OMOP Profiles

LinkML schema for defining the set of profiles, or 'shapes' of data that can be validly populated with clinical endpoints in the OMOP CDM. This is intended to be used for defining the permissible semantic structures that can be used to populate the CDM, such as EAV form, or direct concept identifier slots.

URI: https://athena.ohdsi.org/search-terms/terms/omop_profiles

Name: omop_profiles

Classes

Class	Description
CDMProfiles	A collection of OMOP CDM profiles describing the permissible semantic structu...
CDMSemanticUnits	A collection of named semantic units used for defining permissible values for...
CDMValueSet	A labelled value set defining a set of permissible values for a particular te...
CDMValueSets	A collection of value sets used for defining permissible values for template ...
Concept	Concept that serves as a member of a semantic object
OmopCdmProfile	A compositional profile describing how a particular clinical endpoint is repr...
OmopSemanticObject	Abstract base class for OMOP semantic objects
OmopConcept	A single labelled OMOP concept for use in higher level semantic annotations
OmopEnum	Enumeration (static) of permissible values for a particular slot
OmopGroup	Named group of OMOP concepts defined by their membership in a particular grou...
OmopValueSet	A semantic grouping of mixed types of permissible values for a template slot
OmopTemplate	A compositional semantic template describing how one or more OMOP concepts ar...
OmopTemplates	A collection of OMOP semantic templates for defining complex semantic structu...

Slots

Slot	Description
cdm_profile	Name of a registered OmopCdmProfile to use for this template
cdm_table
class_uri
concept_id	OMOP concept_id
concept_slot
entity_concept	Concept or group of concepts that may populate the CDM concept slot for this ...
enum_members
label
members
name
named_concepts
named_enumerators
named_groups
named_valuesets
notes
parent_concepts	Semantic parent concepts or grouping parents
profiles
role
templates
value_concept	Group of permissible values for value slots (e
value_slot
valueset_members
valueset_name
valuesets

Enumerations

Enumeration	Description
CdmTable	OMOP CDM table to which a semantic template applies

Types

Type	Description
Boolean	A binary (true or false) value
Curie	a compact URI
Date	a date (year, month and day) in an idealized calendar
DateOrDatetime	Either a date or a datetime
Datetime	The combination of a date and time
Decimal	A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double	A real number that conforms to the xsd:double specification
Float	A real number that conforms to the xsd:float specification
Integer	An integer
Jsonpath	A string encoding a JSON Path
Jsonpointer	A string encoding a JSON Pointer
Ncname	Prefix part of CURIE
Nodeidentifier	A URI, CURIE or BNODE that represents a node in a model
Objectidentifier	A URI or CURIE that represents an object in the model
Sparqlpath	A string encoding a SPARQL Property Path
String	A character string
Time	A time object represents a (local) time of day, independent of any particular...
Uri	a complete URI
Uriorcurie	a URI or a CURIE

Subsets

Subset	Description