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 2022-12-09 | 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:
- Examples for this Resource Profile: Condition/phenotype-example-1
Formal Views of Profile Content
Description of Profiles, Differentials, Snapshots and how the different presentations work.
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.
| |||||
| 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
| ||||
| 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() | |
| 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
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.
| |||||
| 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
| ||||
| 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() | |
| 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
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.