - tests: - - not_null - - name: drug_exposure_start_date - type: date - tests: - - not_null - - name: drug_exposure_start_datetime - type: datetime - - name: drug_exposure_end_date - type: date - - name: drug_exposure_end_datetime - type: datetime - - name: drug_type_concept_id - type: integer - tests: - - not_null - - name: drug_source_concept_id - type: integer - - name: drug_source_value - type: string - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: quantity - type: float - - name: refills - type: integer - - name: route_concept_id - type: integer - - name: route_source_value - type: string - - name: sig - type: string - - name: stop_reason - type: string - - name: verbatim_end_date - type: date - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: location - columns: - - name: location_id - type: integer - tests: - - unique - - not_null - - name: address_1 - type: string - - name: address_2 - type: string - - name: city - type: string - - name: state - type: string - - name: county - type: string - - name: zip - type: string - - name: country_concept_id - type: integer - - name: country_source_value - type: string - - name: latitude - type: float - - name: longitude - type: float - - name: location_source_value - type: string - - - name: measurement - columns: - - name: measurement_id - type: integer - tests: - - unique - - not_null - - name: meas_event_field_concept_id - type: integer - - name: measurement_concept_id - type: integer - tests: - - not_null - - name: measurement_date - type: date - tests: - - not_null - - name: measurement_datetime - type: datetime - - name: measurement_event_id - type: bigint - - name: measurement_source_concept_id - type: integer - - name: measurement_source_value - type: string - - name: measurement_type_concept_id - type: integer - tests: - - not_null - - name: operator_concept_id - type: integer - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: range_high - type: float - - name: range_low - type: float - - name: unit_concept_id - type: integer - - name: unit_source_concept_id - type: integer - - name: unit_source_value - type: string - - name: value_as_concept_id - type: integer - - name: value_as_number - type: float - - name: value_source_value - type: string - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: observation - columns: - - name: observation_id - type: integer - tests: - - unique - - not_null - - name: obs_event_field_concept_id - type: integer - - name: observation_concept_id - type: integer - tests: - - not_null - - name: observation_date - type: date - tests: - - not_null - - name: observation_datetime - type: datetime - - name: observation_event_id - type: bigint - - name: observation_source_concept_id - type: integer - - name: observation_source_value - type: string - - name: observation_type_concept_id - type: integer - tests: - - not_null - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: qualifier_concept_id - type: integer - - name: qualifier_source_value - type: string - - name: unit_concept_id - type: integer - - name: unit_source_value - type: string - - name: value_as_concept_id - type: Integer - - name: value_as_number - type: float - - name: value_as_string - type: string - - name: value_source_value - type: string - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: observation_period - columns: - - name: observation_period_id - type: integer - tests: - - unique - - not_null - - name: person_id - type: integer - tests: - - not_null - - name: observation_period_start_date - type: date - tests: - - not_null - - name: observation_period_end_date - type: date - tests: - - not_null - - name: period_type_concept_id - type: integer - tests: - - not_null - - - name: payer_plan_period - columns: - - name: payer_plan_period_id - type: integer - tests: - - unique - - not_null - - name: person_id - type: integer - tests: - - not_null - - name: payer_concept_id - type: integer - - name: payer_source_concept_id - type: integer - - name: payer_source_value - type: string - - name: plan_concept_id - type: integer - - name: plan_source_concept_id - type: integer - - name: plan_source_value - type: string - - name: sponsor_concept_id - type: integer - - name: sponsor_source_concept_id - type: integer - - name: sponsor_source_value - type: string - - name: family_source_value - type: string - - name: payer_plan_period_start_date - type: date - tests: - - not_null - - name: payer_plan_period_end_date - type: date - tests: - - not_null - - name: stop_reason_concept_id - type: integer - - - name: dose_era - columns: - - name: dose_era_id - type: integer - - name: person_id - type: integer - - name: drug_concept_id - type: integer - - name: unit_concept_id - type: integer - - name: dose_value - type: float - - name: dose_era_start_date - type: datetime - - name: dose_era_end_date - type: datetime - - - name: episode - columns: - - name: episode_id - type: integer - tests: - - not_null - - name: person_id - type: integer - tests: - - not_null - - name: episode_concept_id - type: integer - - name: episode_start_date - type: date - tests: - - not_null - - name: episode_start_datetime - type: datetime - - name: episode_end_date - type: date - tests: - - not_null - - name: episode_end_datetime - type: datetime - - name: episode_parent_id - type: integer - - name: episode_number - type: integer - - name: episode_object_concept_id - type: integer - - name: episode_type_concept_id - type: integer - - name: episode_source_value - type: string - - name: episode_source_concept_id - type: integer - - - name: episode_event - columns: - - name: episode_id - type: integer - - name: event_id - type: integer - - name: episode_event_field_concept_id - type: integer - - - name: fact_relationship - columns: - - name: domain_concept_id_1 - type: integer - - name: fact_id_1 - type: integer - - name: domain_concept_id_2 - type: integer - - name: fact_id_2 - type: integer - - name: relationship_concept_id - type: integer - - - name: metadata - columns: - - name: metadata - columns: - - name: metadata_id - type: integer - - name: metadata_concept_id - type: integer - - name: metadata_type_concept_id - type: integer - - name: name - type: string - - name: value_as_string - type: string - - name: value_as_concept_id - type: integer - - name: value_as_number - type: float - - name: metadata_date - type: date - - name: metadata_datetime - type: datetime - - - name: note_nlp - columns: - - name: note_nlp_id - type: integer - - name: note_id - type: integer - - name: section_concept_id - type: integer - - name: snippet - type: string - - name: offset - type: integer - - name: lexical_variant - type: string - - name: note_nlp_concept_id - type: integer - - name: note_nlp_source_concept_id - type: integer - - name: nlp_system - type: string - - name: nlp_date - type: date - - name: nlp_datetime - type: datetime - - name: term_exists - type: string - - name: term_temporal - type: string - - name: term_modifiers - type: string - - - name: note - columns: - - name: note_id - type: integer - - name: person_id - type: integer - - name: note_date - type: date - - name: note_datetime - type: datetime - - name: note_type_concept_id - type: integer - - name: note_class_concept_id - type: integer - - name: note_title - type: string - - name: note_text - type: string - - name: encoding_concept_id - type: integer - - name: language_concept_id - type: integer - - name: provider_id - type: integer - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - name: note_source_value - type: string - - name: note_event_id - type: integer - - name: note_event_field_concept_id - type: integer - - - name: specimen - columns: - - name: specimen_id - type: integer - - name: person_id - type: integer - - name: specimen_concept_id - type: integer - - name: specimen_type_concept_id - type: integer - - name: specimen_date - type: date - - name: specimen_datetime - type: datetime - - name: quantity - type: float - - name: unit_concept_id - type: integer - - name: anatomic_site_concept_id - type: integer - - name: disease_status_concept_id - type: integer - - name: specimen_source_id - type: integer - - name: specimen_source_value - type: string - - name: unit_source_value - type: string - - name: anatomic_site_source_value - type: string - - name: disease_status_source_value - type: string \ No newline at end of file From c81ddc0419ca5e70c9253a45c545006c6451e590 Mon Sep 17 00:00:00 2001 From: Katy Sadowski Date: Sat, 28 Sep 2024 20:58:20 -0400 Subject: [PATCH 7/9] remove omop seeds, rename vocab seeds --- .vscode/settings.json | 1 + dbt_project.yml | 3 - models/omop/_omop__models.yml | 786 ------------------ models/omop/dose_era.sql | 10 +- models/omop/episode.sql | 16 +- models/omop/episode_event.sql | 7 +- models/omop/fact_relationship.sql | 9 +- models/omop/metadata.sql | 12 +- models/omop/note.sql | 19 +- models/omop/note_nlp.sql | 17 +- models/omop/specimen.sql | 18 +- .../vocabulary/_vocabulary__sources.yml | 12 +- seeds/omop/dose_era.csv | 1 - seeds/omop/episode.csv | 1 - seeds/omop/episode_event.csv | 1 - seeds/omop/fact_relationship.csv | 1 - seeds/omop/metadata.csv | 1 - seeds/omop/note.csv | 1 - seeds/omop/note_nlp.csv | 1 - seeds/omop/specimen.csv | 1 - ...ancestor.csv => concept_ancestor_seed.csv} | 0 ...ncept_class.csv => concept_class_seed.csv} | 0 ...ship.csv => concept_relationship_seed.csv} | 0 .../{concept.csv => concept_seed.csv} | 0 ...t_synonym.csv => concept_synonym_seed.csv} | 0 .../{domain.csv => domain_seed.csv} | 0 ...ug_strength.csv => drug_strength_seed.csv} | 0 ...relationship.csv => relationship_seed.csv} | 0 ...map.csv => source_to_concept_map_seed.csv} | 0 .../{vocabulary.csv => vocabulary_seed.csv} | 0 30 files changed, 112 insertions(+), 806 deletions(-) delete mode 100644 models/omop/_omop__models.yml delete mode 100644 seeds/omop/dose_era.csv delete mode 100644 seeds/omop/episode.csv delete mode 100644 seeds/omop/episode_event.csv delete mode 100644 seeds/omop/fact_relationship.csv delete mode 100644 seeds/omop/metadata.csv delete mode 100644 seeds/omop/note.csv delete mode 100644 seeds/omop/note_nlp.csv delete mode 100644 seeds/omop/specimen.csv rename seeds/vocabulary/{concept_ancestor.csv => concept_ancestor_seed.csv} (100%) rename seeds/vocabulary/{concept_class.csv => concept_class_seed.csv} (100%) rename seeds/vocabulary/{concept_relationship.csv => concept_relationship_seed.csv} (100%) rename seeds/vocabulary/{concept.csv => concept_seed.csv} (100%) rename seeds/vocabulary/{concept_synonym.csv => concept_synonym_seed.csv} (100%) rename seeds/vocabulary/{domain.csv => domain_seed.csv} (100%) rename seeds/vocabulary/{drug_strength.csv => drug_strength_seed.csv} (100%) rename seeds/vocabulary/{relationship.csv => relationship_seed.csv} (100%) rename seeds/vocabulary/{source_to_concept_map.csv => source_to_concept_map_seed.csv} (100%) rename seeds/vocabulary/{vocabulary.csv => vocabulary_seed.csv} (100%) diff --git a/.vscode/settings.json b/.vscode/settings.json index 8694f9b..bcd1d7e 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -25,4 +25,5 @@ "packages.yml" ] }, + "dbt.enableNewLineagePanel": true, } diff --git a/dbt_project.yml b/dbt_project.yml index c3440f4..d0fc492 100644 --- a/dbt_project.yml +++ b/dbt_project.yml @@ -26,9 +26,6 @@ seeds: map: +enabled: true +schema: map_seeds - omop: - +enabled: true - +schema: omop_seeds vocabulary: +enabled: true +schema: vocab_seeds diff --git a/models/omop/_omop__models.yml b/models/omop/_omop__models.yml deleted file mode 100644 index a596a74..0000000 --- a/models/omop/_omop__models.yml +++ /dev/null @@ -1,786 +0,0 @@ -version: 2 - -models: - - name: person - columns: - - name: person_id - description: "A unique identifier for each person." - tests: - - unique - - not_null - - name: gender_concept_id - tests: - - not_null - - name: year_of_birth - description: "The year of birth of the person." - tests: - - not_null - - name: month_of_birth - description: "The month of birth of the person." - - name: day_of_birth - description: "The day of birth of the person." - - name: birth_datetime - description: "The date and time of birth of the person." - - name: race_concept_id - tests: - - not_null - - name: ethnicity_concept_id - tests: - - not_null - - name: location_id - description: "A foreign key to the location table." - - name: provider_id - description: "A foreign key to the provider table." - - name: care_site_id - description: "A foreign key to the care site table." - - name: person_source_value - - name: gender_source_value - - name: gender_source_concept_id - - name: race_source_value - - name: race_source_concept_id - - name: ethnicity_source_value - - name: ethnicity_source_concept_id - - - name: care_site - columns: - - name: care_site_id - type: integer - tests: - - unique - - not_null - - name: care_site_name - type: varchar - - name: care_site_source_value - type: varchar - - name: location_id - type: integer - - name: place_of_service_concept_id - type: integer - - name: place_of_service_source_value - type: varchar - - - name: cdm_source - columns: - - name: cdm_etl_reference - type: string - - name: cdm_holder - type: string - tests: - - not_null - - name: cdm_release_date - type: date - tests: - - not_null - - name: cdm_source_abbreviation - type: string - tests: - - not_null - - name: cdm_source_name - type: string - tests: - - not_null - - name: cdm_version - type: string - - name: cdm_version_concept_id - type: integer - tests: - - not_null - - name: source_description - type: string - - name: source_documentation_reference - type: string - - name: source_release_date - type: date - tests: - - not_null - - name: vocabulary_version - type: string - tests: - - not_null - - - name: condition_era - columns: - - name: condition_era_id - type: integer - tests: - - unique - - not_null - - name: condition_concept_id - type: integer - tests: - - not_null - - name: condition_era_start_date - type: datetime - tests: - - not_null - - name: condition_era_end_date - type: datetime - tests: - - not_null - - name: condition_occurrence_count - type: integer - - name: person_id - type: integer - tests: - - not_null - - - name: condition_occurrence - columns: - - name: condition_occurrence_id - type: integer - tests: - - unique - - not_null - - name: condition_concept_id - type: integer - tests: - - not_null - - name: condition_start_date - type: date - tests: - - not_null - - name: condition_start_datetime - type: datetime - - name: condition_end_date - type: date - - name: condition_end_datetime - type: datetime - - name: condition_type_concept_id - type: integer - tests: - - not_null - - name: condition_status_concept_id - type: integer - - name: condition_source_value - type: string - - name: condition_source_concept_id - type: integer - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: stop_reason - type: string - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: cost - columns: - - name: cost_id - type: integer - tests: - - unique - - not_null - - name: amount_allowed - type: float - - name: cost_domain_id - type: string - tests: - - not_null - - name: cost_event_id - type: integer - tests: - - not_null - - name: cost_type_concept_id - type: integer - tests: - - not_null - - name: currency_concept_id - type: integer - - name: drg_concept_id - type: integer - - name: drg_source_value - type: string - - name: paid_by_patient - type: float - - name: paid_by_payer - type: float - - name: paid_by_primary - type: float - - name: paid_dispensing_fee - type: float - - name: paid_ingredient_cost - type: float - - name: paid_patient_coinsurance - type: float - - name: paid_patient_copay - type: float - - name: paid_patient_deductible - type: float - - name: payer_plan_period_id - type: integer - - name: revenue_code_concept_id - type: integer - - name: revenue_code_source_value - type: string - - name: total_charge - type: float - - name: total_cost - type: float - - name: total_paid - type: float - - - name: death - columns: - - name: person_id - type: integer - tests: - - not_null - - name: cause_concept_id - type: integer - - name: cause_source_concept_id - type: integer - - name: cause_source_value - type: string - - name: death_date - type: date - tests: - - not_null - - name: death_datetime - type: datetime - - name: death_type_concept_id - type: integer - - - name: device_exposure - columns: - - name: device_exposure_id - type: integer - tests: - - unique - - not_null - - name: device_concept_id - type: integer - tests: - - not_null - - name: device_exposure_start_date - type: date - tests: - - not_null - - name: device_exposure_start_datetime - type: datetime - - name: device_exposure_end_date - type: date - - name: device_exposure_end_datetime - type: datetime - - name: device_type_concept_id - type: integer - tests: - - not_null - - name: device_source_concept_id - type: integer - - name: device_source_value - type: string - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: quantity - type: integer - - name: unique_device_id - type: string - - name: unit_concept_id - type: integer - - name: unit_source_concept_id - type: integer - - name: unit_source_value - type: string - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: drug_era - columns: - - name: drug_era_id - type: integer - tests: - - unique - - not_null - - name: drug_concept_id - type: integer - tests: - - not_null - - name: drug_era_start_date - type: datetime - tests: - - not_null - - name: drug_era_end_date - type: datetime - tests: - - not_null - - name: drug_exposure_count - type: integer - - name: gap_days - type: integer - - name: person_id - type: integer - tests: - - not_null - - - name: drug_exposure - columns: - - name: drug_exposure_id - type: integer - tests: - - unique - - not_null - - name: drug_concept_id - type: integer - tests: - - not_null - - name: drug_exposure_start_date - type: date - tests: - - not_null - - name: drug_exposure_start_datetime - type: datetime - - name: drug_exposure_end_date - type: date - - name: drug_exposure_end_datetime - type: datetime - - name: drug_type_concept_id - type: integer - tests: - - not_null - - name: drug_source_concept_id - type: integer - - name: drug_source_value - type: string - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: quantity - type: float - - name: refills - type: integer - - name: route_concept_id - type: integer - - name: route_source_value - type: string - - name: sig - type: string - - name: stop_reason - type: string - - name: verbatim_end_date - type: date - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: location - columns: - - name: location_id - type: integer - tests: - - unique - - not_null - - name: address_1 - type: string - - name: address_2 - type: string - - name: city - type: string - - name: state - type: string - - name: county - type: string - - name: zip - type: string - - name: country_concept_id - type: integer - - name: country_source_value - type: string - - name: latitude - type: float - - name: longitude - type: float - - name: location_source_value - type: string - - - name: measurement - columns: - - name: measurement_id - type: integer - tests: - - unique - - not_null - - name: meas_event_field_concept_id - type: integer - - name: measurement_concept_id - type: integer - tests: - - not_null - - name: measurement_date - type: date - tests: - - not_null - - name: measurement_datetime - type: datetime - - name: measurement_event_id - type: bigint - - name: measurement_source_concept_id - type: integer - - name: measurement_source_value - type: string - - name: measurement_type_concept_id - type: integer - tests: - - not_null - - name: operator_concept_id - type: integer - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: range_high - type: float - - name: range_low - type: float - - name: unit_concept_id - type: integer - - name: unit_source_concept_id - type: integer - - name: unit_source_value - type: string - - name: value_as_concept_id - type: integer - - name: value_as_number - type: float - - name: value_source_value - type: string - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: observation - columns: - - name: observation_id - type: integer - tests: - - unique - - not_null - - name: obs_event_field_concept_id - type: integer - - name: observation_concept_id - type: integer - tests: - - not_null - - name: observation_date - type: date - tests: - - not_null - - name: observation_datetime - type: datetime - - name: observation_event_id - type: bigint - - name: observation_source_concept_id - type: integer - - name: observation_source_value - type: string - - name: observation_type_concept_id - type: integer - tests: - - not_null - - name: person_id - type: integer - tests: - - not_null - - name: provider_id - type: integer - - name: qualifier_concept_id - type: integer - - name: qualifier_source_value - type: string - - name: unit_concept_id - type: integer - - name: unit_source_value - type: string - - name: value_as_concept_id - type: Integer - - name: value_as_number - type: float - - name: value_as_string - type: string - - name: value_source_value - type: string - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - - name: observation_period - columns: - - name: observation_period_id - type: integer - tests: - - unique - - not_null - - name: person_id - type: integer - tests: - - not_null - - name: observation_period_start_date - type: date - tests: - - not_null - - name: observation_period_end_date - type: date - tests: - - not_null - - name: period_type_concept_id - type: integer - tests: - - not_null - - - name: payer_plan_period - columns: - - name: payer_plan_period_id - type: integer - tests: - - unique - - not_null - - name: person_id - type: integer - tests: - - not_null - - name: payer_concept_id - type: integer - - name: payer_source_concept_id - type: integer - - name: payer_source_value - type: string - - name: plan_concept_id - type: integer - - name: plan_source_concept_id - type: integer - - name: plan_source_value - type: string - - name: sponsor_concept_id - type: integer - - name: sponsor_source_concept_id - type: integer - - name: sponsor_source_value - type: string - - name: family_source_value - type: string - - name: payer_plan_period_start_date - type: date - tests: - - not_null - - name: payer_plan_period_end_date - type: date - tests: - - not_null - - name: stop_reason_concept_id - type: integer - - - name: dose_era - columns: - - name: dose_era_id - type: integer - - name: person_id - type: integer - - name: drug_concept_id - type: integer - - name: unit_concept_id - type: integer - - name: dose_value - type: float - - name: dose_era_start_date - type: datetime - - name: dose_era_end_date - type: datetime - - - name: episode - columns: - - name: episode_id - type: integer - tests: - - not_null - - name: person_id - type: integer - tests: - - not_null - - name: episode_concept_id - type: integer - - name: episode_start_date - type: date - tests: - - not_null - - name: episode_start_datetime - type: datetime - - name: episode_end_date - type: date - tests: - - not_null - - name: episode_end_datetime - type: datetime - - name: episode_parent_id - type: integer - - name: episode_number - type: integer - - name: episode_object_concept_id - type: integer - - name: episode_type_concept_id - type: integer - - name: episode_source_value - type: string - - name: episode_source_concept_id - type: integer - - - name: episode_event - columns: - - name: episode_id - type: integer - - name: event_id - type: integer - - name: episode_event_field_concept_id - type: integer - - - name: fact_relationship - columns: - - name: domain_concept_id_1 - type: integer - - name: fact_id_1 - type: integer - - name: domain_concept_id_2 - type: integer - - name: fact_id_2 - type: integer - - name: relationship_concept_id - type: integer - - - name: metadata - columns: - - name: metadata - columns: - - name: metadata_id - type: integer - - name: metadata_concept_id - type: integer - - name: metadata_type_concept_id - type: integer - - name: name - type: string - - name: value_as_string - type: string - - name: value_as_concept_id - type: integer - - name: value_as_number - type: float - - name: metadata_date - type: date - - name: metadata_datetime - type: datetime - - - name: note_nlp - columns: - - name: note_nlp_id - type: integer - - name: note_id - type: integer - - name: section_concept_id - type: integer - - name: snippet - type: string - - name: offset - type: integer - - name: lexical_variant - type: string - - name: note_nlp_concept_id - type: integer - - name: note_nlp_source_concept_id - type: integer - - name: nlp_system - type: string - - name: nlp_date - type: date - - name: nlp_datetime - type: datetime - - name: term_exists - type: string - - name: term_temporal - type: string - - name: term_modifiers - type: string - - - name: note - columns: - - name: note_id - type: integer - - name: person_id - type: integer - - name: note_date - type: date - - name: note_datetime - type: datetime - - name: note_type_concept_id - type: integer - - name: note_class_concept_id - type: integer - - name: note_title - type: string - - name: note_text - type: string - - name: encoding_concept_id - type: integer - - name: language_concept_id - type: integer - - name: provider_id - type: integer - - name: visit_occurrence_id - type: integer - - name: visit_detail_id - type: integer - - name: note_source_value - type: string - - name: note_event_id - type: integer - - name: note_event_field_concept_id - type: integer - - - name: specimen - columns: - - name: specimen_id - type: integer - - name: person_id - type: integer - - name: specimen_concept_id - type: integer - - name: specimen_type_concept_id - type: integer - - name: specimen_date - type: date - - name: specimen_datetime - type: datetime - - name: quantity - type: float - - name: unit_concept_id - type: integer - - name: anatomic_site_concept_id - type: integer - - name: disease_status_concept_id - type: integer - - name: specimen_source_id - type: integer - - name: specimen_source_value - type: string - - name: unit_source_value - type: string - - name: anatomic_site_source_value - type: string - - name: disease_status_source_value - type: string \ No newline at end of file diff --git a/models/omop/dose_era.sql b/models/omop/dose_era.sql index 714ffde..7573c7b 100644 --- a/models/omop/dose_era.sql +++ b/models/omop/dose_era.sql @@ -1 +1,9 @@ -SELECT * FROM {{ ref('stg_omop__dose_era') }} +SELECT + CAST(NULL AS INTEGER) AS dose_era_id + , CAST(NULL AS INTEGER) AS person_id + , CAST(NULL AS INTEGER) AS drug_concept_id + , CAST(NULL AS INTEGER) AS unit_concept_id + , CAST(NULL AS FLOAT) AS dose_value + , CAST(NULL AS DATE) AS dose_era_start_date + , CAST(NULL AS DATE) AS dose_era_end_date +WHERE 1 = 0 diff --git a/models/omop/episode.sql b/models/omop/episode.sql index e12b87a..6e7c56c 100644 --- a/models/omop/episode.sql +++ b/models/omop/episode.sql @@ -1 +1,15 @@ -SELECT * FROM {{ ref('stg_omop__episode') }} +SELECT + CAST(NULL AS INTEGER) AS episode_id + , CAST(NULL AS INTEGER) AS person_id + , CAST(NULL AS INTEGER) AS episode_concept_id + , CAST(NULL AS DATE) AS episode_start_date + , CAST(NULL AS TIMESTAMP) AS episode_start_datetime + , CAST(NULL AS DATE) AS episode_end_date + , CAST(NULL AS TIMESTAMP) AS episode_end_datetime + , CAST(NULL AS INTEGER) AS episode_parent_id + , CAST(NULL AS INTEGER) AS episode_number + , CAST(NULL AS INTEGER) AS episode_object_concept_id + , CAST(NULL AS INTEGER) AS episode_type_concept_id + , CAST(NULL AS VARCHAR) AS episode_source_value + , CAST(NULL AS INTEGER) AS episode_source_concept_id +WHERE 1 = 0 diff --git a/models/omop/episode_event.sql b/models/omop/episode_event.sql index 360a4cc..a2cde83 100644 --- a/models/omop/episode_event.sql +++ b/models/omop/episode_event.sql @@ -1 +1,6 @@ -SELECT * FROM {{ ref('stg_omop__episode_event') }} +SELECT + CAST(NULL AS INTEGER) AS episode_event_id + , CAST(NULL AS INTEGER) AS episode_id + , CAST(NULL AS INTEGER) AS event_id + , CAST(NULL AS INTEGER) AS episode_event_field_concept_id +WHERE 1 = 0 diff --git a/models/omop/fact_relationship.sql b/models/omop/fact_relationship.sql index a785da0..52a89d8 100644 --- a/models/omop/fact_relationship.sql +++ b/models/omop/fact_relationship.sql @@ -1 +1,8 @@ -SELECT * FROM {{ ref('stg_omop__fact_relationship') }} +SELECT + CAST(NULL AS INTEGER) AS fact_relationship_id + , CAST(NULL AS INTEGER) AS domain_concept_id_1 + , CAST(NULL AS INTEGER) AS fact_id_1 + , CAST(NULL AS INTEGER) AS domain_concept_id_2 + , CAST(NULL AS INTEGER) AS fact_id_2 + , CAST(NULL AS INTEGER) AS relationship_concept_id +WHERE 1 = 0 diff --git a/models/omop/metadata.sql b/models/omop/metadata.sql index 8b1975c..aae0b5c 100644 --- a/models/omop/metadata.sql +++ b/models/omop/metadata.sql @@ -1 +1,11 @@ -SELECT * FROM {{ ref('stg_omop__metadata') }} +SELECT + CAST(NULL AS INTEGER) AS metadata_id + , CAST(NULL AS INTEGER) AS metadata_concept_id + , CAST(NULL AS INTEGER) AS metadata_type_concept_id + , CAST(NULL AS VARCHAR) AS "name" + , CAST(NULL AS VARCHAR) AS value_as_string + , CAST(NULL AS INTEGER) AS value_as_concept_id + , CAST(NULL AS FLOAT) AS value_as_number + , CAST(NULL AS DATE) AS metadata_date + , CAST(NULL AS TIMESTAMP) AS metadata_datetime +WHERE 1 = 0 diff --git a/models/omop/note.sql b/models/omop/note.sql index ae5e9e2..13175c0 100644 --- a/models/omop/note.sql +++ b/models/omop/note.sql @@ -1 +1,18 @@ -SELECT * FROM {{ ref('stg_omop__note') }} +SELECT + CAST(NULL AS INTEGER) AS note_id + , CAST(NULL AS INTEGER) AS person_id + , CAST(NULL AS DATE) AS note_date + , CAST(NULL AS TIMESTAMP) AS note_datetime + , CAST(NULL AS INTEGER) AS note_type_concept_id + , CAST(NULL AS INTEGER) AS note_class_concept_id + , CAST(NULL AS VARCHAR) AS note_title + , CAST(NULL AS VARCHAR) AS note_text + , CAST(NULL AS INTEGER) AS encoding_concept_id + , CAST(NULL AS INTEGER) AS language_concept_id + , CAST(NULL AS INTEGER) AS provider_id + , CAST(NULL AS INTEGER) AS visit_occurrence_id + , CAST(NULL AS INTEGER) AS visit_detail_id + , CAST(NULL AS VARCHAR) AS note_source_value + , CAST(NULL AS INTEGER) AS note_event_id + , CAST(NULL AS INTEGER) AS note_event_field_concept_id +WHERE 1 = 0 diff --git a/models/omop/note_nlp.sql b/models/omop/note_nlp.sql index bd480bc..f94207d 100644 --- a/models/omop/note_nlp.sql +++ b/models/omop/note_nlp.sql @@ -1 +1,16 @@ -SELECT * FROM {{ ref('stg_omop__note_nlp') }} +SELECT + CAST(NULL AS INTEGER) AS note_nlp_id + , CAST(NULL AS INTEGER) AS note_id + , CAST(NULL AS INTEGER) AS section_concept_id + , CAST(NULL AS VARCHAR) AS snippet + , CAST(NULL AS INTEGER) AS "offset" + , CAST(NULL AS VARCHAR) AS lexical_variant + , CAST(NULL AS INTEGER) AS note_nlp_concept_id + , CAST(NULL AS INTEGER) AS note_nlp_source_concept_id + , CAST(NULL AS VARCHAR) AS nlp_system + , CAST(NULL AS DATE) AS nlp_date + , CAST(NULL AS TIMESTAMP) AS nlp_datetime + , CAST(NULL AS BOOLEAN) AS term_exists + , CAST(NULL AS VARCHAR) AS term_temporal + , CAST(NULL AS VARCHAR) AS term_modifiers +WHERE 1 = 0 diff --git a/models/omop/specimen.sql b/models/omop/specimen.sql index 53e174f..f63a784 100644 --- a/models/omop/specimen.sql +++ b/models/omop/specimen.sql @@ -1 +1,17 @@ -SELECT * FROM {{ ref('stg_omop__specimen') }} +SELECT + CAST(NULL AS INTEGER) AS specimen_id + , CAST(NULL AS INTEGER) AS person_id + , CAST(NULL AS INTEGER) AS specimen_concept_id + , CAST(NULL AS INTEGER) AS specimen_type_concept_id + , CAST(NULL AS DATE) AS specimen_date + , CAST(NULL AS TIMESTAMP) AS specimen_datetime + , CAST(NULL AS FLOAT) AS quantity + , CAST(NULL AS INTEGER) AS unit_concept_id + , CAST(NULL AS INTEGER) AS anatomic_site_concept_id + , CAST(NULL AS INTEGER) AS disease_status_concept_id + , CAST(NULL AS INTEGER) AS specimen_source_id + , CAST(NULL AS VARCHAR) AS specimen_source_value + , CAST(NULL AS VARCHAR) AS unit_source_value + , CAST(NULL AS VARCHAR) AS anatomic_site_source_value + , CAST(NULL AS VARCHAR) AS disease_status_source_value +WHERE 1 = 0 diff --git a/models/staging/vocabulary/_vocabulary__sources.yml b/models/staging/vocabulary/_vocabulary__sources.yml index 3ac308d..a9b0cdf 100644 --- a/models/staging/vocabulary/_vocabulary__sources.yml +++ b/models/staging/vocabulary/_vocabulary__sources.yml @@ -2,15 +2,25 @@ version: 2 sources: - name: vocabulary - schema: "{% if var('seed_source') %}{{ target.schema ~ '_vocab_seeds' }}{% else %}{{ target.schema }}{% endif %}" + schema: "{% if var('seed_source', false) %}{{ target.schema }}_vocab_seeds{% else %}{{ target.schema }}{% endif %}" tables: - name: concept + identifier: "{% if var('seed_source', false) %}concept_seed{% else %}concept{% endif %}" - name: concept_ancestor + identifier: "{% if var('seed_source', false) %}concept_ancestor_seed{% else %}concept_ancestor{% endif %}" - name: concept_class + identifier: "{% if var('seed_source', false) %}concept_class_seed{% else %}concept_class{% endif %}" - name: concept_relationship + identifier: "{% if var('seed_source', false) %}concept_relationship_seed{% else %}concept_relationship{% endif %}" - name: concept_synonym + identifier: "{% if var('seed_source', false) %}concept_synonym_seed{% else %}concept_synonym{% endif %}" - name: domain + identifier: "{% if var('seed_source', false) %}domain_seed{% else %}domain{% endif %}" - name: drug_strength + identifier: "{% if var('seed_source', false) %}drug_strength_seed{% else %}drug_strength{% endif %}" - name: relationship + identifier: "{% if var('seed_source', false) %}relationship_seed{% else %}relationship{% endif %}" - name: vocabulary + identifier: "{% if var('seed_source', false) %}vocabulary_seed{% else %}vocabulary{% endif %}" - name: source_to_concept_map + identifier: "{% if var('seed_source', false) %}source_to_concept_map_seed{% else %}source_to_concept_map{% endif %}" \ No newline at end of file diff --git a/seeds/omop/dose_era.csv b/seeds/omop/dose_era.csv deleted file mode 100644 index 1549128..0000000 --- a/seeds/omop/dose_era.csv +++ /dev/null @@ -1 +0,0 @@ -dose_era_id,person_id,drug_concept_id,unit_concept_id,dose_value,dose_era_start_date,dose_era_end_date \ No newline at end of file diff --git a/seeds/omop/episode.csv b/seeds/omop/episode.csv deleted file mode 100644 index bf89509..0000000 --- a/seeds/omop/episode.csv +++ /dev/null @@ -1 +0,0 @@ -episode_id,person_id,episode_concept_id,episode_start_date,episode_start_datetime,episode_end_date,episode_end_datetime,episode_parent_id,episode_number,episode_object_concept_id,episode_type_concept_id,episode_source_value,episode_source_concept_id \ No newline at end of file diff --git a/seeds/omop/episode_event.csv b/seeds/omop/episode_event.csv deleted file mode 100644 index 4b98c4f..0000000 --- a/seeds/omop/episode_event.csv +++ /dev/null @@ -1 +0,0 @@ -episode_id,event_id,episode_event_field_concept_id \ No newline at end of file diff --git a/seeds/omop/fact_relationship.csv b/seeds/omop/fact_relationship.csv deleted file mode 100644 index 22340e9..0000000 --- a/seeds/omop/fact_relationship.csv +++ /dev/null @@ -1 +0,0 @@ -domain_concept_id_1,fact_id_1,domain_concept_id_2,fact_id_2,relationship_concept_id \ No newline at end of file diff --git a/seeds/omop/metadata.csv b/seeds/omop/metadata.csv deleted file mode 100644 index 5187929..0000000 --- a/seeds/omop/metadata.csv +++ /dev/null @@ -1 +0,0 @@ -metadata_id,metadata_concept_id,metadata_type_concept_id,name,value_as_string,value_as_concept_id,value_as_number,metadata_date,metadata_datetime diff --git a/seeds/omop/note.csv b/seeds/omop/note.csv deleted file mode 100644 index 61973f3..0000000 --- a/seeds/omop/note.csv +++ /dev/null @@ -1 +0,0 @@ -note_id,person_id,note_date,note_datetime,note_type_concept_id,note_class_concept_id,note_title,note_text,encoding_concept_id,language_concept_id,provider_id,visit_occurrence_id,visit_detail_id,note_source_value,note_event_id,note_event_field_concept_id \ No newline at end of file diff --git a/seeds/omop/note_nlp.csv b/seeds/omop/note_nlp.csv deleted file mode 100644 index 3dadbbc..0000000 --- a/seeds/omop/note_nlp.csv +++ /dev/null @@ -1 +0,0 @@ -note_nlp_id,note_id,section_concept_id,snippet,offset,lexical_variant,note_nlp_concept_id,note_nlp_source_concept_id,nlp_system,nlp_date,nlp_datetime,term_exists,term_temporal,term_modifiers \ No newline at end of file diff --git a/seeds/omop/specimen.csv b/seeds/omop/specimen.csv deleted file mode 100644 index 7f2e9c1..0000000 --- a/seeds/omop/specimen.csv +++ /dev/null @@ -1 +0,0 @@ -specimen_id,person_id,specimen_concept_id,specimen_type_concept_id,specimen_date,specimen_datetime,quantity,unit_concept_id,anatomic_site_concept_id,disease_status_concept_id,specimen_source_id,specimen_source_value,unit_source_value,anatomic_site_source_value,disease_status_source_value \ No newline at end of file diff --git a/seeds/vocabulary/concept_ancestor.csv b/seeds/vocabulary/concept_ancestor_seed.csv similarity index 100% rename from seeds/vocabulary/concept_ancestor.csv rename to seeds/vocabulary/concept_ancestor_seed.csv diff --git a/seeds/vocabulary/concept_class.csv b/seeds/vocabulary/concept_class_seed.csv similarity index 100% rename from seeds/vocabulary/concept_class.csv rename to seeds/vocabulary/concept_class_seed.csv diff --git a/seeds/vocabulary/concept_relationship.csv b/seeds/vocabulary/concept_relationship_seed.csv similarity index 100% rename from seeds/vocabulary/concept_relationship.csv rename to seeds/vocabulary/concept_relationship_seed.csv diff --git a/seeds/vocabulary/concept.csv b/seeds/vocabulary/concept_seed.csv similarity index 100% rename from seeds/vocabulary/concept.csv rename to seeds/vocabulary/concept_seed.csv diff --git a/seeds/vocabulary/concept_synonym.csv b/seeds/vocabulary/concept_synonym_seed.csv similarity index 100% rename from seeds/vocabulary/concept_synonym.csv rename to seeds/vocabulary/concept_synonym_seed.csv diff --git a/seeds/vocabulary/domain.csv b/seeds/vocabulary/domain_seed.csv similarity index 100% rename from seeds/vocabulary/domain.csv rename to seeds/vocabulary/domain_seed.csv diff --git a/seeds/vocabulary/drug_strength.csv b/seeds/vocabulary/drug_strength_seed.csv similarity index 100% rename from seeds/vocabulary/drug_strength.csv rename to seeds/vocabulary/drug_strength_seed.csv diff --git a/seeds/vocabulary/relationship.csv b/seeds/vocabulary/relationship_seed.csv similarity index 100% rename from seeds/vocabulary/relationship.csv rename to seeds/vocabulary/relationship_seed.csv diff --git a/seeds/vocabulary/source_to_concept_map.csv b/seeds/vocabulary/source_to_concept_map_seed.csv similarity index 100% rename from seeds/vocabulary/source_to_concept_map.csv rename to seeds/vocabulary/source_to_concept_map_seed.csv diff --git a/seeds/vocabulary/vocabulary.csv b/seeds/vocabulary/vocabulary_seed.csv similarity index 100% rename from seeds/vocabulary/vocabulary.csv rename to seeds/vocabulary/vocabulary_seed.csv From 15809110a5149f5bba0fd6555dc0fe277673c342 Mon Sep 17 00:00:00 2001 From: Lawrence Adams Date: Sun, 29 Sep 2024 08:46:14 +0100 Subject: [PATCH 8/9] chore: remove now redundant omop staging models - these models were used to create empty tables to align with the omop schema by having all tables expected --- models/staging/omop/_omop__models.yml | 9 --------- models/staging/omop/_omop__sources.yml | 14 -------------- models/staging/omop/stg_omop__dose_era.sql | 14 -------------- models/staging/omop/stg_omop__episode.sql | 14 -------------- models/staging/omop/stg_omop__episode_event.sql | 14 -------------- .../staging/omop/stg_omop__fact_relationship.sql | 14 -------------- models/staging/omop/stg_omop__metadata.sql | 14 -------------- models/staging/omop/stg_omop__note.sql | 14 -------------- models/staging/omop/stg_omop__note_nlp.sql | 14 -------------- models/staging/omop/stg_omop__specimen.sql | 14 -------------- 10 files changed, 135 deletions(-) delete mode 100644 models/staging/omop/_omop__models.yml delete mode 100644 models/staging/omop/_omop__sources.yml delete mode 100644 models/staging/omop/stg_omop__dose_era.sql delete mode 100644 models/staging/omop/stg_omop__episode.sql delete mode 100644 models/staging/omop/stg_omop__episode_event.sql delete mode 100644 models/staging/omop/stg_omop__fact_relationship.sql delete mode 100644 models/staging/omop/stg_omop__metadata.sql delete mode 100644 models/staging/omop/stg_omop__note.sql delete mode 100644 models/staging/omop/stg_omop__note_nlp.sql delete mode 100644 models/staging/omop/stg_omop__specimen.sql diff --git a/models/staging/omop/_omop__models.yml b/models/staging/omop/_omop__models.yml deleted file mode 100644 index 9b3a597..0000000 --- a/models/staging/omop/_omop__models.yml +++ /dev/null @@ -1,9 +0,0 @@ -models: - - name: stg_omop__dose_era - - name: stg_omop__episode - - name: stg_omop__episode_event - - name: stg_omop__fact_relationship - - name: stg_omop__metadata - - name: stg_omop__note - - name: stg_omop__note_nlp - - name: stg_omop__specimen \ No newline at end of file diff --git a/models/staging/omop/_omop__sources.yml b/models/staging/omop/_omop__sources.yml deleted file mode 100644 index ce0b8de..0000000 --- a/models/staging/omop/_omop__sources.yml +++ /dev/null @@ -1,14 +0,0 @@ -version: 2 - -sources: - - name: omop - schema: "{{ target.schema ~ '_omop_seeds' }}" - tables: - - name: fact_relationship - - name: dose_era - - name: episode - - name: episode_event - - name: metadata - - name: note - - name: note_nlp - - name: specimen \ No newline at end of file diff --git a/models/staging/omop/stg_omop__dose_era.sql b/models/staging/omop/stg_omop__dose_era.sql deleted file mode 100644 index abf595b..0000000 --- a/models/staging/omop/stg_omop__dose_era.sql +++ /dev/null @@ -1,14 +0,0 @@ -{% set column_names = - dbt_utils.get_filtered_columns_in_relation( source('omop', 'dose_era') ) -%} - - -WITH cte_dose_era_lower AS ( - - SELECT - {{ lowercase_columns(column_names) }} - FROM {{ source('omop','dose_era') }} -) - -SELECT * -FROM cte_dose_era_lower diff --git a/models/staging/omop/stg_omop__episode.sql b/models/staging/omop/stg_omop__episode.sql deleted file mode 100644 index 77d4803..0000000 --- a/models/staging/omop/stg_omop__episode.sql +++ /dev/null @@ -1,14 +0,0 @@ -{% set column_names = - dbt_utils.get_filtered_columns_in_relation( source('omop', 'episode') ) -%} - - -WITH cte_episode_lower AS ( - - SELECT - {{ lowercase_columns(column_names) }} - FROM {{ source('omop','episode') }} -) - -SELECT * -FROM cte_episode_lower diff --git a/models/staging/omop/stg_omop__episode_event.sql b/models/staging/omop/stg_omop__episode_event.sql deleted file mode 100644 index d61563d..0000000 --- a/models/staging/omop/stg_omop__episode_event.sql +++ /dev/null @@ -1,14 +0,0 @@ -{% set column_names = - dbt_utils.get_filtered_columns_in_relation( source('omop', 'episode_event') ) -%} - - -WITH cte_episode_event_lower AS ( - - SELECT - {{ lowercase_columns(column_names) }} - FROM {{ source('omop','episode_event') }} -) - -SELECT * -FROM cte_episode_event_lower diff --git a/models/staging/omop/stg_omop__fact_relationship.sql b/models/staging/omop/stg_omop__fact_relationship.sql deleted file mode 100644 index d40f1fb..0000000 --- a/models/staging/omop/stg_omop__fact_relationship.sql +++ /dev/null @@ -1,14 +0,0 @@ -{% set column_names = - dbt_utils.get_filtered_columns_in_relation( source('omop', 'fact_relationship') ) -%} - - -WITH cte_fact_relationship_lower AS ( - - SELECT - {{ lowercase_columns(column_names) }} - FROM {{ source('omop','fact_relationship') }} -) - -SELECT * -FROM cte_fact_relationship_lower diff --git a/models/staging/omop/stg_omop__metadata.sql b/models/staging/omop/stg_omop__metadata.sql deleted file mode 100644 index 0fca7e4..0000000 --- a/models/staging/omop/stg_omop__metadata.sql +++ /dev/null @@ -1,14 +0,0 @@ -{% set column_names = - dbt_utils.get_filtered_columns_in_relation( source('omop', 'metadata') ) -%} - - -WITH cte_metadata_lower AS ( - - SELECT - {{ lowercase_columns(column_names) }} - FROM {{ source('omop','metadata') }} -) - -SELECT * -FROM cte_metadata_lower diff --git a/models/staging/omop/stg_omop__note.sql b/models/staging/omop/stg_omop__note.sql deleted file mode 100644 index c3d902d..0000000 --- a/models/staging/omop/stg_omop__note.sql +++ /dev/null @@ -1,14 +0,0 @@ -{% set column_names = - dbt_utils.get_filtered_columns_in_relation( source('omop', 'note') ) -%} - - -WITH cte_note_lower AS ( - - SELECT - {{ lowercase_columns(column_names) }} - FROM {{ source('omop','note') }} -) - -SELECT * -FROM cte_note_lower diff --git a/models/staging/omop/stg_omop__note_nlp.sql b/models/staging/omop/stg_omop__note_nlp.sql deleted file mode 100644 index 94b2ea9..0000000 --- a/models/staging/omop/stg_omop__note_nlp.sql +++ /dev/null @@ -1,14 +0,0 @@ -{% set column_names = - dbt_utils.get_filtered_columns_in_relation( source('omop', 'note_nlp') ) -%} - - -WITH cte_note_nlp_lower AS ( - - SELECT - {{ lowercase_columns(column_names) }} - FROM {{ source('omop','note_nlp') }} -) - -SELECT * -FROM cte_note_nlp_lower diff --git a/models/staging/omop/stg_omop__specimen.sql b/models/staging/omop/stg_omop__specimen.sql deleted file mode 100644 index 6ba8a59..0000000 --- a/models/staging/omop/stg_omop__specimen.sql +++ /dev/null @@ -1,14 +0,0 @@ -{% set column_names = - dbt_utils.get_filtered_columns_in_relation( source('omop', 'specimen') ) -%} - - -WITH cte_specimen_lower AS ( - - SELECT - {{ lowercase_columns(column_names) }} - FROM {{ source('omop','specimen') }} -) - -SELECT * -FROM cte_specimen_lower From 417df6a9f2e16aad7aa98cef3933a96b668adf9a Mon Sep 17 00:00:00 2001 From: Katy Sadowski Date: Sun, 29 Sep 2024 14:23:18 -0400 Subject: [PATCH 9/9] vocab models always build --- models/omop/{seed_vocab => }/concept.sql | 2 -- models/omop/{seed_vocab => }/concept_ancestor.sql | 2 -- models/omop/{seed_vocab => }/concept_class.sql | 2 -- models/omop/{seed_vocab => }/concept_relationship.sql | 2 -- models/omop/{seed_vocab => }/concept_synonym.sql | 2 -- models/omop/{seed_vocab => }/domain.sql | 2 -- models/omop/{seed_vocab => }/drug_strength.sql | 2 -- models/omop/{seed_vocab => }/relationship.sql | 2 -- models/omop/source_to_concept_map.sql | 1 + models/omop/{seed_vocab => }/vocabulary.sql | 2 -- 10 files changed, 1 insertion(+), 18 deletions(-) rename models/omop/{seed_vocab => }/concept.sql (51%) rename models/omop/{seed_vocab => }/concept_ancestor.sql (55%) rename models/omop/{seed_vocab => }/concept_class.sql (54%) rename models/omop/{seed_vocab => }/concept_relationship.sql (57%) rename models/omop/{seed_vocab => }/concept_synonym.sql (55%) rename models/omop/{seed_vocab => }/domain.sql (51%) rename models/omop/{seed_vocab => }/drug_strength.sql (54%) rename models/omop/{seed_vocab => }/relationship.sql (53%) create mode 100644 models/omop/source_to_concept_map.sql rename models/omop/{seed_vocab => }/vocabulary.sql (52%) diff --git a/models/omop/seed_vocab/concept.sql b/models/omop/concept.sql similarity index 51% rename from models/omop/seed_vocab/concept.sql rename to models/omop/concept.sql index 93a594e..03f9f2a 100644 --- a/models/omop/seed_vocab/concept.sql +++ b/models/omop/concept.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__concept') }} diff --git a/models/omop/seed_vocab/concept_ancestor.sql b/models/omop/concept_ancestor.sql similarity index 55% rename from models/omop/seed_vocab/concept_ancestor.sql rename to models/omop/concept_ancestor.sql index 84545b3..4757c50 100644 --- a/models/omop/seed_vocab/concept_ancestor.sql +++ b/models/omop/concept_ancestor.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__concept_ancestor') }} diff --git a/models/omop/seed_vocab/concept_class.sql b/models/omop/concept_class.sql similarity index 54% rename from models/omop/seed_vocab/concept_class.sql rename to models/omop/concept_class.sql index cede0f0..0cf991d 100644 --- a/models/omop/seed_vocab/concept_class.sql +++ b/models/omop/concept_class.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__concept_class') }} diff --git a/models/omop/seed_vocab/concept_relationship.sql b/models/omop/concept_relationship.sql similarity index 57% rename from models/omop/seed_vocab/concept_relationship.sql rename to models/omop/concept_relationship.sql index 1763bac..a40fc78 100644 --- a/models/omop/seed_vocab/concept_relationship.sql +++ b/models/omop/concept_relationship.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__concept_relationship') }} diff --git a/models/omop/seed_vocab/concept_synonym.sql b/models/omop/concept_synonym.sql similarity index 55% rename from models/omop/seed_vocab/concept_synonym.sql rename to models/omop/concept_synonym.sql index 1fa6b0b..58fde63 100644 --- a/models/omop/seed_vocab/concept_synonym.sql +++ b/models/omop/concept_synonym.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__concept_synonym') }} diff --git a/models/omop/seed_vocab/domain.sql b/models/omop/domain.sql similarity index 51% rename from models/omop/seed_vocab/domain.sql rename to models/omop/domain.sql index 6a856dd..adeedeb 100644 --- a/models/omop/seed_vocab/domain.sql +++ b/models/omop/domain.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__domain') }} diff --git a/models/omop/seed_vocab/drug_strength.sql b/models/omop/drug_strength.sql similarity index 54% rename from models/omop/seed_vocab/drug_strength.sql rename to models/omop/drug_strength.sql index cd93883..dd76b27 100644 --- a/models/omop/seed_vocab/drug_strength.sql +++ b/models/omop/drug_strength.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__drug_strength') }} diff --git a/models/omop/seed_vocab/relationship.sql b/models/omop/relationship.sql similarity index 53% rename from models/omop/seed_vocab/relationship.sql rename to models/omop/relationship.sql index e54e898..bd7f11d 100644 --- a/models/omop/seed_vocab/relationship.sql +++ b/models/omop/relationship.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__relationship') }} diff --git a/models/omop/source_to_concept_map.sql b/models/omop/source_to_concept_map.sql new file mode 100644 index 0000000..b01ec0c --- /dev/null +++ b/models/omop/source_to_concept_map.sql @@ -0,0 +1 @@ +SELECT * FROM {{ ref('stg_vocabulary__source_to_concept_map') }} diff --git a/models/omop/seed_vocab/vocabulary.sql b/models/omop/vocabulary.sql similarity index 52% rename from models/omop/seed_vocab/vocabulary.sql rename to models/omop/vocabulary.sql index 9f3aedc..ed51f3e 100644 --- a/models/omop/seed_vocab/vocabulary.sql +++ b/models/omop/vocabulary.sql @@ -1,3 +1 @@ -{{ config(enabled=var('seed_source', true)) }} - SELECT * FROM {{ ref('stg_vocabulary__vocabulary') }}