data_elements:
- ordinal: '1.1'
  section: 1. Formal Criteria
  elementName: Pseudonym
  elementCode:
    system: SNOMEDCT
    code: '422549004'
  elementCodeSystem: SNOMEDCT
  dataType: Identifier
  dataSpecification:
  - n/a
  valueSet: null
  fhirExpression_v4_0_1: Patient.identifier.value
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: Individual.id
  recommendedDataSpec_phenopackets: string
  description: The (local) patient-related identification code.
- ordinal: '1.2'
  section: 1. Formal Criteria
  elementName: Date of Admission
  elementCode:
    system: SNOMEDCT
    code: '399423000'
  elementCodeSystem: SNOMEDCT
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: null
  fhirExpression_v4_0_1: Encounter.period.start
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: Individual.time_at_last_encounter
  recommendedDataSpec_phenopackets: TimeElement
  description: The date of admission or data capture of the individual.
- ordinal: '2.1'
  section: 2. Personal Information
  elementName: Date of Birth
  elementCode:
    system: SNOMEDCT
    code: '184099003'
  elementCodeSystem: SNOMEDCT
  dataType: Date
  dataSpecification:
  - YYYY
  - YYYY-MM
  - YYYY-MM-DD
  valueSet: null
  fhirExpression_v4_0_1: Patient.birthDate
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: Individual.date_of_birth
  recommendedDataSpec_phenopackets: TimeElement
  description: The individual's date of birth.
- ordinal: '2.2'
  section: 2. Personal Information
  elementName: Sex at Birth
  elementCode:
    system: LOINC
    code: '76689-9'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Sex at Birth Value Set v2.0.0
  fhirExpression_v4_0_1: Patient.extension:individual-recordedSexOrGender
  recommendedDataSpec_fhir: Recorded Sex Or Gender Type
  phenopacketSchemaElement_v2_0: Individual.sex
  recommendedDataSpec_phenopackets: Sex
  description: The individual's sex that was assigned at birth.
- ordinal: '2.3'
  section: 2. Personal Information
  elementName: Karyotypic Sex
  elementCode:
    system: SNOMEDCT
    code: '1296886006'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSc
  valueSet: Karyotypic Sex Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.value
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: Individual.karyotypic_sex
  recommendedDataSpec_phenopackets: Karyotypic Sex
  description: The chromosomal sex of an individual.
- ordinal: '2.4'
  section: 2. Personal Information
  elementName: Gender Identity
  elementCode:
    system: SNOMEDCT
    code: '263495000'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Gender Identity Value Set v2.0.0
  fhirExpression_v4_0_1: Patient.extension:individual-genderIdentity
  recommendedDataSpec_fhir: Gender Identity
  phenopacketSchemaElement_v2_0: Individual.gender
  recommendedDataSpec_phenopackets: OntologyClass
  description: The self-assigned gender of the individual.
- ordinal: '2.5'
  section: 2. Personal Information
  elementName: Country of Birth
  elementCode:
    system: SNOMEDCT
    code: '370159000'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VS
  valueSet: null
  fhirExpression_v4_0_1: Patient.extension:patient-birthPlace
  recommendedDataSpec_fhir: 'DataType: Address'
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The individual's country of birth.
- ordinal: '3.1'
  section: 3. Patient Status
  elementName: Vital Status
  elementCode:
    system: SNOMEDCT
    code: '278844005'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Vital Status Value Set v2.0.0
  fhirExpression_v4_0_1: Patient.deceased.deceasedBoolean|Observation.value
  recommendedDataSpec_fhir: Boolean|Code
  phenopacketSchemaElement_v2_0: Individual.VitalStatus.status
  recommendedDataSpec_phenopackets: 'Value Set: VitalStatus.Status'
  description: "The individual\u2019s general clinical status orvital status."
- ordinal: '3.2'
  section: 3. Patient Status
  elementName: Time of Death
  elementCode:
    system: SNOMEDCT
    code: '398299004'
  elementCodeSystem: SNOMEDCT
  dataType: Date
  dataSpecification:
  - YYYY
  - YYYY-MM
  - YYYY-MM-DD
  valueSet: null
  fhirExpression_v4_0_1: Patient.deceasedDateTime
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: Individual.VitalStatus.time_of_death
  recommendedDataSpec_phenopackets: TimeElement
  description: "If deceased, the individual\u2019s date of death."
- ordinal: '3.3'
  section: 3. Patient Status
  elementName: Cause of Death
  elementCode:
    system: SNOMEDCT
    code: '184305005'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - ICD-10CM
  valueSet: null
  fhirExpression_v4_0_1: Observation.value.coding.code
  recommendedDataSpec_fhir: Code|CodeableConcept
  phenopacketSchemaElement_v2_0: Individual.VitalStatus.cause_of_death
  recommendedDataSpec_phenopackets: OntologyClass
  description: "If deceased, the individual\u2019s primary cause of death."
- ordinal: '3.4'
  section: 3. Patient Status
  elementName: Age Category
  elementCode:
    system: SNOMEDCT
    code: '105727008'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  valueSet: Age Category Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.value.coding.code
  recommendedDataSpec_fhir: CodableConcept
  phenopacketSchemaElement_v2_0: Individual.time_at_last_encounter
  recommendedDataSpec_phenopackets: TimeElement
  description: The individual's age category at thetime of data capture.
- ordinal: '3.5'
  section: 3. Patient Status
  elementName: Length of Gestation at Birth [weeks+days]
  elementCode:
    system: SNOMEDCT
    code: '412726003'
  elementCodeSystem: SNOMEDCT
  dataType: String
  dataSpecification:
  - XX+X
  valueSet: null
  fhirExpression_v4_0_1: Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity
  recommendedDataSpec_fhir: Quantity
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The duration of the pregnancy in weeks and days,formatted as XX+X (weeks+days).
- ordinal: '3.6'
  section: 3. Patient Status
  elementName: Undiagnosed RD Case
  elementCode:
    system: SNOMEDCT
    code: '723663001'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  valueSet: Undiagnosed RD Case Value Set v2.0.0
  fhirExpression_v4_0_1: (Condition.code)
  recommendedDataSpec_fhir: Code(e.g. ORDO:616874 - Rare disorderwithout a determined
    diagnosis afterfull investigation)
  phenopacketSchemaElement_v2_0: (Disease.term)
  recommendedDataSpec_phenopackets: (OntologyClass (e.g. ORDO:616874 - Rare disorder
    without a determineddiagnosis after full investigation))
  description: Identifies cases where an RD diagnosis has notbeen established.
- ordinal: '4.1'
  section: 4. Care Pathway
  elementName: Encounter Start
  elementCode:
    system: HL7FHIR
    code: 'encounter.period.start'
  elementCodeSystem: HL7FHIR
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: null
  fhirExpression_v4_0_1: Encounter.period.start
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The beginning of an encounter of the individual.
- ordinal: '4.2'
  section: 4. Care Pathway
  elementName: Encounter End
  elementCode:
    system: HL7FHIR
    code: 'encounter.period.end'
  elementCodeSystem: HL7FHIR
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: null
  fhirExpression_v4_0_1: Encounter.period.end
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The end of an encounter of the individual.
- ordinal: '4.3'
  section: 4. Care Pathway
  elementName: Encounter Status
  elementCode:
    system: SNOMEDCT
    code: '305058001'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Encounter Status Value Set v2.0.0
  fhirExpression_v4_0_1: Encounter.status
  recommendedDataSpec_fhir: 'ValueSet: EncounterStatus'
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The status of an encounter of the individual at thetime of data capture.
- ordinal: '4.4'
  section: 4. Care Pathway
  elementName: Encounter Class
  elementCode:
    system: HL7FHIR
    code: encounter.class
  elementCodeSystem: HL7FHIR
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Encounter Class Value Set v2.0.0
  fhirExpression_v4_0_1: Encounter.class
  recommendedDataSpec_fhir: 'ValueSet: EncounterClass'
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The class of an encounter of the individualat the time of data capture.
- ordinal: '5.1'
  section: 5. Disease
  elementName: Disease
  elementCode:
    system: SNOMEDCT
    code: '64572001'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - Ontology Class (MONDO, ORDO, ICD-10, ICD-11, OMIM_g, OMIM_p)
  valueSet: n/a
  fhirExpression_v4_0_1: Condition.code
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: Disease.term
  recommendedDataSpec_phenopackets: OntologyClass
  description: A disease that the individual was affected by. If agenetic diagnosis
    or subtypes were diagnosed, please also provide the respective OMIM_g and OMIM_p
    codes.
- ordinal: '5.2'
  section: 5. Disease
  elementName: Verification Status
  elementCode:
    system: LOINC
    code: '99498-8'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Verification Status Value Set v2.0.0
  fhirExpression_v4_0_1: Condition.verificationStatus
  recommendedDataSpec_fhir: 'ValueSet: Condition Verficication Status'
  phenopacketSchemaElement_v2_0: (Disease.excluded)
  recommendedDataSpec_phenopackets: boolean
  description: The verification status of the disease.
- ordinal: '5.3'
  section: 5. Disease
  elementName: Age at Onset
  elementCode:
    system: SNOMEDCT
    code: '424850005'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Age at Onset Value Set v2.0.0
  fhirExpression_v4_0_1: Condition.onsetString orObservation.valueCodeableConcept
  recommendedDataSpec_fhir: Disease.onset
  phenopacketSchemaElement_v2_0: Disease.onset
  recommendedDataSpec_phenopackets: Disease.onset
  description: The age at the onset of the first symptomsor signs of the disease.
- ordinal: '5.4'
  section: 5. Disease
  elementName: Date of Onset
  elementCode:
    system: SNOMEDCT
    code: '298059007'
  elementCodeSystem: SNOMEDCT
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: n/a
  fhirExpression_v4_0_1: Condition.onset
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: Disease.onset
  recommendedDataSpec_phenopackets: TimeElement
  description: The date at onset of first symptoms orsigns of the disease.
- ordinal: '5.5'
  section: 5. Disease
  elementName: Age at Diagnosis
  elementCode:
    system: SNOMEDCT
    code: '423493009'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Age at Diagnosis Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.value
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: (Disease.onset)
  recommendedDataSpec_phenopackets: (TimeElement)
  description: "The individual\u2019s age when the diagnosis was made."
- ordinal: '5.6'
  section: 5. Disease
  elementName: Date of Diagnosis
  elementCode:
    system: SNOMEDCT
    code: '432213005'
  elementCodeSystem: SNOMEDCT
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: n/a
  fhirExpression_v4_0_1: Condition.recordedDate
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: (Disease.onset)
  recommendedDataSpec_phenopackets: (TimeElement)
  description: The date on which the disease was determined.
- ordinal: '5.7'
  section: 5. Disease
  elementName: Body Site
  elementCode:
    system: SNOMEDCT
    code: '363698007'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Body Site Value Set v2.0.0
  fhirExpression_v4_0_1: Condition.bodySite.coding:SNOMEDCT-ct
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: Disease.primary_site
  recommendedDataSpec_phenopackets: OntologyClass
  description: The specific body site affected by disease is encodedusing all descendants
    of SCT Body Structure (123037004).
- ordinal: '5.8'
  section: 5. Disease
  elementName: Clinical Status
  elementCode:
    system: SNOMEDCT
    code: '263493007'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Clinical Status Value Set v2.0.0
  fhirExpression_v4_0_1: Condition.clinicalStatus
  recommendedDataSpec_fhir: 'ValueSet: ClinicalStatus'
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The clinical status of the disease indicates whetherit is active, inactive,
    or resolved.
- ordinal: '5.9'
  section: 5. Disease
  elementName: Severity
  elementCode:
    system: SNOMEDCT
    code: '246112005'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Severity Value Set v2.0.0
  fhirExpression_v4_0_1: Condition.severity
  recommendedDataSpec_fhir: 'ValueSet: ConditionSeverity'
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The severity of the disease is categorised byclinical evaluation.
- ordinal: 6.1.1
  section: 6. Genetic Findings
  elementName: Genomic Diagnosis
  elementCode:
    system: SNOMEDCT
    code: '106221001'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - OMIM_p
  - MONDO
  valueSet: n/a
  fhirExpression_v4_0_1: Condition.code
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: Interpretation.Diagnosis.disease
  recommendedDataSpec_phenopackets: OntologyClass
  description: The genomic diagnoses can correspond to the diagnoseddisease in (5.1)
    if the same OMIM codes are used.
- ordinal: 6.1.2
  section: 6. Genetic Findings
  elementName: Progress Status of Interpretation
  elementCode:
    system: GA4GH
    code: progress_status
  elementCodeSystem: GA4GH
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Progress Status Value Set v2.0.0
  fhirExpression_v4_0_1: Condition.extension
  recommendedDataSpec_fhir: 'VS: GA4GH ProgressStatus'
  phenopacketSchemaElement_v2_0: Interpretation.progress_status
  recommendedDataSpec_phenopackets: 'ValueSet: ProgressStatus'
  description: The interpretation has a ProgressStatus that refers tothe status of
    the attempted diagnosis.
- ordinal: 6.1.3
  section: 6. Genetic Findings
  elementName: Interpretation Status
  elementCode:
    system: GA4GH
    code: interpretation_status
  elementCodeSystem: GA4GH
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Interpretation Status Value Set v2.0.0
  fhirExpression_v4_0_1: Condition.extension
  recommendedDataSpec_fhir: 'VS: GA4GH InterpretationStatus'
  phenopacketSchemaElement_v2_0: GenomicInterpretation.interpretation_status
  recommendedDataSpec_phenopackets: 'ValueSet: InterpretationStatus'
  description: An enumeration that describes the conclusion made about the genomic
    interpretation.
- ordinal: 6.1.4
  section: 6. Genetic Findings
  elementName: Structural Variant Analysis Method
  elementCode:
    system: LOINC
    code: '81304-8'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VS
  - LOINC
  valueSet: Structural Variant Analysis Method Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.method
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The method used to analyse structural variants in the genome.
- ordinal: 6.1.5
  section: 6. Genetic Findings
  elementName: Reference Genome
  elementCode:
    system: LOINC
    code: '62374-4'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Reference Genome Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.component:reference-sequence-assembly
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The reference genome used for analysing the genetic variant.
- ordinal: 6.1.6
  section: 6. Genetic Findings
  elementName: Genetic Mutation String
  elementCode:
    system: LOINC
    code: 'LP7824-8'
  elementCodeSystem: LOINC
  dataType: String
  dataSpecification:
  - n/a
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.component:Variant.valueString
  recommendedDataSpec_fhir: string
  phenopacketSchemaElement_v2_0: VariationDescriptor.Extension.value
  recommendedDataSpec_phenopackets: string
  description: An unvalidated (HGVS) string that describes the variant change
- ordinal: 6.1.7
  section: 6. Genetic Findings
  elementName: Genomic DNA Change
  elementCode:
    system: LOINC
    code: '81290-9'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - g.HGVS
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.component:Variant.valueCode
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: VariationDescriptor.Expression.value
  recommendedDataSpec_phenopackets: string
  description: The specific change in the genomic DNA sequence encoded with a validated
    g.HGVS expression.
- ordinal: 6.1.8
  section: 6. Genetic Findings
  elementName: Sequence DNA Change
  elementCode:
    system: LOINC
    code: '48004-6'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - c.HGVS
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.component:Variant.valueCode
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: VariationDescriptor.Expression.value
  recommendedDataSpec_phenopackets: string
  description: The specific change in the DNA sequence at the nucleotide level with
    a validated c.HGVS expression.
- ordinal: 6.1.9
  section: 6. Genetic Findings
  elementName: Amino Acid Change
  elementCode:
    system: LOINC
    code: '48005-3'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - p.HGVS
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.component:Variant.valueCode
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: VariationDescriptor.Expression.value
  recommendedDataSpec_phenopackets: string
  description: The specific change in the amino acid sequence resulting from agenetic
    variant as a validated p.HGVS expression.
- ordinal: 6.1.10
  section: 6. Genetic Findings
  elementName: Gene
  elementCode:
    system: LOINC
    code: '48018-6'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - HGNC
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.component:Gene
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: GeneDescriptor.value_id
  recommendedDataSpec_phenopackets: string
  description: The specific gene or genes that were analysed or identified in the
    study.
- ordinal: 6.1.11
  section: 6. Genetic Findings
  elementName: Zygosity
  elementCode:
    system: LOINC
    code: '53034-5'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  - LOINC
  valueSet: Zygosity Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.component:geneticsAllele.State
  recommendedDataSpec_fhir: 'VS: Allelic State'
  phenopacketSchemaElement_v2_0: VariationDescriptor.allelic_state
  recommendedDataSpec_phenopackets: OntologyClass
  description: The zygosity of the genetic variant.
- ordinal: 6.1.12
  section: 6. Genetic Findings
  elementName: Genomic Source Class
  elementCode:
    system: LOINC
    code: '48002-0'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Genomic Source Class Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.component:GenomicSourceClass
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The classification of the genomic source, such as germline, somatic,
    or other origins.
- ordinal: 6.1.13
  section: 6. Genetic Findings
  elementName: DNA Change Type
  elementCode:
    system: LOINC
    code: '48019-4'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VS
  valueSet: DNA Change Type Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.component:Variant.Type
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: "The variant\u2019s type of DNA change, such as point mutation, deletion,\
    \ insertion, or other types."
- ordinal: 6.1.14
  section: 6. Genetic Findings
  elementName: Clinical Significance [ACMG]
  elementCode:
    system: LOINC
    code: '53037-8'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Clinical Significance ACMG Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.component:Variant.Interpretation
  recommendedDataSpec_fhir: ''
  phenopacketSchemaElement_v2_0: VariantInterpretation.acmg_pathogenicity_classification
  recommendedDataSpec_phenopackets: 'ValueSet: AcmgPathogenicityClassification'
  description: The clinical significance of the genetic variant, indicating its impact
    on health and disease.
- ordinal: 6.1.15
  section: 6. Genetic Findings
  elementName: Therapeutic Actionability
  elementCode:
    system: GA4GH
    code: therapeutic_actionability
  elementCodeSystem: GA4GH
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Therapeutic Actionability Value Set v2.0.0
  fhirExpression_v4_0_1: n/a
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: VariantInterpretation.therapeutic_actionability
  recommendedDataSpec_phenopackets: 'ValueSet: TherapeuticActionability'
  description: An enumeration flagging the variant as being a candidate for treatment
    or clinical intervention, which could improve the clinical outcome.
- ordinal: 6.1.16
  section: 6. Genetic Findings
  elementName: Clinical Annotation Level Of Evidence
  elementCode:
    system: LOINC
    code: '93044-6'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Clinical Annotation Level Of Evidence Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.extension:Variant.Interpretation
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: The level of evidence supporting the clinical annotation of the genetic
    variant.
- ordinal: 6.2.1
  section: 6. Phenotypic Feature
  elementName: Phenotypic Feature
  elementCode:
    system: SNOMEDCT
    code: '8116006'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - HPO
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.code
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: PhenotypicFeature.type
  recommendedDataSpec_phenopackets: OntologyClass
  description: An observed physical and clinical characteristicencoded with HPO.
- ordinal: 6.2.2
  section: 6.2 Phenotypic Feature
  elementName: Status
  elementCode:
    system: SNOMEDCT
    code: '363778006'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Phenotype Status Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.status
  recommendedDataSpec_fhir: 'ValueSet: ObservationStatus'
  phenopacketSchemaElement_v2_0: PhenotypicFeature.excluded
  recommendedDataSpec_phenopackets: boolean
  description: The current status of the phenotypic feature, indicating whether it
    is confirmed or refuted.
- ordinal: 6.2.3
  section: 6. Phenotypic Feature
  elementName: Determination Date
  elementCode:
    system: SNOMEDCT
    code: '439272007:704321009=363778006'
  elementCodeSystem: SNOMEDCT
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.effectiveDateTime
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: PhenotypicFeature.onset
  recommendedDataSpec_phenopackets: TimeElement
  description: The date on which the phenotypic feature was observed or recorded.
    We recommend capturing the time acharacteristic was observed.
- ordinal: 6.2.4
  section: 6.2 Phenotypic Feature
  elementName: Resolution Date
  elementCode:
    system: HP
    code: '0034382'
  elementCodeSystem: HP
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.effectiveDateTime
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: PhenotypicFeature.resolution
  recommendedDataSpec_phenopackets: TimeElement
  description: Time at which the feature resolved or abated.
- ordinal: 6.2.5
  section: 6.2 Phenotypic Feature
  elementName: Onset Category
  elementCode:
    system: HP
    code: '0003674'
  elementCodeSystem: HP
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Onset Category Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.category
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: PhenotypicFeature.onset
  recommendedDataSpec_phenopackets: OntologyClass
  description: Time at which the feature was first observed within  HPO onset categories.
- ordinal: 6.2.6
  section: 6.2 Phenotypic Feature
  elementName: Temporal Pattern
  elementCode:
    system: HP
    code: '0011008'
  elementCodeSystem: HP
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Temporal Pattern Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.interpretation
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: PhenotypicFeature.modifiers
  recommendedDataSpec_phenopackets: OntologyClass
  description: The speed at which disease manifestations appear and develop.
- ordinal: 6.2.7
  section: 6.2 Phenotypic Feature
  elementName: Severity
  elementCode:
    system: HP
    code: '0012824'
  elementCodeSystem: HP
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Severity Value Set v2.0.0
  fhirExpression_v4_0_1: Observation.interpretation
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: PhenotypicFeature.severity
  recommendedDataSpec_phenopackets: OntologyClass
  description: A description of the severity of the feature.
- ordinal: 6.2.8
  section: 6. Phenotypic Feature
  elementName: Modifiers
  elementCode:
    system: GA4GH
    code: 'phenotypicfeature.modifier'
  elementCodeSystem: GA4GH
  dataType: Code
  dataSpecification:
  - OntologyClass (HPO, NCBITAXON, SCT)
  valueSet: n/a
  fhirExpression_v4_0_1: 'Suggested: Observation.extension'
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: PhenotypicFeature.modifiers
  recommendedDataSpec_phenopackets: list of OntologyClass
  description: Any number of additional modifiers describing a specific phenotypic
    feature further, such as severity (HP:0012824), clinical modifiers (HP:0012823),
    or linking causative infectious agents using the NCBITAXON Ontology.
- ordinal: 6.2.9
  section: 6.2 Phenotypic Feature
  elementName: Evidence
  elementCode:
    system: GA4GH
    code: 'phenotypicfeature.evidence'
  elementCodeSystem: GA4GH
  dataType: Code
  dataSpecification:
  - ECO
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.method
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: PhenotypicFeature.evidence
  recommendedDataSpec_phenopackets: OntologyClass
  description: The evidence for an assertion of the observation of a type defined
    within the Evidence & Conclusion Ontology (ECO).
- ordinal: 6.3.1
  section: 6.3 Measurement
  elementName: Assay
  elementCode:
    system: NCIT
    code: 'C60819'
  elementCodeSystem: NCIT
  dataType: Code
  dataSpecification:
  - OntologyClass (e.g. LOINC)
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.code
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: Measurement.assay
  recommendedDataSpec_phenopackets: OntologyClass
  description: A class that describes the assay used to producethe measurement.
- ordinal: 6.3.2
  section: 6.3 Measurement
  elementName: Value
  elementCode:
    system: NCIT
    code: 'C25712'
  elementCodeSystem: NCIT
  dataType: Value
  dataSpecification:
  - float
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.value[x]
  recommendedDataSpec_fhir: Quantity|integer
  phenopacketSchemaElement_v2_0: Measurement.measurement_value
  recommendedDataSpec_phenopackets: Quantity[double/float]
  description: The result of the measurement.
- ordinal: 6.3.3
  section: 6.3 Measurement
  elementName: Value Unit
  elementCode:
    system: NCIT
    code: 'C92571'
  elementCodeSystem: NCIT
  dataType: Code
  dataSpecification:
  - UO
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.value[x].unit
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: Measurement.measurement_value
  recommendedDataSpec_phenopackets: OntologyClass
  description: The unit of the result's measurement.
- ordinal: 6.3.4
  section: 6.3 Measurement
  elementName: Interpretation
  elementCode:
    system: NCIT
    code: 'C41255'
  elementCodeSystem: NCIT
  dataType: Code
  dataSpecification:
  - NCIT
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.interpretation
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: 'The interpretation of the measurement (e.g.: Below/Within/Above age-related
    reference range, Absent/Low/Normal, or Positive/Negative).'
- ordinal: 6.3.5
  section: 6.3 Measurement
  elementName: Time Observed
  elementCode:
    system: NCIT
    code: 'C82577'
  elementCodeSystem: NCIT
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: n/a
  fhirExpression_v4_0_1: Observation.effectiveDateTime
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: Measurement.time_observed
  recommendedDataSpec_phenopackets: TimeElement
  description: Time at which the measurement was performed.
- ordinal: 6.3.6
  section: 6.3 Measurement
  elementName: Procedure
  elementCode:
    system: SNOMEDCT
    code: '122869004'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - OntologyClass (e.g. NCIT, SNOMEDCT)
  valueSet: n/a
  fhirExpression_v4_0_1: Procedure.code
  recommendedDataSpec_fhir: Measurement.procedure
  phenopacketSchemaElement_v2_0: Measurement.procedure
  recommendedDataSpec_phenopackets: Measurement.procedure
  description: Clinical procedure performed to acquire the sample used for the measurement.
- ordinal: 6.4.1
  section: 6.4 Family History
  elementName: Family Member Pseudonym
  elementCode:
    system: CustomCode
    code: 'family_member_id'
  elementCodeSystem: CustomCode
  dataType: Identifier
  dataSpecification:
  - n/a
  valueSet: n/a
  fhirExpression_v4_0_1: FamilyMemberHistory.identifier
  recommendedDataSpec_fhir: Identifier
  phenopacketSchemaElement_v2_0: Family.Pedigree.Person.individual_id
  recommendedDataSpec_phenopackets: string
  description: A unique identifier or local pseudonym for the familymember.
- ordinal: 6.4.2
  section: 6.4 Family History
  elementName: Propositus/-a
  elementCode:
    system: SNOMEDCT
    code: '64245008'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Propositus Value Set v2.0.0
  fhirExpression_v4_0_1: n/a
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  recommendedDataSpec_phenopackets: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  description: 'Is the individual the first affected family member who seeks medical
    attention for a genetic disorder, leading to the diagnosis of other family members.
    Disclaimer: The SCT code for propositus (64245008) refers to any  gender.'
- ordinal: 6.4.3
  section: 6.4 Family History
  elementName: Relationship of the Individual to the Propositus
  elementCode:
    system: SNOMEDCT
    code: '408732007'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: Family Relationship To Index Case Value Set v2.0.0
  fhirExpression_v4_0_1: n/a
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  recommendedDataSpec_phenopackets: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  description: 'Specifies the familial relationship of the individual being evaluated
    to the propositus. Disclaimer: The SNOMEDCT code for propositus (64245008) refers
    to any gender.'
- ordinal: 6.4.4
  section: 6.4 Family History
  elementName: Consanguinity
  elementCode:
    system: SNOMEDCT
    code: '842009'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  valueSet: Consanguinity Value Set v2.0.0
  fhirExpression_v4_0_1: n/a
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: Family.consanguinous_parents
  recommendedDataSpec_phenopackets: boolean
  description: The presence of a biological relationship between parents who are related
    by blood, typically as first or second cousins.
- ordinal: 6.4.5
  section: 6.4 Family History
  elementName: Family Member Relationship
  elementCode:
    system: SNOMEDCT
    code: '444018008'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: FamilyMember Value Set v2.0.0
  fhirExpression_v4_0_1: FamilyMemberHistory.relationship.coding
  recommendedDataSpec_fhir: 'ValueSet: FamilyMember'
  phenopacketSchemaElement_v2_0: Family.Pedigree.Person.individual_id
  recommendedDataSpec_phenopackets: string
  description: Specifies the relationship of the selected family member to the patient.
- ordinal: 6.4.6
  section: 6.4 Family
  elementName: Family Member Record Status
  elementCode:
    system: HL7FHIR
    code: 'familymemberhistory.status'
  elementCodeSystem: HL7FHIR
  dataType: Code
  dataSpecification:
  - VS
  valueSet: FamilyHistoryStatus Value Set v2.0.0
  fhirExpression_v4_0_1: FamilyMemberHistory.status
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: "Specifies the record\u2019s status of the family history of a specific\
    \ family member."
- ordinal: 6.4.7
  section: 6.4 Family
  elementName: Family Member Sex
  elementCode:
    system: LOINC
    code: '54123-5'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - VSe
  - VSc
  valueSet: AdministrativeGender Value Set v2.0.0
  fhirExpression_v4_0_1: FamilyMemberHistory.sex
  recommendedDataSpec_fhir: 'ValueSet: AdministrativeGender'
  phenopacketSchemaElement_v2_0: Family.Pedigree.Person.sex
  recommendedDataSpec_phenopackets: 'ValueSet: Sex'
  description: Specifies the sex (or gender) of the specific family member. If possible,
    the sex assigned at birth should be selected.
- ordinal: 6.4.8
  section: 6.4 Family
  elementName: Family Member Age
  elementCode:
    system: LOINC
    code: '54141-7'
  elementCodeSystem: LOINC
  dataType: Integer
  dataSpecification:
  - Integer
  valueSet: n/a
  fhirExpression_v4_0_1: FamilyMemberHistory.ageAge
  recommendedDataSpec_fhir: Age
  phenopacketSchemaElement_v2_0: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  recommendedDataSpec_phenopackets: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  description: Records the current age of the selected family member.
- ordinal: 6.4.9
  section: 6.4 Family
  elementName: Family Member Date of Birth
  elementCode:
    system: LOINC
    code: '54124-3'
  elementCodeSystem: LOINC
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: n/a
  fhirExpression_v4_0_1: FamilyMemberHistory.bornDate
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  recommendedDataSpec_phenopackets: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  description: Records the date of birth of the selected family member.
- ordinal: 6.4.10
  section: 6.4 Family
  elementName: Family Member Deceased
  elementCode:
    system: SNOMEDCT
    code: '740604001'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  valueSet: Deceased Value Set v2.0.0
  fhirExpression_v4_0_1: FamilyMemberHistory.deceased.deceasedBoolean
  recommendedDataSpec_fhir: boolean
  phenopacketSchemaElement_v2_0: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  recommendedDataSpec_phenopackets: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  description: Indicates whether the selected family member is deceased.
- ordinal: 6.4.11
  section: 6.4 Family
  elementName: Family Member Cause of Death
  elementCode:
    system: LOINC
    code: '54112-8'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - ICD10CM
  valueSet: n/a
  fhirExpression_v4_0_1: FamilyMemberHistory.condition.code & FamilyMemberHistory.condition.contributedToDeath
  recommendedDataSpec_fhir: Code
  phenopacketSchemaElement_v2_0: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  recommendedDataSpec_phenopackets: "(Family.relatives \u2192 1 Phenopacket per family\
    \ member)"
  description: Records the cause of death of the selected deceasedfamily member.
- ordinal: 6.4.12
  section: 6.4 Family
  elementName: Family Member Deceased Age
  elementCode:
    system: LOINC
    code: '92662-6'
  elementCodeSystem: LOINC
  dataType: Integer
  dataSpecification:
  - Integer
  valueSet: n/a
  fhirExpression_v4_0_1: FamilyMemberHistory.deceasedAge
  recommendedDataSpec_fhir: Family.relatives
  phenopacketSchemaElement_v2_0: Family.relatives
  recommendedDataSpec_phenopackets: Family.relatives
  description: Records the age at which the selected family member died.
- ordinal: 6.4.13
  section: 6.4 Family
  elementName: Family Member Disease
  elementCode:
    system: LOINC
    code: '75315-2'
  elementCodeSystem: LOINC
  dataType: Code
  dataSpecification:
  - Ontology Class
  - ORDO
  - ICD-10-CM
  - ICD-11
  - MONDO
  - OMIM_p
  valueSet: n/a
  fhirExpression_v4_0_1: FamilyMemberHistory.condition.code
  recommendedDataSpec_fhir: Family.relatives
  phenopacketSchemaElement_v2_0: Family.relatives
  recommendedDataSpec_phenopackets: Family.relatives
  description: Indicates whether the selected family member is affected by the same
    rare disease as the individual.
- ordinal: '7.1'
  section: 7. Consent
  elementName: Consent Status
  elementCode:
    system: SNOMEDCT
    code: '309370004'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VS
  valueSet: Consent Status Value Set v2.0.0
  fhirExpression_v4_0_1: Consent.status
  recommendedDataSpec_fhir: 'ValueSet: ConsentStatus'
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: Indicates the current status of the consent.
- ordinal: '7.2'
  section: 7. Consent
  elementName: Consent Date
  elementCode:
    system: HL7FHIR
    code: 'consent.datetime'
  elementCodeSystem: HL7FHIR
  dataType: Date
  dataSpecification:
  - YYYY-MM-DD
  valueSet: n/a
  fhirExpression_v4_0_1: Consent.dateTime
  recommendedDataSpec_fhir: DateTime
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: Records the date when the consent was given.
- ordinal: '7.3'
  section: 7. Consent
  elementName: Health Policy Monitoring
  elementCode:
    system: SNOMEDCT
    code: '386318002'
  elementCodeSystem: SNOMEDCT
  dataType: String
  dataSpecification:
  - n/a
  valueSet: n/a
  fhirExpression_v4_0_1: Consent.policy
  recommendedDataSpec_fhir: string
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: References to the policies that are included in thisconsent scope.
- ordinal: '7.4'
  section: 7. Consent
  elementName: Agreement to be Contacted for Research
  elementCode:
    system: CustomCode
    code: 'consent_contact_research'
  elementCodeSystem: CustomCode
  dataType: Code
  dataSpecification:
  - VSe
  valueSet: Contact for Research Value Set v2.0.0
  fhirExpression_v4_0_1: Consent.scope.coding
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: Indicates whether the patient agrees to be contacted for research.
- ordinal: '7.5'
  section: 7. Consent
  elementName: Consent to the Reuse of Data
  elementCode:
    system: CustomCode
    code: 'conset_data_reuse'
  elementCodeSystem: CustomCode
  dataType: Code
  dataSpecification:
  - VSe
  valueSet: Data Reuse Consent Value Set v2.0.0
  fhirExpression_v4_0_1: Consent.scope.coding
  recommendedDataSpec_fhir: CodeableConcept
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: Indicates whether the patient consents to the reuse of their data.
- ordinal: '7.6'
  section: 7. Consent
  elementName: Biological Sample
  elementCode:
    system: SNOMEDCT
    code: '123038009'
  elementCodeSystem: SNOMEDCT
  dataType: Code
  dataSpecification:
  - VSe
  valueSet: Biological Sample Consent Value Set v2.0.0
  fhirExpression_v4_0_1: n/a
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: Indicates whether a patient's biological sample is available for research.
- ordinal: '7.7'
  section: 7. Consent
  elementName: Link to a Biobank
  elementCode:
    system: CustomCode
    code: 'biobank_link'
  elementCodeSystem: CustomCode
  dataType: String
  dataSpecification:
  - n/a
  valueSet: n/a
  fhirExpression_v4_0_1: n/a
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: If there is a biological sample, this data element indicates the link
    to the biobank of the individual's biological sample.
- ordinal: '8.1'
  section: 8. Disability
  elementName: Classification of Functioning / Disability
  elementCode:
    system: CustomCode
    code: 'icf_score'
  elementCodeSystem: CustomCode
  dataType: Code
  dataSpecification:
  - ICF
  valueSet: n/a
  fhirExpression_v4_0_1: n/a
  recommendedDataSpec_fhir: n/a
  phenopacketSchemaElement_v2_0: n/a
  recommendedDataSpec_phenopackets: n/a
  description: Specifies the classification of the individualss functioning or disability
    according to the International Classification of Functioning, Disability and Health
    (ICF).
