Scope and Usage

The Phenotype profile is used to associate a patient with one or more phenotypic observations. These observations can be either present or absent and will likely have an age associated with when the phenotype was observed.

The primary code system employed by this profile is Human Phenotype Ontology.

• Differential Table
• Key Elements Table
• Snapshot Table
• Statistics/References
• All

This structure is derived from Condition

Name	Flags	Card.	Type	Description & Constraints
Condition		0..*	Condition	Detailed information about conditions, problems or diagnoses
code		0..1	CodeableConcept	Identification of the condition, problem or diagnosis Binding: Phenotype Codes (required)
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet
Condition.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology)

Name	Flags	Card.	Type	Description & Constraints
Condition	C	0..*	Condition	Detailed information about conditions, problems or diagnoses
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
clinicalStatus	?!ΣC	0..1	CodeableConcept	active | recurrence | relapse | inactive | remission | resolved Binding: ConditionClinicalStatusCodes (required): The clinical status of the condition or diagnosis.
verificationStatus	?!ΣC	0..1	CodeableConcept	unconfirmed | provisional | differential | confirmed | refuted | entered-in-error Binding: ConditionVerificationStatus (required): The verification status to support or decline the clinical status of the condition or diagnosis.
code	Σ	0..1	CodeableConcept	Identification of the condition, problem or diagnosis Binding: Phenotype Codes (required)
subject	Σ	1..1	Reference(Patient | Group)	Who has the condition?
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Condition.clinicalStatus	required	ConditionClinicalStatusCodes
Condition.verificationStatus	required	ConditionVerificationStatus
Condition.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology)

Constraints

Id	Grade	Path(s)	Details	Requirements
con-3	best practice	Condition	Condition.clinicalStatus SHALL be present if verificationStatus is not entered-in-error and category is problem-list-item : clinicalStatus.exists() or verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() or category.select($this='problem-list-item').empty()
con-4	error	Condition	If condition is abated, then clinicalStatus must be either inactive, resolved, or remission : abatement.empty() or clinicalStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-clinical' and (code='resolved' or code='remission' or code='inactive')).exists()
con-5	error	Condition	Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error : verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').empty() or clinicalStatus.empty()
dom-2	error	Condition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Condition	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Condition	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Condition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Condition	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Name	Flags	Card.	Type	Description & Constraints
Condition	C	0..*	Condition	Detailed information about conditions, problems or diagnoses
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	External Ids for this condition
clinicalStatus	?!ΣC	0..1	CodeableConcept	active | recurrence | relapse | inactive | remission | resolved Binding: ConditionClinicalStatusCodes (required): The clinical status of the condition or diagnosis.
verificationStatus	?!ΣC	0..1	CodeableConcept	unconfirmed | provisional | differential | confirmed | refuted | entered-in-error Binding: ConditionVerificationStatus (required): The verification status to support or decline the clinical status of the condition or diagnosis.
category		0..*	CodeableConcept	problem-list-item | encounter-diagnosis Binding: ConditionCategoryCodes (extensible): A category assigned to the condition.
severity		0..1	CodeableConcept	Subjective severity of condition Binding: Condition/DiagnosisSeverity (preferred): A subjective assessment of the severity of the condition as evaluated by the clinician.
code	Σ	0..1	CodeableConcept	Identification of the condition, problem or diagnosis Binding: Phenotype Codes (required)
bodySite	Σ	0..*	CodeableConcept	Anatomical location, if relevant Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
subject	Σ	1..1	Reference(Patient | Group)	Who has the condition?
encounter	Σ	0..1	Reference(Encounter)	Encounter created as part of
onset[x]	Σ	0..1		Estimated or actual date, date-time, or age
onsetDateTime			dateTime
onsetAge			Age
onsetPeriod			Period
onsetRange			Range
onsetString			string
abatement[x]	C	0..1		When in resolution/remission
abatementDateTime			dateTime
abatementAge			Age
abatementPeriod			Period
abatementRange			Range
abatementString			string
recordedDate	Σ	0..1	dateTime	Date record was first recorded
recorder	Σ	0..1	Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)	Who recorded the condition
asserter	Σ	0..1	Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)	Person who asserts this condition
stage	C	0..*	BackboneElement	Stage/grade, usually assessed formally
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
summary	C	0..1	CodeableConcept	Simple summary (disease specific) Binding: ConditionStage (example): Codes describing condition stages (e.g. Cancer stages).
assessment	C	0..*	Reference(ClinicalImpression | DiagnosticReport | Observation)	Formal record of assessment
type		0..1	CodeableConcept	Kind of staging Binding: ConditionStageType (example): Codes describing the kind of condition staging (e.g. clinical or pathological).
evidence	C	0..*	BackboneElement	Supporting evidence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	0..*	CodeableConcept	Manifestation/symptom Binding: ManifestationAndSymptomCodes (example): Codes that describe the manifestation or symptoms of a condition.
detail	ΣC	0..*	Reference(Resource)	Supporting information found elsewhere
note		0..*	Annotation	Additional information about the Condition
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Condition.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding
Condition.clinicalStatus	required	ConditionClinicalStatusCodes
Condition.verificationStatus	required	ConditionVerificationStatus
Condition.category	extensible	ConditionCategoryCodes
Condition.severity	preferred	Condition/DiagnosisSeverity
Condition.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology)
Condition.bodySite	example	SNOMEDCTBodyStructures
Condition.stage.summary	example	ConditionStage
Condition.stage.type	example	ConditionStageType
Condition.evidence.code	example	ManifestationAndSymptomCodes

Constraints

Id	Grade	Path(s)	Details	Requirements
con-1	error	Condition.stage	Stage SHALL have summary or assessment : summary.exists() or assessment.exists()
con-2	error	Condition.evidence	evidence SHALL have code or details : code.exists() or detail.exists()
con-3	best practice	Condition	Condition.clinicalStatus SHALL be present if verificationStatus is not entered-in-error and category is problem-list-item : clinicalStatus.exists() or verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() or category.select($this='problem-list-item').empty()
con-4	error	Condition	If condition is abated, then clinicalStatus must be either inactive, resolved, or remission : abatement.empty() or clinicalStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-clinical' and (code='resolved' or code='remission' or code='inactive')).exists()
con-5	error	Condition	Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error : verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').empty() or clinicalStatus.empty()
dom-2	error	Condition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Condition	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Condition	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Condition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Condition	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Differential View

This structure is derived from Condition

Name	Flags	Card.	Type	Description & Constraints
Condition		0..*	Condition	Detailed information about conditions, problems or diagnoses
code		0..1	CodeableConcept	Identification of the condition, problem or diagnosis Binding: Phenotype Codes (required)
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet
Condition.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology)

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Condition	C	0..*	Condition	Detailed information about conditions, problems or diagnoses
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
clinicalStatus	?!ΣC	0..1	CodeableConcept	active | recurrence | relapse | inactive | remission | resolved Binding: ConditionClinicalStatusCodes (required): The clinical status of the condition or diagnosis.
verificationStatus	?!ΣC	0..1	CodeableConcept	unconfirmed | provisional | differential | confirmed | refuted | entered-in-error Binding: ConditionVerificationStatus (required): The verification status to support or decline the clinical status of the condition or diagnosis.
code	Σ	0..1	CodeableConcept	Identification of the condition, problem or diagnosis Binding: Phenotype Codes (required)
subject	Σ	1..1	Reference(Patient | Group)	Who has the condition?
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Condition.clinicalStatus	required	ConditionClinicalStatusCodes
Condition.verificationStatus	required	ConditionVerificationStatus
Condition.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology)

Constraints

Id	Grade	Path(s)	Details	Requirements
con-3	best practice	Condition	Condition.clinicalStatus SHALL be present if verificationStatus is not entered-in-error and category is problem-list-item : clinicalStatus.exists() or verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() or category.select($this='problem-list-item').empty()
con-4	error	Condition	If condition is abated, then clinicalStatus must be either inactive, resolved, or remission : abatement.empty() or clinicalStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-clinical' and (code='resolved' or code='remission' or code='inactive')).exists()
con-5	error	Condition	Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error : verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').empty() or clinicalStatus.empty()
dom-2	error	Condition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Condition	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Condition	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Condition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Condition	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
Condition	C	0..*	Condition	Detailed information about conditions, problems or diagnoses
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	External Ids for this condition
clinicalStatus	?!ΣC	0..1	CodeableConcept	active | recurrence | relapse | inactive | remission | resolved Binding: ConditionClinicalStatusCodes (required): The clinical status of the condition or diagnosis.
verificationStatus	?!ΣC	0..1	CodeableConcept	unconfirmed | provisional | differential | confirmed | refuted | entered-in-error Binding: ConditionVerificationStatus (required): The verification status to support or decline the clinical status of the condition or diagnosis.
category		0..*	CodeableConcept	problem-list-item | encounter-diagnosis Binding: ConditionCategoryCodes (extensible): A category assigned to the condition.
severity		0..1	CodeableConcept	Subjective severity of condition Binding: Condition/DiagnosisSeverity (preferred): A subjective assessment of the severity of the condition as evaluated by the clinician.
code	Σ	0..1	CodeableConcept	Identification of the condition, problem or diagnosis Binding: Phenotype Codes (required)
bodySite	Σ	0..*	CodeableConcept	Anatomical location, if relevant Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
subject	Σ	1..1	Reference(Patient | Group)	Who has the condition?
encounter	Σ	0..1	Reference(Encounter)	Encounter created as part of
onset[x]	Σ	0..1		Estimated or actual date, date-time, or age
onsetDateTime			dateTime
onsetAge			Age
onsetPeriod			Period
onsetRange			Range
onsetString			string
abatement[x]	C	0..1		When in resolution/remission
abatementDateTime			dateTime
abatementAge			Age
abatementPeriod			Period
abatementRange			Range
abatementString			string
recordedDate	Σ	0..1	dateTime	Date record was first recorded
recorder	Σ	0..1	Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)	Who recorded the condition
asserter	Σ	0..1	Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)	Person who asserts this condition
stage	C	0..*	BackboneElement	Stage/grade, usually assessed formally
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
summary	C	0..1	CodeableConcept	Simple summary (disease specific) Binding: ConditionStage (example): Codes describing condition stages (e.g. Cancer stages).
assessment	C	0..*	Reference(ClinicalImpression | DiagnosticReport | Observation)	Formal record of assessment
type		0..1	CodeableConcept	Kind of staging Binding: ConditionStageType (example): Codes describing the kind of condition staging (e.g. clinical or pathological).
evidence	C	0..*	BackboneElement	Supporting evidence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	0..*	CodeableConcept	Manifestation/symptom Binding: ManifestationAndSymptomCodes (example): Codes that describe the manifestation or symptoms of a condition.
detail	ΣC	0..*	Reference(Resource)	Supporting information found elsewhere
note		0..*	Annotation	Additional information about the Condition
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Condition.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding
Condition.clinicalStatus	required	ConditionClinicalStatusCodes
Condition.verificationStatus	required	ConditionVerificationStatus
Condition.category	extensible	ConditionCategoryCodes
Condition.severity	preferred	Condition/DiagnosisSeverity
Condition.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology)
Condition.bodySite	example	SNOMEDCTBodyStructures
Condition.stage.summary	example	ConditionStage
Condition.stage.type	example	ConditionStageType
Condition.evidence.code	example	ManifestationAndSymptomCodes

Constraints

Id	Grade	Path(s)	Details	Requirements
con-1	error	Condition.stage	Stage SHALL have summary or assessment : summary.exists() or assessment.exists()
con-2	error	Condition.evidence	evidence SHALL have code or details : code.exists() or detail.exists()
con-3	best practice	Condition	Condition.clinicalStatus SHALL be present if verificationStatus is not entered-in-error and category is problem-list-item : clinicalStatus.exists() or verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() or category.select($this='problem-list-item').empty()
con-4	error	Condition	If condition is abated, then clinicalStatus must be either inactive, resolved, or remission : abatement.empty() or clinicalStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-clinical' and (code='resolved' or code='remission' or code='inactive')).exists()
con-5	error	Condition	Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error : verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').empty() or clinicalStatus.empty()
dom-2	error	Condition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Condition	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Condition	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Condition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Condition	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

This structure is derived from Condition

Summary

Phenotype Code

The Condition.code must have one Coding from the Human Phenotype Ontology. For cases where there is no ideal HPO code to suit a researcher’s needs, users may use a general HPO code as the first entry in the code array and one or more codes from other systems which are more technically accurate.

Phenotype Present/Absent

Condition.verificationStatus is used to convey presence/absence of a given phenotype using a subset of the Hl7 codes as follows:

recordedDate vs onset

Depending on the data available the condition may be tagged using recordedDate or onset.

Condition.recordedDate is described as “date record was first recorded” and, therefore, is expected to be the earliest date associated with the ascertainment of the diagnosis. Condition.onset is expected only for cases where there is confidence that the date is an actual onset date. Both dates should be provided as relativeDateTime relative to the patient’s birth date.