Class: Procedure

A clinical procedure performed on a subject. By preference a single concept to indicate both the procedure and the body site should be used. In cases where this is not possible, the body site should be indicated using a separate ontology class. e.g. {"code":{"NCIT:C51585": "Biopsy of Soft Palate"}} {"code":{"NCIT:C28743": "Punch Biopsy"}, "body_site":{"UBERON:0003403": "skin of forearm"}} - a punch biopsy of the skin from the forearm FHIR mapping: Procedure (https://www.hl7.org/fhir/procedure.html)

URI: phenopackets:Procedure

erDiagram Procedure { } TimeElement { string timestamp } OntologyClass { string id string label } TimeInterval { string end string start } GestationalAge { integer days integer weeks } AgeRange { } Age { string iso8601duration } Procedure ||--|o OntologyClass : "bodySite" Procedure ||--|o OntologyClass : "code" Procedure ||--|o TimeElement : "performed" TimeElement ||--|o Age : "age" TimeElement ||--|o AgeRange : "ageRange" TimeElement ||--|o GestationalAge : "gestationalAge" TimeElement ||--|o TimeInterval : "interval" TimeElement ||--|o OntologyClass : "ontologyClass" AgeRange ||--|o Age : "end" AgeRange ||--|o Age : "start"

Slots

Name	Cardinality and Range	Description	Inheritance
bodySite	0..1 OntologyClass	FHIR mapping: Procedure	direct
code	0..1 OntologyClass	FHIR mapping: Procedure	direct
performed	0..1 TimeElement	When the procedure was performed	direct

Usages

used by	used in	type	used
Measurement	procedure	range	Procedure
Biosample	procedure	range	Procedure
MedicalAction	procedure	range	Procedure

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/linkml/phenopackets/phenopackets

Mappings

Mapping Type	Mapped Value
self	phenopackets:Procedure
native	phenopackets:Procedure

LinkML Source

Direct

name: Procedure
description: 'A clinical procedure performed on a subject. By preference a single
  concept to indicate both the procedure and the body site should be used. In cases
  where this is not possible, the body site should be indicated using a separate ontology
  class. e.g. {"code":{"NCIT:C51585": "Biopsy of Soft Palate"}} {"code":{"NCIT:C28743":
  "Punch Biopsy"}, "body_site":{"UBERON:0003403": "skin of forearm"}} - a punch biopsy
  of the skin from the forearm FHIR mapping: Procedure (https://www.hl7.org/fhir/procedure.html)'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  bodySite:
    name: bodySite
    annotations:
      rank:
        tag: rank
        value: 2
    description: 'FHIR mapping: Procedure.bodySite'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Procedure
    - RadiationTherapy
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  code:
    name: code
    annotations:
      rank:
        tag: rank
        value: 1
    description: 'FHIR mapping: Procedure.code'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Procedure
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  performed:
    name: performed
    annotations:
      rank:
        tag: rank
        value: 3
    description: When the procedure was performed.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Procedure
    range: TimeElement
    inlined: true
    inlined_as_list: true

Induced

name: Procedure
description: 'A clinical procedure performed on a subject. By preference a single
  concept to indicate both the procedure and the body site should be used. In cases
  where this is not possible, the body site should be indicated using a separate ontology
  class. e.g. {"code":{"NCIT:C51585": "Biopsy of Soft Palate"}} {"code":{"NCIT:C28743":
  "Punch Biopsy"}, "body_site":{"UBERON:0003403": "skin of forearm"}} - a punch biopsy
  of the skin from the forearm FHIR mapping: Procedure (https://www.hl7.org/fhir/procedure.html)'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  bodySite:
    name: bodySite
    annotations:
      rank:
        tag: rank
        value: 2
    description: 'FHIR mapping: Procedure.bodySite'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: bodySite
    owner: Procedure
    domain_of:
    - Procedure
    - RadiationTherapy
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  code:
    name: code
    annotations:
      rank:
        tag: rank
        value: 1
    description: 'FHIR mapping: Procedure.code'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: code
    owner: Procedure
    domain_of:
    - Procedure
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  performed:
    name: performed
    annotations:
      rank:
        tag: rank
        value: 3
    description: When the procedure was performed.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: performed
    owner: Procedure
    domain_of:
    - Procedure
    range: TimeElement
    inlined: true
    inlined_as_list: true