ISO/IEC 23092-3:2022

Information technology — Genomic information representation — Part 3: Metadata and application programming interfaces (APIs)

This document specifies information metadata, auxiliary fields, SAM interoperability, protection metadata and programming interfaces of genomic information. It defines: — metadata storage and interpretation for the different encapsulation levels as specified in ISO/IEC 23092-1 (in Clause 6); — protection elements providing confidentiality, integrity and privacy rules at the different encapsulation levels specified in ISO/IEC 23092-1 (in Clause 7); — how to associate auxiliary fields to encoded reads (in Clause 8); — mechanisms for backward compatibility with existing SAM content, and exportation to this format (in Annex C); — interfaces to access genomic information coded in compliance with ISO/IEC 23092-1 and ISO/IEC 23092-2 (in subclause 8.1).

Technologie de l'information — Représentation des informations génomiques — Partie 3: Métadonnées et interfaces de programmation d'application (API)

General Information

• Status: Published
• Publication Date: 24-Oct-2022
• ICS: 35.040.99 - Other standards related to information coding
• Technical Committee: ISO/IEC JTC 1/SC 29 - Coding of audio, picture, multimedia and hypermedia information
• Drafting Committee: ISO/IEC JTC 1/SC 29/WG 8 - MPEG Genomic coding
• Current Stage: 9092 - International Standard to be revised
• Completion Date: 24-Jul-2023

Relations

• Revises: ISO/IEC 23092-3:2020 - Information technology — Genomic information representation — Part 3: Metadata and application programming interfaces (APIs)
• Effective Date: 22-May-2021

Standards Content (Sample)

INTERNATIONAL ISO/IEC
STANDARD 23092-3
Second edition
2022-10
Information technology — Genomic
information representation —
Part 3:
Metadata and application
programming interfaces (APIs)
Technologie de l'information — Représentation des informations
génomiques —
Partie 3: Métadonnées et interfaces de programmation d'application
(API)
Reference number
ISO/IEC 23092-3:2022(E)
© ISO/IEC 2022

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ISO/IEC 23092-3:2022(E)
COPYRIGHT PROTECTED DOCUMENT
© ISO/IEC 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
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Published in Switzerland
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ISO/IEC 23092-3:2022(E)
Contents Page
Foreword .v
Introduction . vi
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 2
4 Abbreviated terms . 2
5 Conventions . 2
5.1 Character encoding . 2
5.2 Bit Ordering . 2
5.3 Syntax functions and data types . 3
5.4 Graphic notations . 3
6 Information metadata . 4
6.1 General . 4
6.2 Dataset group metadata . 4
6.3 Reference metadata . 5
6.4 Dataset metadata . 5
6.5 Metadata protection . 7
6.6 Mechanism for extensions of the metadata set . 7
6.6.1 General . 7
6.6.2 Example for dataset metadata extensions . 8
6.6.3 Example for obfuscating labels . 8
6.6.4 Example for obfuscating sequences . 8
6.7 Metadata profiles . 8
6.7.1 General . 8
6.7.2 Example of metadata profile — Run. 8
6.7.3 Example of metadata profile — Genomic data commons . 9
7 Protection metadata .10
7.1 General . 10
7.2 Encryption of gen_info elements and blocks . 10
7.2.1 General . 10
7.2.2 EncryptionParameters carried in dataset group protection . 10
7.2.3 EncryptionParameters carried in dataset protection .12
7.2.4 Key retrieval .15
7.2.5 Decryption . 16
7.3 Privacy rules for the use of the genomic information . 18
7.3.1 General . 18
7.3.2 Example of use of privacy rules . 19
7.4 Digital signature of gen_info elements and blocks . 19
7.4.1 General . 19
7.4.2 Signatures carried in dataset group protection . . 19
7.4.3 Signatures carried in dataset protection . 20
7.4.4 Signatures carried in access unit protection . 21
7.4.5 Signatures carried in descriptor stream protection .22
8 Access unit information .22
8.1 General .22
8.2 genAuxRecord . 22
8.3 genAux . 24
8.4 genTag . 24
9 Decoding process for metadata .25
9.1 General . 25
9.2 Initialization of parameters . 26
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ISO/IEC 23092-3:2022(E)
9.2.1 General . 26
9.2.2 Properties . 26
9.2.3 Parameters . 27
9.2.4 Constants .28
9.2.5 Process .28
9.3 Macros . 30
9.4 Decoding process . 32
10 Application programming interfaces (APIs) .40
10.1 General .40
10.2 Structure of the API.40
10.3 Detailed specification of the API .40
10.3.1 Data types .40
10.3.2 Return codes . 41
10.3.3 Metadata fields . . 41
10.3.4 Output structures . 42
10.3.5 Filters.49
10.3.6 Genomic information . 53
10.3.7 Metadata .58
10.3.8 Protection . 59
10.3.9 Reference . 61
10.3.10 Statistics . 62
Annex A (normative) XML schemas corresponding to metadata information and protection
elements .65
Annex B (informative) XML schemas and XML-based data .66
Annex C (informative) SAM interoperability .76
Annex D (informative) Example of key transport .83
Bibliography .87
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ISO/IEC 23092-3:2022(E)
Foreword
ISO (the International Organization for Standardization) and IEC (the International Electrotechnical
Commission) form the specialized system for worldwide standardization. National bodies that are
members of ISO or IEC participate in the development of International Standards through technical
committees established by the respective organization to deal with particular fields of technical
activity. ISO and IEC technical committees collaborate in fields of mutual interest. Other international
organizations, governmental and non-governmental, in liaison with ISO and IEC, also take part in the
work.
The procedures used to develop this document and those intended for its further maintenance
are described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria
needed for the different types of document should be noted. This document was drafted in
accordance with the editorial rules of the ISO/IEC Directives, Part 2 (see www.iso.org/directives or
www.iec.ch/members_experts/refdocs).
Attention is drawn to the possibility that some of the elements of this document may be the subject
of patent rights. ISO and IEC shall not be held responsible for identifying any or all such patent
rights. Details of any patent rights identified during the development of the document will be in the
Introduction and/or on the ISO list of patent declarations received (see www.iso.org/patents) or the IEC
list of patent declarations received (see https://patents.iec.ch).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO's adherence to
the World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT) see
www.iso.org/iso/foreword.html. In the IEC, see www.iec.ch/understanding-standards.
This document was prepared by Joint Technical Committee ISO/IEC JTC 1, Information technology,
Subcommittee SC 29, Coding of audio, picture, multimedia and hypermedia information.
This second edition cancels and replaces the first edition (ISO/IEC 23092-3:2020), which has been
technically revised.
The main changes are as follows:
— A few upper/lower case changes in identifiers for consistency.
— Some clarifications on the notation (new subclauses 5.2 and 5.4).
— Minor changes on data structures and parameters.
— A few fixes on references to annexes, tables and subclauses.
— Adding a subclause (7.2.3.3.1.3) to describe the “URI unaligned” for consistency.
— Some corrections in Table 15 including its splitting into 2 tables.
A list of all parts in the ISO/IEC 23092 series can be found on the the ISO and IEC websites.
Any feedback or questions on this document should be directed to the user’s national standards
body. A complete listing of these bodies can be found at www.iso.org/members.html and
www.iec.ch/national-committees.
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ISO/IEC 23092-3:2022(E)
Introduction
The advent of high-throughput sequencing (HTS) technologies has the potential to boost the adoption
of genomic information in everyday practice, ranging from biological research to personalized genomic
medicine in the clinic. As a consequence, the volume of generated data has increased dramatically
during the last few years, and an even more pronounced growth is expected in the near future.
At the moment, genomic information is mostly exchanged through a variety of data formats, such as
FASTA/FASTQ for unaligned sequencing reads and SAM/BAM/CRAM for aligned reads. With respect to
such formats, the ISO/IEC 23092 series provides a new solution for the representation and compression
of genome sequencing information by:
— specifying an abstract representation of the sequencing data rather than a specific format with its
direct implementation;
— being designed at a time point when technologies and use cases are more mature. This permits the
addressing of one limitation of the textual SAM format, for which incremental ad-hoc addition of
features followed along the years, resulting in an overall redundant and suboptimal format which
at the same time results not general and unnecessarily complicated;
— normatively separating free-field user-defined information with no clear semantics from the
normative genomic data representation. This allows a fully interoperable and automatic exchange
of information between different data producers;
— allowing multiplexing of relevant metadata information with the data since data and metadata are
partitioned at different conceptual levels;
— following a strict and supervised development process which has proven successful in the last
30 years in the domain of digital media for the transport format, the file format, the compressed
representation and the application program interfaces.
This document provides the enabling technology that will allow the community to create an ecosystem
of novel, interoperable solutions in the field of genomic information processing. In particular, it offers:
— consistent, general and properly designed format definitions and data structures to store sequencing
and alignment information. A robust framework which can be used as a foundation to implement
different compression algorithms;
— speed and flexibility in the selective access to coded data, by means of newly designed data clustering
and optimized storage methodologies;
— low latency in data transmission and consequent fast availability at remote locations, based on
transmission protocols inspired by real-time application domains;
— built-in privacy and protection of sensitive information, thanks to a flexible framework which allows
customizable secured access at all layers of the data hierarchy;
— reliability of the technology and interoperability among tools and systems, owing to the provision
of a normative procedure to assess conformance to the standard on an exhaustive dataset;
— support to the implementation of a complete ecosystem of compliant devices and applications,
through the availability of a normative reference implementation covering the totality of the
specification.
The fundamental structure of the ISO/IEC 23092 series data representation is the genomic record. The
genomic record is a data structure consisting of either a single sequence read, or a paired sequence
read, and its associated sequencing and alignment information; it may contain detailed mapping and
alignment data, a single or paired read identifier (read name) and quality values.
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ISO/IEC 23092-3:2022(E)
Without breaking traditional approaches, the genomic record introduced in the ISO/IEC 23092 series
provides a more compact, simpler and manageable data structure grouping all the information related
to a single DNA template, from simple sequencing data to sophisticated alignment information.
The genomic record, although it is an appropriate logic data structure for interaction and manipulation of
coded information, is not a suitable atomic data structure for compression. To achieve high compression
ratios, it is necessary to group genomic records into clusters and to transform the information of the
same type into sets of descriptors structured into homogeneous blocks. Furthermore, when dealing
with selective data access, the genomic record is a too small unit to allow effective and fast information
retrieval.
For these reasons, this document introduces the concept of access unit, which is the fundamental
structure for coding and access to information in the compressed domain.
The access unit is the smallest data structure that can be decoded by a decoder compliant with
ISO/IEC 23092-2. An access unit is composed of one block for each descriptor used to represent the
information of its genomic records; therefore, a block payload is the coded representation of all the data
of the same type (i.e. a descriptor) in a cluster.
In addition to clusters of genomic records compressed into access units, reads are further classified in
six data classes: five classes are defined according to the result of their alignment against one or more
reference sequences; the sixth class contains either reads that could not be mapped or raw sequencing
data. The classification of sequence reads into classes enables to develop powerful selective data access.
In fact, access units inherit a specific data characterization (e.g. perfect matches in Class P, substitutions
in Class M, indels in Class I, half-mapped reads in Class HM) from the genomic records composing them,
and thus constitute a data structure capable of providing powerful filtering capability for the efficient
support of many different use cases.
Access units are the fundamental, finest grain data structure in terms of content protection and in
terms of metadata association. In other words, each access unit can be protected individually and
independently. Figure 1 shows how access units, blocks and genomic records relate to each other in the
ISO/IEC 23092 series data structure.
Figure 1 — Access units, blocks and genomic records
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ISO/IEC 23092-3:2022(E)
Figure 2 — High-level data structure: datasets and dataset group
A dataset is a coded data structure containing headers and one or more access units. Typical datasets
could, for example, contain the complete sequencing of an individual, or a portion of it. Other datasets
could contain, for example, a reference genome or a subset of its chromosomes. Datasets are grouped in
dataset groups, as shown in Figure 2.
A simplified diagram of the dataset decoding process is shown in Figure 3.
Figure 3 — Decoding process
The International Organization for Standardization (ISO) and International Electrotechnical
Commission (IEC) draw attention to the fact that it is claimed that compliance with this document may
involve the use of a patent.
ISO and IEC take no position concerning the evidence, validity and scope of this patent right.
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ISO/IEC 23092-3:2022(E)
The holder of this patent right has assured ISO and IEC that he/she is willing to negotiate licences under
reasonable and non-discriminatory terms and conditions with applicants throughout the world. In this
respect, the statement of the holder of this patent right is registered with ISO and IEC. Information may
be obtained from the patent database available at www.iso.org/patents.
Attention is drawn to the possibility that some of the elements of this document may be the subject
of patent rights other than those in the patent database. ISO and IEC shall not be held responsible for
identifying any or all such patent rights.
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INTERNATIONAL STANDARD ISO/IEC 23092-3:2022(E)
Information technology — Genomic information
representation —
Part 3:
Metadata and application programming interfaces (APIs)
1 Scope
This document specifies information metadata, auxiliary fields, SAM interoperability, protection
metadata and programming interfaces of genomic information. It defines:
— metadata storage and interpretation for the different encapsulation levels as specified in
ISO/IEC 23092-1 (in Clause 6);
— protection elements providing confidentiality, integrity and privacy rules at the different
encapsulation levels specified in ISO/IEC 23092-1 (in Clause 7);
— how to associate auxiliary fields to encoded reads (in Clause 8);
— mechanisms for backward compatibility with existing SAM content, and exportation to this format
(in Annex C);
— interfaces to access genomic information coded in compliance with ISO/IEC 23092-1 and
ISO/IEC 23092-2 (in subclause 8.1).
2 Normative references
The following documents are referred to in the text in such a way that some or all of their content
constitutes requirements of this document. For dated references, only the edition cited applies. For
undated references, the latest edition of the referenced document (including any amendments) applies.
ISO/IEC 23092-1:2020, Information technology — Genomic information representation — Part 1:
Transport and storage of genomic information
ISO/IEC 23092-2:2019, Information technology — Genomic information representation — Part 2: Coding
of genomic information
IEEE, 754-2008, IEEE Standard for Floating-Point Arithmetic, August 2008, Available: https:// ieeexplore
.ieee .org/ document/ 4610935
IETF, RFC 8017, PKCS #1: RSA Cryptography Specifications Version 2.2, November 2016, Available:
https:// tools .ietf .org/ html/ rfc8017
IETF, RFC 8018, PKCS #5: Password-Based Cryptography Specification Version 2.1, January 2017,
Available: https:// tools .ietf .org/ html/ rfc2898https:// tools .ietf .org/ html/ rfc8018
IETF, RFC 3394, Advanced Encryption Standard (AES) Key Wrap Algorithm, September 2002, Available:
https:// tools .ietf .org/ html/ rfc3394
OASIS, eXtensible Access Control Markup Language (XACML) Version 3.0, 2013, Available: http:// docs
.oasis -open .org/ xacml/ 3 .0/ xacml -3 .0 -core -spec -cs -01 -en .pdf
W3C XPath, XML Path Language, Version 1.0, 16 November 1999, Available: https:// www .w3 .org/ TR/
xpath -10/
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