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