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
Slices for coding		1..*	Coding	Code defined by a terminology system Slice: Ordered, Open At End by pattern:code
coding:pheno-code		1..*	Coding	Code defined by a terminology system
code		0..1	code	Symbol in syntax defined by the system Binding: Phenotype Codes (required)
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
Condition.code.coding:pheno-code.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology) https://nih-ncpi.github.io/ncpi-fhir-ig/ValueSet/phenotype-codes from this IG

Name	Flags	Card.	Type	Description & Constraints
Condition	C	0..*	Condition	Detailed information about conditions, problems or diagnoses con-3: Condition.clinicalStatus SHOULD be present if verificationStatus is not entered-in-error and category is problem-list-item con-4: If condition is abated, then clinicalStatus must be either inactive, resolved, or remission con-5: Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error
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.
subject	Σ	1..1	Reference(Patient | Group)	Who has the condition?
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Condition.clinicalStatus	required	ConditionClinicalStatusCodes http://hl7.org/fhir/ValueSet/condition-clinical|4.3.0 from the FHIR Standard
Condition.verificationStatus	required	ConditionVerificationStatus http://hl7.org/fhir/ValueSet/condition-ver-status|4.3.0 from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
con-3	best practice	Condition	Condition.clinicalStatus SHOULD be present if verificationStatus is not entered-in-error and category is problem-list-item : verificationStatus.empty().not() and verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').exists().not() and category.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-category' and code='problem-list-item').exists() implies clinicalStatus.empty().not()
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.exists() and ('#'+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(uri) = '#').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 con-3: Condition.clinicalStatus SHOULD be present if verificationStatus is not entered-in-error and category is problem-list-item con-4: If condition is abated, then clinicalStatus must be either inactive, resolved, or remission con-5: Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error
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): IETF language tag Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources dom-r4b: Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems
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: Condition/Problem/DiagnosisCodes (example): Identification of the condition or diagnosis.
id		0..1	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
Slices for coding	Σ	1..*	Coding	Code defined by a terminology system Slice: Ordered, Open At End by pattern:code
coding:pheno-code	Σ	1..*	Coding	Code defined by a terminology system
id		0..1	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
system	Σ	0..1	uri	Identity of the terminology system
version	Σ	0..1	string	Version of the system - if relevant
code	Σ	0..1	code	Symbol in syntax defined by the system Binding: Phenotype Codes (required)
display	Σ	0..1	string	Representation defined by the system
userSelected	Σ	0..1	boolean	If this coding was chosen directly by the user
text	Σ	0..1	string	Plain text representation of the concept
bodySite	Σ	0..*	CodeableConcept	Anatomical location, if relevant Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
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 con-1: Stage SHALL have summary or assessment
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 con-2: evidence SHALL have code or details
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	URI
Condition.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard
Condition.clinicalStatus	required	ConditionClinicalStatusCodes http://hl7.org/fhir/ValueSet/condition-clinical|4.3.0 from the FHIR Standard
Condition.verificationStatus	required	ConditionVerificationStatus http://hl7.org/fhir/ValueSet/condition-ver-status|4.3.0 from the FHIR Standard
Condition.category	extensible	ConditionCategoryCodes http://hl7.org/fhir/ValueSet/condition-category from the FHIR Standard
Condition.severity	preferred	Condition/DiagnosisSeverity http://hl7.org/fhir/ValueSet/condition-severity from the FHIR Standard
Condition.code	example	Condition/Problem/DiagnosisCodes http://hl7.org/fhir/ValueSet/condition-code from the FHIR Standard
Condition.code.coding:pheno-code.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology) https://nih-ncpi.github.io/ncpi-fhir-ig/ValueSet/phenotype-codes from this IG
Condition.bodySite	example	SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard
Condition.stage.summary	example	ConditionStage http://hl7.org/fhir/ValueSet/condition-stage from the FHIR Standard
Condition.stage.type	example	ConditionStageType http://hl7.org/fhir/ValueSet/condition-stage-type from the FHIR Standard
Condition.evidence.code	example	ManifestationAndSymptomCodes http://hl7.org/fhir/ValueSet/manifestation-or-symptom from the FHIR Standard

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 SHOULD be present if verificationStatus is not entered-in-error and category is problem-list-item : verificationStatus.empty().not() and verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').exists().not() and category.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-category' and code='problem-list-item').exists() implies clinicalStatus.empty().not()
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.exists() and ('#'+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(uri) = '#').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()
dom-r4b	warning	Condition.contained	Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems : ($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)
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
Slices for coding		1..*	Coding	Code defined by a terminology system Slice: Ordered, Open At End by pattern:code
coding:pheno-code		1..*	Coding	Code defined by a terminology system
code		0..1	code	Symbol in syntax defined by the system Binding: Phenotype Codes (required)
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
Condition.code.coding:pheno-code.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology) https://nih-ncpi.github.io/ncpi-fhir-ig/ValueSet/phenotype-codes from this IG

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Condition	C	0..*	Condition	Detailed information about conditions, problems or diagnoses con-3: Condition.clinicalStatus SHOULD be present if verificationStatus is not entered-in-error and category is problem-list-item con-4: If condition is abated, then clinicalStatus must be either inactive, resolved, or remission con-5: Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error
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.
subject	Σ	1..1	Reference(Patient | Group)	Who has the condition?
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Condition.clinicalStatus	required	ConditionClinicalStatusCodes http://hl7.org/fhir/ValueSet/condition-clinical|4.3.0 from the FHIR Standard
Condition.verificationStatus	required	ConditionVerificationStatus http://hl7.org/fhir/ValueSet/condition-ver-status|4.3.0 from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
con-3	best practice	Condition	Condition.clinicalStatus SHOULD be present if verificationStatus is not entered-in-error and category is problem-list-item : verificationStatus.empty().not() and verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').exists().not() and category.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-category' and code='problem-list-item').exists() implies clinicalStatus.empty().not()
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.exists() and ('#'+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(uri) = '#').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 con-3: Condition.clinicalStatus SHOULD be present if verificationStatus is not entered-in-error and category is problem-list-item con-4: If condition is abated, then clinicalStatus must be either inactive, resolved, or remission con-5: Condition.clinicalStatus SHALL NOT be present if verification Status is entered-in-error
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): IETF language tag Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources dom-r4b: Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems
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: Condition/Problem/DiagnosisCodes (example): Identification of the condition or diagnosis.
id		0..1	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
Slices for coding	Σ	1..*	Coding	Code defined by a terminology system Slice: Ordered, Open At End by pattern:code
coding:pheno-code	Σ	1..*	Coding	Code defined by a terminology system
id		0..1	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
system	Σ	0..1	uri	Identity of the terminology system
version	Σ	0..1	string	Version of the system - if relevant
code	Σ	0..1	code	Symbol in syntax defined by the system Binding: Phenotype Codes (required)
display	Σ	0..1	string	Representation defined by the system
userSelected	Σ	0..1	boolean	If this coding was chosen directly by the user
text	Σ	0..1	string	Plain text representation of the concept
bodySite	Σ	0..*	CodeableConcept	Anatomical location, if relevant Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
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 con-1: Stage SHALL have summary or assessment
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 con-2: evidence SHALL have code or details
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	URI
Condition.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard
Condition.clinicalStatus	required	ConditionClinicalStatusCodes http://hl7.org/fhir/ValueSet/condition-clinical|4.3.0 from the FHIR Standard
Condition.verificationStatus	required	ConditionVerificationStatus http://hl7.org/fhir/ValueSet/condition-ver-status|4.3.0 from the FHIR Standard
Condition.category	extensible	ConditionCategoryCodes http://hl7.org/fhir/ValueSet/condition-category from the FHIR Standard
Condition.severity	preferred	Condition/DiagnosisSeverity http://hl7.org/fhir/ValueSet/condition-severity from the FHIR Standard
Condition.code	example	Condition/Problem/DiagnosisCodes http://hl7.org/fhir/ValueSet/condition-code from the FHIR Standard
Condition.code.coding:pheno-code.code	required	PhenotypeCodes (a valid code from Human Phenotype Ontology) https://nih-ncpi.github.io/ncpi-fhir-ig/ValueSet/phenotype-codes from this IG
Condition.bodySite	example	SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard
Condition.stage.summary	example	ConditionStage http://hl7.org/fhir/ValueSet/condition-stage from the FHIR Standard
Condition.stage.type	example	ConditionStageType http://hl7.org/fhir/ValueSet/condition-stage-type from the FHIR Standard
Condition.evidence.code	example	ManifestationAndSymptomCodes http://hl7.org/fhir/ValueSet/manifestation-or-symptom from the FHIR Standard

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 SHOULD be present if verificationStatus is not entered-in-error and category is problem-list-item : verificationStatus.empty().not() and verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code='entered-in-error').exists().not() and category.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-category' and code='problem-list-item').exists() implies clinicalStatus.empty().not()
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.exists() and ('#'+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(uri) = '#').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()
dom-r4b	warning	Condition.contained	Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems : ($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)
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

Mandatory: 0 element (2 nested mandatory elements)

Slices

This structure defines the following Slices:

• The element Condition.code.coding is sliced based on the value of pattern:code (ordered, Open at End)

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.