Bunnycore API referenceEntities

core.entities

source

This script describes the entities used by the database connection.

Concept

class Concept(
  concept_id = Column(Integer, primary_key=True),
  concept_name = Column(String(255), nullable=False),
  domain_id = Column(String(20), nullable=False),
  vocabulary_id = Column(String(20), nullable=False),
  concept_class_id = Column(String(20), nullable=False),
  standard_concept = Column(String(1), nullable=True),
  concept_code = Column(String(50), nullable=False),
  valid_start_date = Column(Date, nullable=False),
  valid_end_date = Column(Date, nullable=False),
  invalid_reason = Column(String(1), nullable=True),
)

A sqlalchemy.orm.DeclarativeBase class representing the concept table of the OMOP-CDM

Person

class Person(
    person_id = Column(Integer, primary_key=True)
    gender_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=False
    )
    year_of_birth = Column(Integer, nullable=False)
    month_of_birth = Column(Integer, nullable=True)
    day_of_birth = Column(Integer, nullable=True)
    birth_datetime = Column(DateTime, nullable=True)
    race_concept_id = Column(Integer, ForeignKey("concept.concept_id"), nullable=False)
    ethnicity_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=False
    )
    location_id = Column(Integer, nullable=True)
    provider_id = Column(Integer, nullable=True)
    care_site_id = Column(Integer, nullable=True)
    person_source_value = Column(String(50), nullable=True)
    gender_source_value = Column(String(50), nullable=True)
    gender_source_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
    race_source_value = Column(String(50), nullable=True)
    race_source_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
    ethnicity_source_value = Column(String(50), nullable=True)
    ethnicity_source_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
)

A sqlalchemy.orm.DeclarativeBase class representing the person table of the OMOP-CDM

Measurement

class Measurement(
  measurement_id = Column(Integer, primary_key=True)
  person_id = Column(Integer, ForeignKey("person.person_id"), nullable=False)
  measurement_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=False
  )
  measurement_date = Column(Date, nullable=False)
  measurement_datetime = Column(DateTime, nullable=True)
  measurement_time = Column(String(10), nullable=True)
  measurement_type_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=False
  )
  operator_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=True
  )
  value_as_number = Column(Numeric, nullable=True)
  value_as_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=True
  )
  unit_concept_id = Column(Integer, ForeignKey("concept.concept_id"), nullable=True)
  range_low = Column(Numeric, nullable=True)
  range_high = Column(Numeric, nullable=True)
  provider_id = Column(Integer, nullable=True)
  visit_occurrence_id = Column(Integer, nullable=True)
  visit_detail_id = Column(Integer, nullable=True)
  measurement_source_value = Column(String(50), nullable=True)
  measurement_source_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=True
  )
  unit_source_value = Column(String(50), nullable=True)
  unit_source_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=True
  )
  value_source_value = Column(String(50), nullable=True)
  measurement_event_id = Column(BigInteger, nullable=True)
  meas_event_field_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=True
  )
)

ConditionOccurrence

class ConditionOccurrence(
    condition_occurrence_id = Column(Integer, primary_key=True)
    person_id = Column(Integer, ForeignKey("person.person_id"), nullable=False)
    condition_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=False
    )
    condition_start_date = Column(Date, nullable=False)
    condition_start_datetime = Column(DateTime, nullable=True)
    condition_end_date = Column(Date, nullable=True)
    condition_end_datetime = Column(DateTime, nullable=True)
    condition_type_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=False
    )
    condition_status_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
    stop_reason = Column(String(20), nullable=True)
    provider_id = Column(Integer, nullable=True)
    visit_occurrence_id = Column(Integer, nullable=True)
    visit_detail_id = Column(Integer, nullable=True)
    condition_source_value = Column(String(50), nullable=True)
    condition_source_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
    condition_status_source_value = Column(String(50), nullable=True)
)

Observation

class Observation(
    observation_id = Column(Integer, primary_key=True)
    person_id = Column(Integer, ForeignKey("person.person_id"), nullable=False)
    observation_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=False
    )
    observation_date = Column(Date, nullable=False)
    observation_datetime = Column(DateTime, nullable=True)
    observation_type_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=False
    )
    value_as_number = Column(Numeric, nullable=True)
    value_as_string = Column(String(60), nullable=True)
    value_as_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
    qualifier_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
    unit_concept_id = Column(Integer, ForeignKey("concept.concept_id"), nullable=True)
    provider_id = Column(Integer, nullable=True)
    visit_occurrence_id = Column(Integer, nullable=True)
    visit_detail_id = Column(Integer, nullable=True)
    observation_source_value = Column(String(50), nullable=True)
    observation_source_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
    unit_source_value = Column(String(50), nullable=True)
    qualifier_source_value = Column(String(50), nullable=True)
    value_source_value = Column(String(50), nullable=True)
    observation_event_id = Column(BigInteger, nullable=True)
    obs_event_field_concept_id = Column(
        Integer, ForeignKey("concept.concept_id"), nullable=True
    )
)

ProcedureOccurrence

class ProcedureOccurrence(
  procedure_occurrence_id = Column(Integer, primary_key=True)
  person_id = Column(Integer, ForeignKey("person.person_id"), nullable=False)
  procedure_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=False
  )
  procedure_date = Column(Date, nullable=False)
  procedure_datetime = Column(DateTime, nullable=True)
  procedure_end_date = Column(Date, nullable=True)
  procedure_end_datetime = Column(DateTime, nullable=True)
  procedure_type_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=False
  )
  modifier_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=True
  )
  quantity = Column(Integer, nullable=True)
  provider_id = Column(Integer, nullable=True)
  visit_occurrence_id = Column(Integer, nullable=True)
  visit_detail_id = Column(Integer, nullable=True)
  procedure_source_value = Column(String(50), nullable=True)
  procedure_source_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=True
  )
  modifier_source_value = Column(String(50), nullable=True)
)

DrugExposure

class DrugExposure(
  drug_exposure_id = Column(Integer, primary_key=True)
  person_id = Column(Integer, ForeignKey("person.person_id"), nullable=False)
  drug_concept_id = Column(Integer, ForeignKey("concept.concept_id"), nullable=False)
  drug_exposure_start_date = Column(Date, nullable=False)
  drug_exposure_start_datetime = Column(DateTime, nullable=True)
  drug_exposure_end_date = Column(Date, nullable=False)
  drug_exposure_end_datetime = Column(DateTime, nullable=True)
  verbatim_end_date = Column(Date, nullable=True)
  drug_type_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=False
  )
  stop_reason = Column(String(20), nullable=True)
  refills = Column(Integer, nullable=True)
  quantity = Column(Numeric, nullable=True)
  days_supply = Column(Integer, nullable=True)
  sig = Column(Text, nullable=True)
  route_concept_id = Column(Integer, ForeignKey("concept.concept_id"), nullable=True)
  lot_number = Column(String(50), nullable=True)
  provider_id = Column(Integer, nullable=True)
  visit_occurrence_id = Column(Integer, nullable=True)
  visit_detail_id = Column(Integer, nullable=True)
  drug_source_value = Column(String(50), nullable=True)
  drug_source_concept_id = Column(
      Integer, ForeignKey("concept.concept_id"), nullable=True
  )
  route_source_value = Column(String(50), nullable=True)
  dose_unit_source_value = Column(String(50), nullable=True)
)

Relationships

imported by query_solvers

Db ManagerEnums