{ "version": "v2_0_0", "dataElements": [ { "ordinal": "1.1", "section": "1. Formal Criteria", "elementName": "Pseudonym", "elementCode": "422549004", "elementCodeSystem": "SNOMED", "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": "399423000", "elementCodeSystem": "SNOMED", "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": "184099003", "elementCodeSystem": "SNOMED", "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": "281053000", "elementCodeSystem": "SNOMED", "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": "1296886006", "elementCodeSystem": "SNOMED", "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": "263495000", "elementCodeSystem": "SNOMED", "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": "370159000", "elementCodeSystem": "SNOMED", "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": "278844005", "elementCodeSystem": "SNOMED", "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": "398299004", "elementCodeSystem": "SNOMED", "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": "184305005", "elementCodeSystem": "SNOMED", "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": "105727008", "elementCodeSystem": "SNOMED", "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": "412726003", "elementCodeSystem": "SNOMED", "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": "723663001", "elementCodeSystem": "SNOMED", "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": "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": "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": "305058001", "elementCodeSystem": "SNOMED", "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": "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": "64572001", "elementCodeSystem": "SNOMED", "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": "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": "424850005", "elementCodeSystem": "SNOMED", "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": "298059007", "elementCodeSystem": "SNOMED", "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": "423493009", "elementCodeSystem": "SNOMED", "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": "432213005", "elementCodeSystem": "SNOMED", "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": "363698007", "elementCodeSystem": "SNOMED", "dataType": "Code", "dataSpecification": [ "VS" ], "valueSet": "Body Site Value Set v2.0.0", "fhirExpression_v4_0_1": "Condition.bodySite.coding:snomed-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": "263493007", "elementCodeSystem": "SNOMED", "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": "246112005", "elementCodeSystem": "SNOMED", "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": "106221001", "elementCodeSystem": "SNOMED", "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": "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": "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": "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": "62374-4", "elementCodeSystem": "LOINC", "dataType": "Code", "dataSpecification": [ "VS" ], "valueSet": "Reference Genome Value Set v2.0.0", "fhirExpression_v4_0_1": "MolecularSequence.referenceSeqId", "recommendedDataSpec_fhir": "CodeableConcept", "phenopacketSchemaElement_v2_0": "VariationDescriptor.vrs_ref_allele_seq", "recommendedDataSpec_phenopackets": "string", "description": "The reference genome used for analysing the genetic variant." }, { "ordinal": "6.1.6", "section": "6. Genetic Findings", "elementName": "Genetic Mutation String", "elementCode": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "8116006", "elementCodeSystem": "SNOMED", "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": "363778006", "elementCodeSystem": "SNOMED", "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": "439272007:704321009=363778006", "elementCodeSystem": "SNOMED", "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "122869004", "elementCodeSystem": "SNOMED", "dataType": "Code", "dataSpecification": [ "OntologyClass (e.g. NCIT, SNOMED)" ], "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": "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": "64245008", "elementCodeSystem": "SNOMED", "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": "408732007", "elementCodeSystem": "SNOMED", "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 SNOMED code for propositus (64245008) refers to any gender." }, { "ordinal": "6.4.4", "section": "6.4 Family History", "elementName": "Consanguinity", "elementCode": "842009", "elementCodeSystem": "SNOMED", "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": "444018008", "elementCodeSystem": "SNOMED", "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": "familymemberhistory.status", "elementCodeSystem": "HL7FHIR", "dataType": "Code", "dataSpecification": [ "VS" ], "valueSet": "FamilyHistoryStatus Value Set v2.0.0", "fhirExpression_v4_0_1": "FamilyMemberHistory.status", "recommendedDataSpec_fhir": null, "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": "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": "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": "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": "740604001", "elementCodeSystem": "SNOMED", "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": "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": "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": "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": "309370004", "elementCodeSystem": "SNOMED", "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": "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": "386318002", "elementCodeSystem": "SNOMED", "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": "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": "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": "123038009", "elementCodeSystem": "SNOMED", "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": "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": "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)." } ] }