ISO 4454:2022
Genomics informatics — Phenopackets: A format for phenotypic data exchange
This document specifies a uniform, machine-readable, phenotypic description of an individual, patient or sample in the context of rare disease, common/complex disease or cancer.
It is applicable to academic, clinical and commercial research, as well as clinical diagnostics. While intended for human data collection, it can be used in other areas (e.g. mouse research). It does not define the phenotypic information that needs to be collected for a particular use but represents that information in an appropriately descriptive manner that allows it to be computationally exchanged between systems.
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Foreword
Introduction
1 Scope
2 Normative references
3 Terms and definitions
4 Abbreviated terms
5 Phenopackets Schema and Requirements
5.1 Phenopacket Schema
5.2 Requirement Levels
5.2.1 General
5.2.2 Multiplicity
5.3 Ontology Use
6 Phenopacket Schema Top-Level Elements
6.1 Phenopacket
6.1.1 General
6.1.2 id
6.1.3 subject
6.1.4 phenotypic_features
6.1.5 measurements
6.1.6 biosamples
6.1.7 interpretation
6.1.8 diseases
6.1.9 medical_actions
6.1.10 files
6.1.11 meta_data
6.2 Family
6.2.1 General
6.2.2 id
6.2.3 proband
6.2.4 relatives
6.2.5 pedigree
6.2.6 files
6.2.7 meta_data
6.3 Cohort
6.3.1 General
6.3.2 id
6.3.3 description
6.3.4 members
6.3.5 files
6.3.6 meta_data
7 Phenopackets Building Blocks
7.1 General
7.2 Age
7.3 AgeRange
7.4 Biosample
7.4.1 General
7.4.2 id
7.4.3 individual_id
7.4.4 derived_from_id
7.4.5 description
7.4.6 sampled_tissue
7.4.7 sample_type
7.4.8 phenotypic_features
7.4.9 measurements
7.4.10 taxonomy
7.4.11 time_at_collection
7.4.12 histological_diagnosis
7.4.13 tumor_progression
7.4.14 tumor_grade
7.4.15 pathological_stage
7.4.16 pathological_tnm_finding
7.4.17 diagnostic_markers
7.4.18 procedure
7.4.19 files
7.4.20 material_sample
7.4.21 sample_processing
7.4.22 sample_storage
7.5 ComplexValue
7.5.1 General
7.5.2 typed_quantities
7.6 Disease
7.6.1 General
7.6.2 term
7.6.3 excluded
7.6.4 onset
7.6.5 resolution
7.6.6 disease_stage
7.6.7 clinical_tnm_finding
7.6.8 primary_site
7.6.9 laterality
7.7 DoseInterval
7.7.1 General
7.7.2 quantity
7.7.3 schedule_frequency
7.7.4 interval
7.8 DrugType
7.8.1 General
7.9 Evidence
7.9.1 General
7.9.2 evidence_code
7.9.3 Reference
7.10 ExternalReference
7.10.1 General
7.10.2 id
7.10.3 reference
7.10.4 description
7.11 File
7.11.1 General
7.11.2 uri
7.11.3 individual_to_file_identifiers
7.11.4 file_attributes
7.12 GeneDescriptor
7.12.1 General
7.12.2 value_id
7.12.3 symbol
7.12.4 description
7.12.5 alternate_ids
7.12.6 alternate_symbols
7.12.7 xrefs
7.13 GenomicInterpretation
7.13.1 General
7.13.2 subject_or_biosample_id
7.13.3 interpretation_status
7.13.4 call
7.14 GestationalAge
7.14.1 General
7.15 Individual
7.15.1 General
7.15.2 id
7.15.3 alternate_ids
7.15.4 date_of_birth
7.15.5 time_at_last_encounter
7.15.6 vital_status
7.15.7 sex
7.15.8 karyotypic_sex
7.15.9 gender
7.15.10 taxonomy
7.16 Interpretation
7.16.1 General
7.16.2 id
7.16.3 progress_status
7.16.4 diagnosis
7.16.5 summary
7.17 KaryotypicSex
7.18 Measurement
7.18.1 General
7.18.2 description
7.18.3 assay
7.18.4 value
7.18.5 time_observed
7.18.6 procedure
7.19 MedicalAction
7.19.1 General
7.19.2 action
7.19.3 treatment_target
7.19.4 treatment_intent
7.19.5 response_to_treatment
7.19.6 adverse_events
7.19.7 treatment_termination_reason
7.20 MetaData
7.20.1 General
7.20.2 created
7.20.3 created_by
7.20.4 submitted_by
7.20.5 resources
7.20.6 updates
7.20.7 phenopacket_schema_version
7.20.8 external_references
7.21 OntologyClass
7.21.1 General
7.21.2 id
7.21.3 label
7.22 Pedigree
7.22.1 General
7.22.2 persons
7.23 PhenotypicFeature
7.23.1 General
7.23.2 description
7.23.3 type
7.23.4 excluded
7.23.5 severity
7.23.6 modifiers
7.23.7 onset
7.23.8 resolution
7.23.9 evidence
7.24 Procedure
7.24.1 General
7.24.2 code
7.24.3 body site
7.24.4 performed
7.25 Quantity
7.25.1 General
7.25.2 unit
7.25.3 value
7.25.4 reference_range
7.26 RadiationTherapy
7.26.1 General
7.26.2 modality
7.26.3 body_site
7.26.4 dosage
7.26.5 fractions
7.27 ReferenceRange
7.27.1 General
7.27.2 unit
7.27.3 low
7.27.4 high
7.28 Resource
7.28.1 General
7.28.2 id
7.28.3 name
7.28.4 url
7.28.5 version
7.28.6 namespace_prefix
7.28.7 iriPrefix
7.28.8 CURIE
7.28.9 Identifier resolution
7.29 Sex
7.30 TherapeuticRegimen
7.30.1 General
7.30.2 identifier
7.30.3 start_time
7.30.4 end_time
7.30.5 regimen_status
7.31 TimeElement
7.31.1 General
7.31.2 gestational_age
7.31.3 age
7.31.4 age_range
7.31.5 ontology_class
7.31.6 timestamp
7.31.7 interval
7.32 TimeInterval
7.32.1 General
7.32.2 start
7.32.3 end
7.33 Timestamp
7.34 Treatment
7.34.1 General
7.34.2 agent
7.34.3 route_of_administration
7.34.4 dose_intervals
7.34.5 drug_type
7.34.6 cumulative_dose
7.35 Update
7.35.1 General
7.35.2 timestamp
7.35.3 updated_by
7.35.4 comment
7.36 Value
7.36.1 General
7.36.2 value
7.37 VariationDescriptor
7.37.1 General
7.37.2 id
7.37.3 variation
7.37.4 label
7.37.5 description
7.37.6 gene_context
7.37.7 expression
7.37.8 vcf_record
7.37.9 xrefs
7.37.10 alternate_labels
7.37.11 extensions
7.37.12 molecule_context
7.37.13 structural_type
7.37.14 vrs_ref_allele_seq
7.37.15 allelic_state
7.38 VariantInterpretation
7.38.1 General
7.38.2 acmg_pathogenicity_classification
7.38.3 therapeutic_actionability
7.38.4 variant
7.39 VitalStatus
7.39.1 General
7.39.2 status
7.39.3 time_of_death
7.39.4 cause_of_death
7.39.5 survival_time_in_days
Annex A (informative) Working with Phenopackets
Annex B (informative) Ontologies
Annex C (informative) Rare Disease Example
Annex D (informative) Cancer Example
Annex E (informative) COVID-19 Example
Bibliography
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Foreword
Introduction
1 Scope
2 Normative references
3 Terms and definitions
4 Abbreviated terms
5 Phenopackets Schema and Requirements
5.1 Phenopacket Schema
5.2 Requirement Levels
5.2.1 General
5.2.2 Multiplicity
5.3 Ontology Use
6 Phenopacket Schema Top-Level Elements
6.1 Phenopacket
6.1.1 General
6.1.2 id
6.1.3 subject
6.1.4 phenotypic_features
6.1.5 measurements
6.1.6 biosamples
6.1.7 interpretation
6.1.8 diseases
6.1.9 medical_actions
6.1.10 files
6.1.11 meta_data
6.2 Family
6.2.1 General
6.2.2 id
6.2.3 proband
6.2.4 relatives
6.2.5 pedigree
6.2.6 files
6.2.7 meta_data
6.3 Cohort
6.3.1 General
6.3.2 id
6.3.3 description
6.3.4 members
6.3.5 files
6.3.6 meta_data
7 Phenopackets Building Blocks
7.1 General
7.2 Age
7.3 AgeRange
7.4 Biosample
7.4.1 General
7.4.2 id
7.4.3 individual_id
7.4.4 derived_from_id
7.4.5 description
7.4.6 sampled_tissue
7.4.7 sample_type
7.4.8 phenotypic_features
7.4.9 measurements
7.4.10 taxonomy
7.4.11 time_at_collection
7.4.12 histological_diagnosis
7.4.13 tumor_progression
7.4.14 tumor_grade
7.4.15 pathological_stage
7.4.16 pathological_tnm_finding
7.4.17 diagnostic_markers
7.4.18 procedure
7.4.19 files
7.4.20 material_sample
7.4.21 sample_processing
7.4.22 sample_storage
7.5 ComplexValue
7.5.1 General
7.5.2 typed_quantities
7.6 Disease
7.6.1 General
7.6.2 term
7.6.3 excluded
7.6.4 onset
7.6.5 resolution
7.6.6 disease_stage
7.6.7 clinical_tnm_finding
7.6.8 primary_site
7.6.9 laterality
7.7 DoseInterval
7.7.1 General
7.7.2 quantity
7.7.3 schedule_frequency
7.7.4 interval
7.8 DrugType
7.8.1 General
7.9 Evidence
7.9.1 General
7.9.2 evidence_code
7.9.3 Reference
7.10 ExternalReference
7.10.1 General
7.10.2 id
7.10.3 reference
7.10.4 description
7.11 File
7.11.1 General
7.11.2 uri
7.11.3 individual_to_file_identifiers
7.11.4 file_attributes
7.12 GeneDescriptor
7.12.1 General
7.12.2 value_id
7.12.3 symbol
7.12.4 description
7.12.5 alternate_ids
7.12.6 alternate_symbols
7.12.7 xrefs
7.13 GenomicInterpretation
7.13.1 General
7.13.2 subject_or_biosample_id
7.13.3 interpretation_status
7.13.4 call
7.14 GestationalAge
7.14.1 General
7.15 Individual
7.15.1 General
7.15.2 id
7.15.3 alternate_ids
7.15.4 date_of_birth
7.15.5 time_at_last_encounter
7.15.6 vital_status
7.15.7 sex
7.15.8 karyotypic_sex
7.15.9 gender
7.15.10 taxonomy
7.16 Interpretation
7.16.1 General
7.16.2 id
7.16.3 progress_status
7.16.4 diagnosis
7.16.5 summary
7.17 KaryotypicSex
7.18 Measurement
7.18.1 General
7.18.2 description
7.18.3 assay
7.18.4 value
7.18.5 time_observed
7.18.6 procedure
7.19 MedicalAction
7.19.1 General
7.19.2 action
7.19.3 treatment_target
7.19.4 treatment_intent
7.19.5 response_to_treatment
7.19.6 adverse_events
7.19.7 treatment_termination_reason
7.20 MetaData
7.20.1 General
7.20.2 created
7.20.3 created_by
7.20.4 submitted_by
7.20.5 resources
7.20.6 updates
7.20.7 phenopacket_schema_version
7.20.8 external_references
7.21 OntologyClass
7.21.1 General
7.21.2 id
7.21.3 label
7.22 Pedigree
7.22.1 General
7.22.2 persons
7.23 PhenotypicFeature
7.23.1 General
7.23.2 description
7.23.3 type
7.23.4 excluded
7.23.5 severity
7.23.6 modifiers
7.23.7 onset
7.23.8 resolution
7.23.9 evidence
7.24 Procedure
7.24.1 General
7.24.2 code
7.24.3 body site
7.24.4 performed
7.25 Quantity
7.25.1 General
7.25.2 unit
7.25.3 value
7.25.4 reference_range
7.26 RadiationTherapy
7.26.1 General
7.26.2 modality
7.26.3 body_site
7.26.4 dosage
7.26.5 fractions
7.27 ReferenceRange
7.27.1 General
7.27.2 unit
7.27.3 low
7.27.4 high
7.28 Resource
7.28.1 General
7.28.2 id
7.28.3 name
7.28.4 url
7.28.5 version
7.28.6 namespace_prefix
7.28.7 iriPrefix
7.28.8 CURIE
7.28.9 Identifier resolution
7.29 Sex
7.30 TherapeuticRegimen
7.30.1 General
7.30.2 identifier
7.30.3 start_time
7.30.4 end_time
7.30.5 regimen_status
7.31 TimeElement
7.31.1 General
7.31.2 gestational_age
7.31.3 age
7.31.4 age_range
7.31.5 ontology_class
7.31.6 timestamp
7.31.7 interval
7.32 TimeInterval
7.32.1 General
7.32.2 start
7.32.3 end
7.33 Timestamp
7.34 Treatment
7.34.1 General
7.34.2 agent
7.34.3 route_of_administration
7.34.4 dose_intervals
7.34.5 drug_type
7.34.6 cumulative_dose
7.35 Update
7.35.1 General
7.35.2 timestamp
7.35.3 updated_by
7.35.4 comment
7.36 Value
7.36.1 General
7.36.2 value
7.37 VariationDescriptor
7.37.1 General
7.37.2 id
7.37.3 variation
7.37.4 label
7.37.5 description
7.37.6 gene_context
7.37.7 expression
7.37.8 vcf_record
7.37.9 xrefs
7.37.10 alternate_labels
7.37.11 extensions
7.37.12 molecule_context
7.37.13 structural_type
7.37.14 vrs_ref_allele_seq
7.37.15 allelic_state
7.38 VariantInterpretation
7.38.1 General
7.38.2 acmg_pathogenicity_classification
7.38.3 therapeutic_actionability
7.38.4 variant
7.39 VitalStatus
7.39.1 General
7.39.2 status
7.39.3 time_of_death
7.39.4 cause_of_death
7.39.5 survival_time_in_days
Annex A (informative) Working with Phenopackets
Annex B (informative) Ontologies
Annex C (informative) Rare Disease Example
Annex D (informative) Cancer Example
Annex E (informative) COVID-19 Example
Bibliography