BS ISO 4454:2022

$215.11

Genomics informatics. Phenopackets: A format for phenotypic data exchange

Published By	Publication Date	Number of Pages
BSI	2022	102

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Categories: 35.240.80 - IT applications in health care technology, BSI

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Description

PDF Catalog

PDF Pages	PDF Title
2	undefined
10	Foreword
11	Introduction
13	1 Scope 2 Normative references 3 Terms and definitions
16	4 Abbreviated terms
17	5 Phenopackets Schema and Requirements 5.1 Phenopacket Schema
23	5.2 Requirement Levels 5.2.1 General 5.2.2 Multiplicity
24	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
25	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
26	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
27	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
28	7.2 Age 7.3 AgeRange 7.4 Biosample 7.4.1 General
30	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
31	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
32	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
33	7.6 Disease 7.6.1 General 7.6.2 term 7.6.3 excluded
34	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
35	7.7.2 quantity 7.7.3 schedule_frequency 7.7.4 interval 7.8 DrugType 7.8.1 General
36	7.9 Evidence 7.9.1 General 7.9.2 evidence_code 7.9.3 Reference 7.10 ExternalReference 7.10.1 General
37	7.10.2 id 7.10.3 reference 7.10.4 description 7.11 File 7.11.1 General
38	7.11.2 uri 7.11.3 individual_to_file_identifiers 7.11.4 file_attributes 7.12 GeneDescriptor 7.12.1 General
39	7.12.2 value_id
40	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
41	7.13.2 subject_or_biosample_id 7.13.3 interpretation_status 7.13.4 call 7.14 GestationalAge 7.14.1 General
42	7.15 Individual 7.15.1 General 7.15.2 id
43	7.15.3 alternate_ids 7.15.4 date_of_birth 7.15.5 time_at_last_encounter
44	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
45	7.16.2 id 7.16.3 progress_status
46	7.16.4 diagnosis 7.16.5 summary 7.17 KaryotypicSex
47	7.18 Measurement 7.18.1 General
48	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
49	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
50	7.20.2 created 7.20.3 created_by 7.20.4 submitted_by 7.20.5 resources
51	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
52	7.22 Pedigree 7.22.1 General 7.22.2 persons
54	7.23 PhenotypicFeature 7.23.1 General 7.23.2 description 7.23.3 type
55	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
56	7.24.2 code 7.24.3 body site 7.24.4 performed 7.25 Quantity 7.25.1 General
57	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
58	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
59	7.28.2 id
60	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
61	7.28.9 Identifier resolution 7.29 Sex 7.30 TherapeuticRegimen 7.30.1 General
62	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
63	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
64	7.32.2 start 7.32.3 end 7.33 Timestamp 7.34 Treatment 7.34.1 General
66	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
67	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
70	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
71	7.37.9 xrefs 7.37.10 alternate_labels 7.37.11 extensions 7.37.12 molecule_context 7.37.13 structural_type
72	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
73	7.38.3 therapeutic_actionability 7.38.4 variant 7.39 VitalStatus 7.39.1 General 7.39.2 status
74	7.39.3 time_of_death 7.39.4 cause_of_death 7.39.5 survival_time_in_days
75	Annex A (informative) Working with Phenopackets
83	Annex B (informative) Ontologies
86	Annex C (informative) Rare Disease Example
89	Annex D (informative) Cancer Example
93	Annex E (informative) COVID-19 Example
98	Bibliography

Additional information

Status	Definitive
Pages	102
Publication Date	2022-07-22
ISBN	978 0 539 14689 9
Standard Number	BS ISO 4454:2022
Title	Genomics informatics. Phenopackets: A format for phenotypic data exchange
Identical National Standard Of	ISO 4454
Descriptors	Information, Data, Measurement, Blocks, Samples
Publisher	BSI
Committee	IST/35
ICS Codes	35.240.80 - IT applications in health care technology

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BS ISO 4454:2022

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