iTeh StandardsiTeh Standards
EURUSD
Your shopping cart is empty.
ISO

ISO 4454:2022

(Main)

Genomics informatics — Phenopackets: A format for phenotypic data exchange

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.

Titre manque

General Information

Status
Published
Publication Date
06-Jul-2022
ICS
35.240.80 - IT applications in health care technology
Technical Committee
ISO/TC 215/SC 1 - Genomics Informatics
Drafting Committee
ISO/TC 215/SC 1/WG 1 - Genomics data sharing
Current Stage
6060 - International Standard published
Start Date
07-Jul-2022
Due Date
22-Jul-2023
Completion Date
07-Jul-2022
Ref Project

Buy Standard

ISO 4454:2022 - Genomics informatics — Phenopackets: A format for phenotypic data exchange Released:7. 07. 2022ISO 4454:2022 - Genomics informatics — Phenopackets: A format for phenotypic data exchange Released:7. 07. 2022
PreviousNext
Standard
ISO 4454:2022 - Genomics informatics — Phenopackets: A format for phenotypic data exchange Released:7. 07. 2022
English language
86 pages
sale 15% off
Preview
sale 15% off
Preview

Standards Content (Sample)

INTERNATIONAL ISO
STANDARD 4454
First edition
2022-07
Genomics informatics —
Phenopackets: A format for
phenotypic data exchange
Reference number
ISO 4454:2022(E)
© ISO 2022

---------------------- Page: 1 ----------------------
ISO 4454:2022(E)
COPYRIGHT PROTECTED DOCUMENT
© ISO 2022
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may
be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting on
the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address below
or ISO’s member body in the country of the requester.
ISO copyright office
CP 401 • Ch. de Blandonnet 8
CH-1214 Vernier, Geneva
Phone: +41 22 749 01 11
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland
ii
  © ISO 2022 – All rights reserved

---------------------- Page: 2 ----------------------
ISO 4454:2022(E)
Contents Page
Foreword .viii
Introduction .ix
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Abbreviated terms . 4
5 Phenopackets Schema and Requirements . 5
5.1 Phenopacket Schema . 5
5.2 Requirement Levels. 11
5.2.1 General . 11
5.2.2 Multiplicity . 11
5.3 Ontology Use .12
6 Phenopacket Schema Top-Level Elements.12
6.1 Phenopacket .12
6.1.1 General .12
6.1.2 id .12
6.1.3 subject . 12
6.1.4 phenotypic_features .13
6.1.5 measurements .13
6.1.6 biosamples .13
6.1.7 interpretation . 13
6.1.8 diseases .13
6.1.9 medical_actions . 13
6.1.10 files . 13
6.1.11 meta_data .13
6.2 Family .13
6.2.1 General .13
6.2.2 id . 14
6.2.3 proband . 14
6.2.4 relatives . 14
6.2.5 pedigree . 14
6.2.6 files . 14
6.2.7 meta_data . 14
6.3 Cohort . 15
6.3.1 General .15
6.3.2 id . 15
6.3.3 description . 15
6.3.4 members .15
6.3.5 files . 15
6.3.6 meta_data .15
7 Phenopackets Building Blocks .15
7.1 General . 15
7.2 Age . 16
7.3 AgeRange . 16
7.4 Biosample . 16
7.4.1 General . 16
7.4.2 id . 18
7.4.3 individual_id . 18
7.4.4 derived_from_id . 18
7.4.5 description . 18
7.4.6 sampled_tissue . 18
7.4.7 sample_type . 18
iii
© ISO 2022 – All rights reserved

---------------------- Page: 3 ----------------------
ISO 4454:2022(E)
7.4.8 phenotypic_features . 18
7.4.9 measurements . 18
7.4.10 taxonomy . 19
7.4.11 time_at_collection . 19
7.4.12 histological_diagnosis . 19
7.4.13 tumor_progression . 19
7.4.14 tumor_grade . 19
7.4.15 pathological_stage . 19
7.4.16 pathological_tnm_finding . 19
7.4.17 diagnostic_markers . 19
7.4.18 procedure . . 19
7.4.19 files . 19
7.4.20 material_sample . 20
7.4.21 sample_processing . .20
7.4.22 sample_storage . 20
7.5 ComplexValue . 20
7.5.1 General .20
7.5.2 typed_quantities . . .20
7.6 Disease . 21
7.6.1 General . 21
7.6.2 term . 21
7.6.3 excluded . 21
7.6.4 onset .22
7.6.5 resolution . 22
7.6.6 disease_stage . 22
7.6.7 clinical_tnm_finding . .22
7.6.8 primary_site . 22
7.6.9 laterality . 22
7.7 DoseInterval . 22
7.7.1 General .22
7.7.2 quantity .23
7.7.3 schedule_frequency . 23
7.7.4 interval . 23
7.8 DrugType .23
7.8.1 General .23
7.9 Evidence . 24
7.9.1 General . 24
7.9.2 evidence_code . 24
7.9.3 Reference . 24
7.10 ExternalReference . 24
7.10.1 General . 24
7.10.2 id . 25
7.10.3 reference . 25
7.10.4 description . 25
7.11 File . 25
7.11.1 General . 25
7.11.2 uri . 26
7.11.3 individual_to_file_identifiers . 26
7.11.4 file_attributes .26
7.12 GeneDescriptor . 26
7.12.1 General . 26
7.12.2 value_id . 27
7.12.3 symbol .28
7.12.4 description .28
7.12.5 alternate_ids . .28
7.12.6 alternate_symbols .28
7.12.7 xrefs .28
7.13 GenomicInterpretation .28
iv
  © ISO 2022 – All rights reserved

---------------------- Page: 4 ----------------------
ISO 4454:2022(E)
7.13.1 General .28
7.13.2 subject_or_biosample_id .29
7.13.3 interpretation_status .29
7.13.4 call .29
7.14 GestationalAge .29
7.14.1 General .29
7.15 Individual . 30
7.15.1 General .30
7.15.2 id .30
7.15.3 alternate_ids . . 31
7.15.4 date_of_birth . 31
7.15.5 time_at_last_encounter . 31
7.15.6 vital_status . 32
7.15.7 sex . 32
7.15.8 karyotypic_sex . 32
7.15.9 gender . . 32
7.15.10 taxonomy . 32
7.16 Interpretation . 32
7.16.1 General . 32
7.16.2 id . 33
7.16.3 progress_status .33
7.16.4 diagnosis .34
7.16.5 summary .34
7.17 KaryotypicSex .34
7.18 Measurement . 35
7.18.1 General . 35
7.18.2 description . 36
7.18.3 assay .36
7.18.4 value .36
7.18.5 time_observed .36
7.18.6 procedure . . 36
7.19 MedicalAction. 36
7.19.1 General .36
7.19.2 action . 37
7.19.3 treatment_target . 37
7.19.4 treatment_intent .
...

Questions, Comments and Discussion

Ask us and Technical Secretary will try to provide an answer. You can facilitate discussion about the standard in here.

This May Also Interest You

ISO
ISO/TS 23357:2023(Main)
Genomics informatics — Clinical genomics data sharing specification for next-generation sequencing

This document specifies clinical sequencing information generated by massive parallel sequencing technology for sharing health information via massively parallel sequencing. This document covers the data fields and their metadata from the generation of sequence reads and base calling to variant evaluation and assertion for archiving reproducibility during health information exchange of clinical sequence information. However, the specimen collection, processing and storage, DNA extraction and DNA processing and library preparation, and the generation of test report are not in the scope of this document. This document hence defines the data types, relationship, optionality, cardinalities and bindings of terminology of the data. In essence, this document specifies: — the required data fields and their metadata from generation of sequence reads and base calling to variant evaluation and assertion for sharing clinical genomic sequencing data files generated by massively parallel sequencing technology, as shown in Figure 1; — the sequencing information from human samples using DNA sequencing by massively parallel sequencing technologies for clinical practice.

  • Technical specification
    14 pages
    English language
    sale 15% off
  • Draft
    14 pages
    English language
    sale 15% off
  • Draft
    14 pages
    English language
    sale 15% off
ISO
ISO/TS 8392:2023(Main)
Genomics informatics — Description rules for genomic data for genetic detection products and services

This document specifies requirements on the category definition and quality assessment of genomic data, including the content structure, attribute and description rules of data format, and the compilation rules of data format. This document applies to all the genomic data used for human genetic detection products and services. This document applies to genomic data processing and analysis, and to the quality evaluation/assessment of genomic data.

  • Technical specification
    17 pages
    English language
    sale 15% off
  • Draft
    17 pages
    English language
    sale 15% off
  • Draft
    17 pages
    English language
    sale 15% off
  • Draft
    13 pages
    English language
    sale 15% off
  • Draft
    13 pages
    English language
    sale 15% off
ISO
ISO/TS 4425:2023(Main)
Genomics informatics — Data elements and their metadata for describing the microsatellite instability (MSI) information of clinical massive parallel DNA sequencing

This document identifies data elements and metadata to represent the information about microsatellite instability (MSI) for reporting the value of the biomarker using clinical massive parallel DNA sequencing. This document covers information about the MSI test result and related data, such as used resources, data generation condition, and data processing information which are helpful to clinical diagnosis and research. This document is not intended — for defining experimental protocols or methods for calculating the value of microsatellite instability (MSI), — for the other biological species than human resource, or — for the Sanger sequencing methods.

  • Technical specification
    20 pages
    English language
    sale 15% off
  • Draft
    21 pages
    English language
    sale 15% off
  • Draft
    21 pages
    English language
    sale 15% off
ISO
ISO/TS 22690:2021(Main)
Genomics informatics — Reliability assessment criteria for high-throughput gene-expression data

This document specifies reliability assessment criteria for high-throughput gene-expression data. It is applicable to assessing the accuracy, reproducibility, and comparability of gene-expression data that are generated from microarray, next-generation sequencing, and other forms of high-throughput technologies. This document identifies the quality-related data for the process of the next-generation sequencing of RNA (RNA-seq). The sequencing platform covered by this document is limited to short-read sequencers. The use of RNA-seq for mutation detection and virus identification is outside of the scope of this document. This document is applicable to human health associated species such as human, cell lines, and preclinical animals. Other biological species are outside the scope of this document. From a biological point of view, expression profiles of all genetic sequences including genes, transcripts, isoforms, exons, and junctions are within the scope of this document

  • Technical specification
    11 pages
    English language
    sale 15% off
  • Draft
    11 pages
    English language
    sale 15% off
ISO
ISO 21393:2021(Main)
Genomics informatics — Omics Markup Language (OML)

This document is applicable to the data exchange format that is designed to facilitate exchanging omics data around the world without forcing changes of any database schema. This document specifies the characteristics of OML from the following perspectives. From an informatics perspective, OML defines the data exchange format based on XML. This document gives guidelines for the specifications of the data exchange format, but this document excludes the database schema itself. From a molecular side of view, this document is applicable to all kinds of omics data, while this document excludes the details of the molecules (e.g., details of genomic sequence variations or whole genomic sequence). This document is also applicable to the molecular annotations including clinical concerns and relations with other omics concerns. From an application side of view, this document is applicable to the clinical field including clinical practice, preventive medicine, translational research, and clinical research including drug discovery. This document does not apply to basic research and other scientific fields. From a biological species side of view, this document is applicable to the human health-associated species as human, preclinical animals, and cell lines. This document does not apply to the other biological species.

  • Standard
    46 pages
    English language
    sale 15% off
  • Standard
    48 pages
    French language
    sale 15% off
  • Draft
    48 pages
    English language
    sale 15% off
ISO
ISO/TS 22693:2021(Main)
Genomics informatics — Structured clinical gene fusion report in electronic health records

The document defines the data elements and their necessary metadata to implement a structured clinical gene fusion report whose data are generated by next generation sequencing technologies. This document — describes the reporting guideline for RNA sequencing approaches focusing on detecting novel and known fusion partners, — defines the required data fields and their metadata for a structured clinical gene fusion report, — defines the optional data fields and their metadata, — covers the fusion gene from human specimen using whole transcriptome sequencing by next generation sequencing technologies for clinical practice and translational research, — does not cover the fusion gene detection using DNA sequencing methods, — does not cover the basic research and other scientific areas, — does not cover the other biological species, — does not cover the Sanger sequencing methods, and — does not cover the other structural variations. This document only defines the data elements and their metadata for the structured clinical sequencing report in electronic health records. Therefore, its layout can be designed based on the institutional decision if all elements are included as in this document.

  • Technical specification
    21 pages
    English language
    sale 15% off
  • Draft
    21 pages
    English language
    sale 15% off
ISO
ISO/TS 22692:2020(Main)
Genomics informatics— Quality control metrics for DNA sequencing

This document identifies quality metrics for the detection of DNA variants using next generation sequencing (NGS) technology. It also defines the data types, relationships, optionality, cardinalities and terminology bindings of the data. This document provides a basis for sharing and for the application of "high quality" genomic data and contributes to the realization of the precision medicine and the development of relevant industries. This document is intended to serve as a catalogue of sequencing data elements used to address quality metrics for various clinical, industrial and commercial applications. The exchange of these data allows researchers, commercial entities, and regulatory bodies to assess for the purpose of selective utilization of the data by setting application-specific quality criteria This document is not intended for — sequencing methods other than NGS, such as the Sanger sequencing, — targets other than genome, such as transcriptome or proteome, or — specimens of species other than humans.

  • Technical specification
    15 pages
    English language
    sale 15% off
  • Draft
    15 pages
    English language
    sale 15% off
ISO
ISO/TS 20428:2017(Main)
Health informatics — Data elements and their metadata for describing structured clinical genomic sequence information in electronic health records

ISO/TS 20428:2017 defines the data elements and their necessary metadata to implement a structured clinical genomic sequencing report and their metadata in electronic health records particularly focusing on the genomic data generated by next generation sequencing technology. ISO/TS 20428:2017 - defines the composition of a structured clinical sequencing report (see Clause 5), - defines the required data fields and their metadata for a structured clinical sequencing report (see Clause 6), - defines the optional data (see Clause 7), - covers the DNA-level variation from human samples using whole genome sequencing, whole exome sequencing, and targeted sequencing (disease-targeted gene panels) by next generation sequencing technologies. Though whole transcriptome sequencing and other technologies are important to provide better patient care and enable precision medicine, this document only deals with DNA-level changes, - covers mainly clinical applications and clinical research such as clinical trials and translational research which uses clinical data. However, the necessary steps such as de-identification or consent from patient should be applied. The basic research and other scientific areas are outside the scope of this document, - does not cover the other biological species, i.e. genomes of viruses and microbes, and - does not cover the Sanger sequencing methods.

  • Technical specification
    33 pages
    English language
    sale 15% off
ISO
ISO 25720:2009(Main)
Health informatics — Genomic Sequence Variation Markup Language (GSVML)

ISO 25720:2009 is applicable to the data exchange format that is designed to facilitate the exchange of the genomic sequence variation data around the world, without forcing change of any database schema. From an informatics perspective, GSVML defines the data exchange format based on XML. The scope of ISO 25720:2009 is the data exchange format, but the database schema itself is outside the scope of this International Standard. From a biological point of view, all genetic sequence variations are taken into consideration and are within the scope of this International Standard, while polymorphisms, especially SNP, are the main focus of this International Standard. In other words, the annotations of variation as clinical concerns and -omics concerns are within the scope of ISO 25720:2009. Though SNPs exist in various biological species, the scope of this International Standard covers the human health associated species as human, cell line, and preclinical animals. The other biological species are outside the scope of ISO 25720:2009. The clinical field is within the scope of this International Standard, but the basic research fields and other scientific fields are outside the scope of ISO 25720:2009. Here, clinical research including drug discovery is within the scope of this International Standard. As for supposed application fields, our main focus is in human health including clinical practice, preventive medicine, translational research and clinical researches.

  • Standard
    132 pages
    English language
    sale 15% off
  • Standard
    132 pages
    English language
    sale 15% off
ISO
ISO/TS 23357:2023(Main)
Genomics informatics — Clinical genomics data sharing specification for next-generation sequencing

This document specifies clinical sequencing information generated by massive parallel sequencing technology for sharing health information via massively parallel sequencing. This document covers the data fields and their metadata from the generation of sequence reads and base calling to variant evaluation and assertion for archiving reproducibility during health information exchange of clinical sequence information. However, the specimen collection, processing and storage, DNA extraction and DNA processing and library preparation, and the generation of test report are not in the scope of this document. This document hence defines the data types, relationship, optionality, cardinalities and bindings of terminology of the data. In essence, this document specifies: — the required data fields and their metadata from generation of sequence reads and base calling to variant evaluation and assertion for sharing clinical genomic sequencing data files generated by massively parallel sequencing technology, as shown in Figure 1; — the sequencing information from human samples using DNA sequencing by massively parallel sequencing technologies for clinical practice.

  • Technical specification
    14 pages
    English language
    sale 15% off
  • Draft
    14 pages
    English language
    sale 15% off
  • Draft
    14 pages
    English language
    sale 15% off