omop

OMOP Common Data Model [source].

Install and mount omop in a new instance:

>>> pip install omop
>>> lamin init --storage ./test-omop --schema omop

Import the package:

>>> import omop

Registries:

CareSite()	Uniquely identified healthcare delivery unit or an organizational unit, where healthcare services are provided.
CdmSource()	Source database and the process details used to transform the data into the OMOP Common Data Model.
Cohort()	Records of subjects that satisfy a given set of criteria for a duration of time.
CohortDefinition()	Records defining a Cohort derived from the data through the associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT table.
Concept()	The Standardized Vocabularies contain records, or Concepts, that uniquely express clinical information in all domain tables of the CDM.
ConceptAncestor()	Hierarchical relationships between Concepts.
ConceptRelationship()	Records that define direct relationships between any two Concepts and the nature or type of the relationship.
ConceptSynonym()	Alternate names and descriptions for Concepts.
ConditionEra()	Span of time when the Person is assumed to have a given condition.
ConditionOccurrence()	Records of Events of a Person.
Cost()	Records containing the cost of any medical event recorded in one of the OMOP clinical event tables.
Death()	Clinical event for how and when a Person dies.
DeviceExposure()	Information about a persons exposure to a foreign physical object or instrument.
Domain()	OMOP-defined Domains the Concepts of the Standardized Vocabularies can belong to.
DoseEra()	Span of time when the Person is assumed to be exposed to a constant dose of a specific active ingredient.
DrugEra()	Span of time when the Person is assumed to be exposed to a particular active ingredient.
DrugExposure()	Records about the exposure to a Drug ingested or otherwise introduced into the body.
DrugStrength()	Amount or concentration and associated units of a specific ingredient contained within a particular drug product.
Episode()	Aggregates lower-level clinical events into a higher-level abstraction representing clinically and analytically relevant disease phases, outcomes and treatments.
EpisodeEvent()	The EPISODE_EVENT table connects qualifying clinical events to the appropriate EPISODE entry.
FactRelationship()	Records about the relationships between facts stored as records in any table of the CDM.
Location()	Capture physical location or address information of Persons and Care Sites.
Measurement()	Records of Measurements, i.e. structured values (numerical or categorical) obtained through systematic and standardized examination or testing of a Person or Persons sample.
Metadata()	Metadata information about a dataset that has been transformed to the OMOP Common Data Model.
Note()	Unstructured information that was recorded by a provider about a patient in free text notes on a given date.
NoteNlp()	Encodes all output of NLP on clinical notes.
Observation()	Clinical facts about a Person obtained in the context of examination, questioning or a procedure.
ObservationPeriod()	Records which define spans of time during which two conditions are expected to hold.
PayerPlanPeriod()	Details of the period of time that a Person is continuously enrolled under a specific health Plan benefit structure from a given Payer.
Person()	Identity management for all Persons in the database.
ProcedureOccurrence()	Records of activities or processes ordered by, or carried out by, a healthcare provider on the patient with a diagnostic or therapeutic purpose.
Provider()	Uniquely identified healthcare providers.
Relationship()	All types of relationships that can be used to associate any two concepts in the CONCEPT_RELATIONSHP table.
SourceToConceptMap()	The source to concept map table is a legacy data structure within the OMOP Common Data Model.
Specimen()	The specimen domain contains the records identifying biological samples from a person.
VisitDetail()	Optional table used to represents details of each record in the parent VISIT_OCCURRENCE table.
VisitOccurrence()	Events where Persons engage with the healthcare system for a duration of time.
Vocabulary()	Vocabularies collected from various sources or created de novo by the OMOP community.