NCPI FHIR Implementation Guide
0.2.0 - ci-build

NCPI FHIR Implementation Guide - Local Development build (v0.2.0). See the Directory of published versions

Resource Profile: NCPI Phenotype

Official URL: https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/phenotype Version: 0.2.0
Draft as of 2023-08-08 Computable Name: Phenotype

Representation of phenotypic observations (present or absent)

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.

Usage:

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

This structure is derived from Condition

NameFlagsCard.TypeDescription & Constraintsdoco
.. Condition 0..*ConditionDetailed information about conditions, problems or diagnoses
... code 0..1CodeableConceptIdentification of the condition, problem or diagnosis
Binding: Phenotype Codes (required)

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSet
Condition.coderequiredPhenotypeCodes (a valid code from Human Phenotype Ontology)
NameFlagsCard.TypeDescription & Constraintsdoco
.. Condition C0..*ConditionDetailed information about conditions, problems or diagnoses
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... clinicalStatus ?!ΣC0..1CodeableConceptactive | recurrence | relapse | inactive | remission | resolved
Binding: ConditionClinicalStatusCodes (required): The clinical status of the condition or diagnosis.

... code Σ0..1CodeableConceptIdentification of the condition, problem or diagnosis
Binding: Phenotype Codes (required)
... subject Σ1..1Reference(Patient | Group)Who has the condition?

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Condition.clinicalStatusrequiredConditionClinicalStatusCodes
Condition.verificationStatusrequiredConditionVerificationStatus
Condition.coderequiredPhenotypeCodes (a valid code from Human Phenotype Ontology)

Constraints

IdGradePath(s)DetailsRequirements
con-3best practiceConditionCondition.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-4errorConditionIf 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-5errorConditionCondition.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-2errorConditionIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorConditionIf 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-4errorConditionIf 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-5errorConditionIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceConditionA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Condition C0..*ConditionDetailed information about conditions, problems or diagnoses
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Ids for this condition
... clinicalStatus ?!ΣC0..1CodeableConceptactive | recurrence | relapse | inactive | remission | resolved
Binding: ConditionClinicalStatusCodes (required): The clinical status of the condition or diagnosis.

... verificationStatus ?!ΣC0..1CodeableConceptunconfirmed | 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..*CodeableConceptproblem-list-item | encounter-diagnosis
Binding: ConditionCategoryCodes (extensible): A category assigned to the condition.


... severity 0..1CodeableConceptSubjective severity of condition
Binding: Condition/DiagnosisSeverity (preferred): A subjective assessment of the severity of the condition as evaluated by the clinician.

... code Σ0..1CodeableConceptIdentification of the condition, problem or diagnosis
Binding: Phenotype Codes (required)
... bodySite Σ0..*CodeableConceptAnatomical location, if relevant
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.


... subject Σ1..1Reference(Patient | Group)Who has the condition?
... encounter Σ0..1Reference(Encounter)Encounter created as part of
... onset[x] Σ0..1Estimated or actual date, date-time, or age
.... onsetDateTimedateTime
.... onsetAgeAge
.... onsetPeriodPeriod
.... onsetRangeRange
.... onsetStringstring
... abatement[x] C0..1When in resolution/remission
.... abatementDateTimedateTime
.... abatementAgeAge
.... abatementPeriodPeriod
.... abatementRangeRange
.... abatementStringstring
... recordedDate Σ0..1dateTimeDate record was first recorded
... recorder Σ0..1Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)Who recorded the condition
... asserter Σ0..1Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)Person who asserts this condition
... stage C0..*BackboneElementStage/grade, usually assessed formally
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... summary C0..1CodeableConceptSimple summary (disease specific)
Binding: ConditionStage (example): Codes describing condition stages (e.g. Cancer stages).

.... assessment C0..*Reference(ClinicalImpression | DiagnosticReport | Observation)Formal record of assessment
.... type 0..1CodeableConceptKind of staging
Binding: ConditionStageType (example): Codes describing the kind of condition staging (e.g. clinical or pathological).

... evidence C0..*BackboneElementSupporting evidence
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code ΣC0..*CodeableConceptManifestation/symptom
Binding: ManifestationAndSymptomCodes (example): Codes that describe the manifestation or symptoms of a condition.


.... detail ΣC0..*Reference(Resource)Supporting information found elsewhere
... note 0..*AnnotationAdditional information about the Condition

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Condition.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Condition.clinicalStatusrequiredConditionClinicalStatusCodes
Condition.verificationStatusrequiredConditionVerificationStatus
Condition.categoryextensibleConditionCategoryCodes
Condition.severitypreferredCondition/DiagnosisSeverity
Condition.coderequiredPhenotypeCodes (a valid code from Human Phenotype Ontology)
Condition.bodySiteexampleSNOMEDCTBodyStructures
Condition.stage.summaryexampleConditionStage
Condition.stage.typeexampleConditionStageType
Condition.evidence.codeexampleManifestationAndSymptomCodes

Constraints

IdGradePath(s)DetailsRequirements
con-1errorCondition.stageStage SHALL have summary or assessment
: summary.exists() or assessment.exists()
con-2errorCondition.evidenceevidence SHALL have code or details
: code.exists() or detail.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

This structure is derived from Condition

Summary

Differential View

This structure is derived from Condition

NameFlagsCard.TypeDescription & Constraintsdoco
.. Condition 0..*ConditionDetailed information about conditions, problems or diagnoses
... code 0..1CodeableConceptIdentification of the condition, problem or diagnosis
Binding: Phenotype Codes (required)

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSet
Condition.coderequiredPhenotypeCodes (a valid code from Human Phenotype Ontology)

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Condition C0..*ConditionDetailed information about conditions, problems or diagnoses
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... clinicalStatus ?!ΣC0..1CodeableConceptactive | recurrence | relapse | inactive | remission | resolved
Binding: ConditionClinicalStatusCodes (required): The clinical status of the condition or diagnosis.

... code Σ0..1CodeableConceptIdentification of the condition, problem or diagnosis
Binding: Phenotype Codes (required)
... subject Σ1..1Reference(Patient | Group)Who has the condition?

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Condition.clinicalStatusrequiredConditionClinicalStatusCodes
Condition.verificationStatusrequiredConditionVerificationStatus
Condition.coderequiredPhenotypeCodes (a valid code from Human Phenotype Ontology)

Constraints

IdGradePath(s)DetailsRequirements
con-3best practiceConditionCondition.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-4errorConditionIf 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-5errorConditionCondition.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-2errorConditionIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorConditionIf 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-4errorConditionIf 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-5errorConditionIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceConditionA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Condition C0..*ConditionDetailed information about conditions, problems or diagnoses
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Ids for this condition
... clinicalStatus ?!ΣC0..1CodeableConceptactive | recurrence | relapse | inactive | remission | resolved
Binding: ConditionClinicalStatusCodes (required): The clinical status of the condition or diagnosis.

... verificationStatus ?!ΣC0..1CodeableConceptunconfirmed | 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..*CodeableConceptproblem-list-item | encounter-diagnosis
Binding: ConditionCategoryCodes (extensible): A category assigned to the condition.


... severity 0..1CodeableConceptSubjective severity of condition
Binding: Condition/DiagnosisSeverity (preferred): A subjective assessment of the severity of the condition as evaluated by the clinician.

... code Σ0..1CodeableConceptIdentification of the condition, problem or diagnosis
Binding: Phenotype Codes (required)
... bodySite Σ0..*CodeableConceptAnatomical location, if relevant
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.


... subject Σ1..1Reference(Patient | Group)Who has the condition?
... encounter Σ0..1Reference(Encounter)Encounter created as part of
... onset[x] Σ0..1Estimated or actual date, date-time, or age
.... onsetDateTimedateTime
.... onsetAgeAge
.... onsetPeriodPeriod
.... onsetRangeRange
.... onsetStringstring
... abatement[x] C0..1When in resolution/remission
.... abatementDateTimedateTime
.... abatementAgeAge
.... abatementPeriodPeriod
.... abatementRangeRange
.... abatementStringstring
... recordedDate Σ0..1dateTimeDate record was first recorded
... recorder Σ0..1Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)Who recorded the condition
... asserter Σ0..1Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)Person who asserts this condition
... stage C0..*BackboneElementStage/grade, usually assessed formally
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... summary C0..1CodeableConceptSimple summary (disease specific)
Binding: ConditionStage (example): Codes describing condition stages (e.g. Cancer stages).

.... assessment C0..*Reference(ClinicalImpression | DiagnosticReport | Observation)Formal record of assessment
.... type 0..1CodeableConceptKind of staging
Binding: ConditionStageType (example): Codes describing the kind of condition staging (e.g. clinical or pathological).

... evidence C0..*BackboneElementSupporting evidence
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code ΣC0..*CodeableConceptManifestation/symptom
Binding: ManifestationAndSymptomCodes (example): Codes that describe the manifestation or symptoms of a condition.


.... detail ΣC0..*Reference(Resource)Supporting information found elsewhere
... note 0..*AnnotationAdditional information about the Condition

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Condition.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Condition.clinicalStatusrequiredConditionClinicalStatusCodes
Condition.verificationStatusrequiredConditionVerificationStatus
Condition.categoryextensibleConditionCategoryCodes
Condition.severitypreferredCondition/DiagnosisSeverity
Condition.coderequiredPhenotypeCodes (a valid code from Human Phenotype Ontology)
Condition.bodySiteexampleSNOMEDCTBodyStructures
Condition.stage.summaryexampleConditionStage
Condition.stage.typeexampleConditionStageType
Condition.evidence.codeexampleManifestationAndSymptomCodes

Constraints

IdGradePath(s)DetailsRequirements
con-1errorCondition.stageStage SHALL have summary or assessment
: summary.exists() or assessment.exists()
con-2errorCondition.evidenceevidence SHALL have code or details
: code.exists() or detail.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

This structure is derived from Condition

Summary

 

Other representations of profile: CSV, Excel, Schematron

Notes:

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:

Present/Absent Verification Status
Present Confirmed
Absent Refuted
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.