ISO/IEC 23092-1:2020

Information technology - Genomic information representation - Part 1: Transport and storage of genomic information

This document specifies data formats for both transport and storage of genomic information, including the conversion process.

Technologie de l'information — Représentation des informations génomiques — Partie 1: Transport et stockage des informations génomiques

General Information

• Status: Published
• Publication Date: 19-Oct-2020
• 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 - Coding of audio, picture, multimedia and hypermedia information
• Current Stage: 9599 - Withdrawal of International Standard
• Start Date: 24-Jan-2025
• Completion Date: 30-Oct-2025

Relations

• Revised: ISO/IEC 23092-1:2025 - Information technology - Genomic information representation - Part 1: Transport and storage of genomic information
• Effective Date: 06-Jun-2022
• Revises: ISO/IEC 23092-1:2019 - Information technology - Genomic information representation - Part 1: Transport and storage of genomic information
• Effective Date: 23-Apr-2020

Overview - ISO/IEC 23092-1:2020 (Genomic information representation - Transport and storage)

ISO/IEC 23092-1:2020 defines a standardized framework for the transport and storage of genomic information, focusing on data formats, syntax/semantics and the conversion process between transport and file formats. Designed for the era of high-throughput sequencing (HTS), this standard introduces an abstract, interoperable representation of sequencing and alignment data to enable efficient compression, selective access and secure multiplexing of metadata with genomic data.

Key topics and technical requirements

• Genomic record model: A compact logical unit that groups a single or paired read with associated sequencing, alignment and quality information.
• Access units and clustering: Access units are the smallest decodable units in the compressed domain; genomic records are grouped into clusters for high compression and fast selective access.
• Data classes: Reads are categorized into six classes (five alignment-based classes plus an unmapped/raw class) to enable targeted filtering and retrieval.
• File and transport format structures: Detailed definitions for headers, dataset groups, datasets, access units, blocks, indexing and descriptor streams that distinguish file-format vs transport-format elements.
• Syntax, semantics and bit-level rules: Specifications include tabular syntax conventions, bit ordering and syntax functions to ensure precise encoding/decoding.
• Selective access strategies: Mechanisms for efficient partial retrieval of sequences without full decompression.
• Conversion and depacketization: Reference procedures to convert transport format to file format and vice versa.
• Privacy, metadata and protection: Framework for multiplexing metadata and applying layered protection and access control.
• Conformance and reference implementation: A normative reference implementation and conformance procedure support interoperability and validation.

Practical applications and who uses it

ISO/IEC 23092-1:2020 is intended for organizations and professionals working with large-scale genomic datasets:

• Bioinformatics software developers implementing compressed genomic formats and APIs
• Sequencing centers and core labs managing HTS data storage and transmission
• Cloud and archival storage providers optimizing genomic data transport and retrieval
• Clinical labs and EHR/informatics vendors requiring secure, interoperable genomic exchange
• Data repositories, research consortia and regulators focused on data standardization and compliance

Practical benefits include improved compression efficiency, lower network latency for genomic transfers, fast selective access for specific analyses, clearer separation of free-text metadata from core genomic data, and built-in mechanisms for secure sharing.

Related standards and references

• ISO/IEC 23092 series (other parts cover compression, decoding and APIs) - see ISO/IEC 23092-2 for decoder definitions referenced by this part.
• Common genomic formats and interoperability points: FASTA, FASTQ, SAM/BAM/CRAM (contextual comparison).
• Annex references such as IETF RFC 3986 (URI syntax) for transport-related considerations.

Keywords: ISO/IEC 23092-1:2020, genomic information representation, genomic data transport, genomic data storage, access unit, genomic record, selective access, compression, HTS, interoperability.

Standards Content (Sample)

INTERNATIONAL ISO/IEC
STANDARD 23092-1
Second edition
2020-10
Information technology — Genomic
information representation —
Part 1:
Transport and storage of genomic
information
Technologie de l'information — Représentation des informations
génomiques —
Partie 1: Transport et stockage des informations génomiques
Reference number
©
ISO/IEC 2020
© ISO/IEC 2020
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: [phone]
Email: [e-mail]
Website: www.iso.org
Published in Switzerland
ii © ISO/IEC 2020 – All rights reserved

Contents Page
Foreword .iv
Introduction .v
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Mathematical operators . 4
4.1 Arithmetic operators . 4
4.2 Logical operators . 4
4.3 Relational operators . 4
4.4 Bitwise operators. 4
4.5 Assignment . 5
4.6 Unary operators . 5
5 Structure of coded genomic data . 5
5.1 Genomic records . 5
5.2 Data classes . 6
5.3 Access units . 6
5.4 Datasets . 7
5.5 Selective access . 7
6 Data format . 7
6.1 Format structure . 7
6.1.1 General. 7
6.1.2 Box order . 9
6.2 Syntax and semantics .10
6.2.1 Method of specifying syntax in tabular form .10
6.2.2 Bit ordering .11
6.2.3 Specification of syntax functions .11
6.3 Syntax for representation .11
6.4 Output data unit .12
6.5 Data structures common to file format and transport format .13
6.5.1 File header .13
6.5.2 Dataset group.13
6.5.3 Dataset .22
6.5.4 Access unit .30
6.5.5 Block .36
6.6 Data structures specific to file format .37
6.6.1 General.37
6.6.2 Indexing .37
6.6.3 Descriptor stream .41
6.6.4 Offset .42
6.7 Data structures specific to transport format .43
6.7.1 General.43
6.7.2 Data streams .43
6.7.3 Dataset mapping table list .44
6.7.4 Dataset mapping table .44
6.7.5 Packet .46
6.8 Reference procedure to convert transport format to file format .47
Annex A (informative) IETF RFC 3986 specification summary .50
Annex B (informative) Selective access strategies .51
Annex C (informative) Depacketization process .54
Bibliography .56
© ISO/IEC 2020 – All rights reserved iii

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).
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 http:// 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.
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 23092-1:2019), which has been
technically revised.
The main changes compared to the previous edition are as follows:
— reference box syntax and semantics have been updated;
— syntax, semantics and decoding process for cluster signatures has been fixed;
— the scope of some parameters has been changed from dataset_header to dataset_parameter_set;
— new dataset_group_ID and dataset_ID fields have been added to the metadata and protection boxes;
— minor fixes in transport format;
— editorial changes.
A list of all parts in the ISO/IEC 23092 series can be found on the ISO website.
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.
iv © ISO/IEC 2020 – All rights reserved

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 clinics. 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
addressing one limitation of the textual SAM format, for which the incremental ad-hoc addition of
features followed along the years, resulting in an overall redundant and suboptimal format which
was unnecessarily complicated.
— Separating free-field user-defined information with no clear semantics from the 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.
The ISO/IEC 23092 series 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 procedure to assess conformance to this document 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
ISO/IEC 23092 series.
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.
© ISO/IEC 2020 – All rights reserved v

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 the development of 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
vi © ISO/IEC 2020 – All rights reserved

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
This document defines the syntax and semantics of the data formats for both transport and storage of
genomic information. According to this document, the compressed sequencing data can be multiplexed
into a bitstream suitable for packetization for real-time transport over typical network protocols. In
storage use cases, coded data can be encapsulated into a file format with the possibility to organize
blocks per descriptor stream or per access units, to further optimize the selective access performance
© ISO/IEC 2020 – All rights reserved vii

to the type of data access required by the different application scenarios. This document further
provides a reference process to convert a transport stream into a file format and vice versa.
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.
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.
viii © ISO/IEC 2020 – All rights reserved

INTERNATIONAL STANDARD ISO/IEC 23092-1:2020(E)
Information technology — Genomic information
representation —
Part 1:
Transport and storage of genomic information
1 Scope
This document specifies data formats for both transport and storage of genomic information, including
the conversion process.
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 10646, Information technology — Universal Coded Character Set (UCS)
ISO/IEC 23092-2, Information technology — Genomic information representation — Part 2: Coding of
genomic information
ISO/IEC 23092-3, Information technology — Genomic information representation — Part 3: Metadata and
application programming interfaces (APIs)
IETF RFC 3986, Uniform Resource Identifier (URI): Generic Syntax
IETF RFC 7320, URI Design and Ownership
3 Terms and definitions
For the purposes of this document, the following terms and definitions apply.
ISO and IEC maintain terminological databases for use in standardization at the following addresses:
— ISO Online browsing platform: available at https:// www .iso .org/ obp
— IEC Electropedia: available at http:// www .electropedia .org/
3.1
access unit
logical data structure containing a coded representation of genomic information to facilitate bit stream
access and manipulation
3.2
access unit covered region
genomic range comprised between the access unit start position and the access unit end position,
inclusive
3.3
access unit start position
position of the left-most mapped base among the first alignments of all genomic records contained in
the access unit, irrespective of the strand
© ISO/IEC 2020 – All rights reserved 1

3.4
access unit end position
position of the right-most mapped base among the first alignments of all genomic records contained in
the access unit, irrespective of the strand
3.5
access unit range
genomic range comprised between the access unit start position and the right-most genomic record
position among all genomic records contained in the access unit
3.6
access unit covered region
genomic range comprised between the access unit start position and the access unit end position
inclusive
3.7
alignment
information describing the similarity between a sequence (typically a sequencing read) and a reference
sequence (for instance, a reference genome)
3.8
box
object-oriented building unit defined by a unique type identifier and length
3.9
cluster
aggregation of genomic records
3.10
cluster signature
signature
sequence of nucleotides that is common to most or all genomic records belonging to a cluster
3.11
container box
box (3.8) whose sole purpose is to contain and group a set of related boxes
3.12
data stream
set of packets (3.20) transporting the same data type
3.13
extended access unit start position
position of the left-most mapped base among all alignments of all genomic records contained in the
access unit, irrespective of the strand
3.14
extended access unit end position
position of the right-most mapped base among all alignments of all genomic records contained in the
access unit, irrespective of the strand
3.15
file format
set of data structures for the storage of coded information
3.16
genomic position
position
integer number representing the zero-based position of a nucleotide within a reference sequence
2 © ISO/IEC 2020 – All rights reserved

3.17
genomic region
region
genomic interval between a start nucleotide position and an end nucleotide position, inclusive
3.18
genomic range
range
interval of positions on a reference sequence defined by a start position s and an end position e such
that s ≤ e; the start and the end positions of a genomic range are always included in the range
3.19
mapped base
base of the aligned read that either matches the corresponding base on the reference sequence or can
be turned into the corresponding base on the reference sequence via a substitution
3.20
packet
transmission unit transporting segments of any of the data structures defined in this document
3.21
reference genome
representative example of the sequences for a species’ genetic material
Note 1 to entry: Genetic material meaning the sequences of the DNA molecules present in a typical cell of that
species.
3.22
reference sequence
nucleic acid sequence with biological relevance
Note 1 to entry: Each reference sequence is indexed by a one-dimensional integer coordinate system whereby
each integer within range identifies a single nucleotide. Coordinate values can only be equal to or larger than
zero. The coordinate system in the context of this standard is zero-based (i.e. the first nucleotide has coordinate 0
and it is said to be at position 0) and linearly increasing within the string from left to right.
3.23
genomic segment
segment
contiguous sequence of nucleotides, typically output of the sequencing process and sequenced from one
strand of a template
3.24
sequence read
read
readout, by a specific technology more or less prone to errors, of a continuous part of a nucleic acid
molecule extracted from an organic sample
3.25
syntax field
element of data represented in the data format
3.26
template
genomic sequence that is produced by a sequencing machine as a single unit
Note 1 to entry: A template can be made of one or more segments, being called single-end sequencing read when
it only has one segment and paired-end sequencing read when it has two segments.
3.27
transport format
set of data structures for the transport of coded information
© ISO/IEC 2020 – All rights reserved 3

3.28
variable
parameter either inferred from syntax fields or locally defined in a process description
4 Mathematical operators
NOTE The mathematical operators used in this document are similar to those used in the C programming
language. However, integer division with truncation and rounding are specifically defined. The bitwise operators
are defined assuming two's-complement representation of integers. Numbering and counting loops generally
begin from 0.
4.1 Arithmetic operators
+ addition
− subtraction (as a binary operator) or negation (as a unary operator)
++ increment
* multiplication
/ integer division with truncation of the result toward 0 (for example, 7/4 and −7/−4 are truncat-
ed to 1 and −7/4 and 7/−4 are truncated to −1)
4.2 Logical operators
|| logical OR
&& logical AND
! logical NOT
4.3 Relational operators
> greater than
≥ greater than or equal to
< less than
≤ less than or equal to
== equal to
!= not equal to
4.4 Bitwise operators
& AND
| OR
>> shift right with sign extension
<< shift left with 0 fill
4 © ISO/IEC 2020 – All rights reserved

4.5 Assignment
= assignment operator
4.6 Unary operators
sizeof(N) size in bytes of N, where N is either a data structure or a data type
5 Structure of coded genomic data
5.1 Genomic records
The genomic record, in this document, is a data structure consisting of either a single sequence read, or
paired sequence reads, and its associated sequencing and alignment information. The genomic record
may contain detailed mapping and alignment data, a single or paired read identifier (read name) and
quality values.
When alignment information is present, the genomic record position is defined as the position of the
left-most mapped base of the genomic record on the reference genome. Genomic record positions are
0-based in the ISO/IEC 23092 series. In case of multiple alignments, the position of the first alignment
in the record is considered; in such a case, the first alignment shall be the one with the leftmost position
among all the alignments with the best score.
In case of unmapped reads (i.e. no alignment information present) the notion of position does not apply
to the genomic record.
In case of aligned content, bases that are present in the reads of the genomic record and not present in
the reference sequence (insertions) and bases preserved by the alignment process but not mapped on
the reference sequence (soft clips) do not have mapping positions.
Table 1 enumerates all the types of data that a genomic record can contain. ISO/IEC 23092-2 defines
technology that allows coding all and only those types of data into a set of descriptors; data, and
consequently descriptors, which are mandatory or optional, are also specified in ISO/IEC 23092-2, as
well as how they are used to represent multiple alignments.
Table 1 — Genomic records
Data Semantics
Record identifier name of the record (e.g. read names)
Sequence reads sequencing readout, as one or more strings of bases
Quality values quality scores of the sequence reads
Strandedness information about the strandedness of each read of the Record
Length length of the sequence reads
Position position on the reference genome of the left-most mapped genomic record base
Pairing position or distance of the mate reads (e.g. in a pair)
Flags technical, additional alignment information (duplicates, proper pairs, failures)
Mismatches information about position and type of each mismatch in mapped records
Clips information about clipped bases (soft and hard clips) in mapped records
Mapping scores mapping scores for an alignment
Multiple alignments information about the number of alignments and the alternative alignment
information about each segment of the record
Group read group the genomic record belongs to
© ISO/IEC 2020 – All rights reserved 5

ISO/IEC 23092-2 defines an output record format for all types of data in Table 1. These records shall be
generated by decoders compliant to ISO/IEC 23092-2 as output of the decoding process.
5.2 Data classes
Six data classes are specified to classify genomic records according to the result of the mapping of the
encoded sequence reads against one or more reference sequences.
In the case of more than one read in a template, if both reads are mapped, the genomic record belongs
to the class of the read with the highest class_ID. In case of multiple alignments, the genomic record
belongs to the class of the first alignment in the record.
The data classes and their descriptions are specified in Table 2.
Table 2 — Data classes
Class ID Class name Record content
1 CLASS_P Only reads perfectly matching to the reference sequence.
2 CLASS_N Reads perfectly matching to the reference sequence or containing mismatches
which are unknown bases only.
3 CLASS_M Reads perfectly matching to the reference sequence or containing substitu-
tions or unknown bases, but no insertions, no deletions, no splices and no
clipped bases.
4 CLASS_I Reads perfectly matching to the reference sequence or containing substitu-
tions, unknown bases, insertions, deletions, splices or clipped bases.
5 CLASS_HM Paired-end reads with only one mapped read.
6 CLASS_U Unmapped reads only.
Genomic records of each data class are coded by means of several descriptors; conversely, a descriptor
is a coding element needed to represent part of the information. Descriptors for each data class are
specified in ISO/IEC 23092-2.
Descriptors are coded in blocks. Blocks are defined in subclause 6.5.5. A sequence of block payloads
of a single descriptor composes a descriptor stream. All block payloads in a descriptor stream contain
compressed descriptors of a single type representing reads of the same data class.
5.3 Access units
Access units (AUs) are data structures containing a coded representation of genomic information and
optionally related metadata to facilitate the bitstream access and manipulation. An access unit contains
either genomic records belonging to the same data class or a fragment of a reference sequence.
The access unit is the smallest data organization that can be decoded by a decoder compliant with
ISO/IEC 23092-2.
Access units are orthogonal to descriptor streams: an access unit is composed of all and only those
blocks of the descriptor streams that are necessary to decode the information contained in a cluster of
records of a given data class.
An access unit can be of several types according to the class of the coded data.
6 © ISO/IEC 2020 – All rights reserved

Table 3 — Access unit type
Access unit type Class of data
Name Value
P_TYPE_AU 1 CLASS_P
N_TYPE_AU 2 CLASS_N
M_TYPE_AU 3 CLASS_M
I_TYPE_AU 4 CLASS_I
HM_TYPE_AU 5 CLASS_HM
U_TYPE_AU 6 CLASS_U
Depending on the type of coded information, an access unit can be decoded either independently of any
other access unit or using information contained in other access units.
5.4 Datasets
A dataset is a data structure containing headers and access units. The set of access units composing the
dataset constitutes the dataset payload.
One or more datasets are assembled into a dataset group.
5.5 Selective access
In the case of selective access to a genomic region comprised between a start genomic position and an
end genomic position the decoder shall return: a) all the access units whose covered region overlaps the
region defined by start and end with at least one base, and the parameter sets that are needed to decode
them; b) at least the reference portion that is necessary to decode the access units identified in a).
In the case of selective access to signed content identified by a U_cluster_signature signature the
decoder shall return all the access units whose signature corresponds to U_cluster_signature, and the
parameter sets that are needed to decode them. Examples of selective access strategies are described
in Annex B.
6 Data format
6.1 Format structure
6.1.1 General
Table 4 presents the overall data structures and hierarchical encapsulation levels.
Boxes that may occur at the top-level are shown in the left-most column; indentation is used to show
possible containment. Not all boxes need be used in all files; the mandatory boxes are marked with an
asterisk (*) in the Mandatory column: such column refers to the relevant scope (File and/or Transport).
Optional boxes are represented with dashed borders in Figure 4 and Figure 5. Mandatory boxes are
represented with solid borders. When no entry is present in the Scope column, scope is both File and
Transport. See the specification of each individual box for the assumptions when the optional boxes are
not present. If the box key is represented in italic format in Table 4, the corresponding box is represented
either with no Key and no Length, but only Value in the gen_info format, as specified in subclause 6.3,
for all boxes but offset, or as specified in subclause 6.6.5.1 for the offset box.
© ISO/IEC 2020 – All rights reserved 7

Table 4 — Format structure and encapsulation levels
Box key (with hierarchical level) Subclause Scope Mandatory
flhd 6.5.1 *
dgcn 6.5.2 File *
dghd 6.5.2.2 *
rfgn 6.5.2.3
rfmd 6.5.2.4
labl 6.5.2.5
lbll 6.5.2.5.4
dgmd 6.5.2.6
dgpr 6.5.2.7
dmtl 6.7.3 Transport *
dtcn 6.5.3.1 File *
dthd 6.5.3.2 *
mitb 6.6.2.1 File
pars 6.5.3.5 *
dtmd 6.5.3.3
dtpr 6.5.3.4
dmtb 6.7.4 Transport *
dscn 6.6.3.1 File
dshd 6.6.3.2 File
dspr 6.6.3.3 File
aucn 6.5.4.1 *
auhd 6.5.4.3 *
auin 6.5.4.4
aupr 6.5.4.5
block 6.5.5 *
block_header 6.5.5.2
offset offset 6.6.4 File
packet 6.7.5 Transport *
packet_header 6.7.5.2 Transport *

8 © ISO/IEC 2020 – All rights reserved

Figure 4 — Data structures hierarchy for storage
Figure 5 — Data structures hierarchy for transport
In transport format, any box represented in Figure 5 shall be encapsulated in one or more packets, as
specified in subclause 6.7.5. The dataset group and dataset are represented in Figure 5 for clarity, but
the corresponding container boxes (dgcn and dtcn) do not exist in transport format.
6.1.2 Box order
In order to improve interoperability, the following rules shall be followed for the order of boxes:
© ISO/IEC 2020 – All rights reserved 9

In file format
1) The container boxes (dataset group, dataset, access unit and descriptor stream) shall be ordered
according to the hierarchy specified in Table 4.
2) The box order inside the containers dgcn, dtcn, dscn, and aucn is specified in Table 9, Table 19,
Table 25 and Table 32, respectively.
3) The file header box ‘flhd’ shall occur before any variable-length box.
4) When present, the offset box ‘offs’, as specified in subclause 6.6.4, enables an indirect addressing of
boxes, which, while logically respecting the ordering specified in this subclause, may be physically
located in a different position in the file.
5) The contiguity of child boxes inside the containers dgcn, dtcn, dscn, and aucn shall not be broken by
any box external to the container box, apart from the offset box, as specified in subclause 6.6.4.
In transport format
1) The dataset_mapping_table_list, dataset_mapping_table and file header boxes shall be decoded
first, and then all other boxes according to the hierarchy specified in Table 4.
3) It is recommended to transmit the boxes in hierarchical order, as specified in Table 4.
4) It is recommended, when possible, to interleave boxes with hierarchical level equal to 1 (second
column in Table 4) and belonging to different dataset groups, and the dthd boxes belonging to
different datasets, before transmitting all other boxes.
6.2 Syntax and semantics
6.2.1 Method of specifying syntax in tabular form
Table 5 lists the constructs that are used to express the conditions when data elements are present.
NOTE This syntax uses the convention that a variable or expression evaluating to a non-zero value is
equivalent to a condition that is true.
Table 5 — Constructs used to express the conditions when data elements are present
Construct Description
If the condition is true, then the first group of data
if (condition) {
elements occurs next in the bitstream.
data_element
. . .
}
If the condition is not true, then the second group of
else {
data elements occurs next in the bitstream.
data_element
. . .
}
The group of data elements occurs n times. Conditional
for (i=0;i constructs within the group of data elements may depend on
data_element
the value of the loop control variable i, which is equal
to zero for the first occurrence, incremented to 1 for the
. . .
second occurrence, and so forth.
}
As noted, the group of data elements may contain nested conditional constructs. For compactness, the
{} are omitted when only one data element follows. Collections of data elements are represented as
listed in Table 6.
10 © ISO/IEC 2020 – All rights reserved

Table 6 — Syntax used to represent collections of data elements
data_element[] data_element[] is an array of data. The number of data
elements is indicated by the semantics.
th
data_element[n] data_element[n] is the n+1 element of an array of data.
th th
data_element[m][n] data_element[m][n] is the m+1 ,n+1 element of a two-
dimensional array of data.
th th th
data_element[l][m][n] data_element[l][m][n] is the l+1 , m+1 ,n+1 element
of a three-dimensional array of data.
6.2.2 Bit ordering
The bit order of syntax fields in the syntax tables is specified to start with the most significant bit
(MSB) and proceed to the least significant bit (LSB).
6.2.3 Specification of syntax functions
byte_aligned( ) is specified as follows:
— If the current position in the bitstream is on a byte boundary, i.e., the next bit in the bitstream is the
first bit in a byte, the return value of byte_aligned( ) is equal to TRUE.
— Otherwise, the return value of byte_aligned( ) is equal to FALSE.
read_bits( n ) reads the next n bits from the bitstream and advances the bitstream pointer by n bit
positions. When n is equal to 0, read_bits( n ) is specified to return a value equal to 0 and to not advance
the bitstream pointer.
The following data types specify the parsing process of each syntax element:
— f(n): fixed-pattern bit string using n bits written (from left to right) with the left bit first. The parsing
process for this data type is specified by the return value of the function read_bits( n ).
— u(n): unsigned integer using n bits. When n is "v" in the syntax table, the number of bits varies in a
manner dependent on the value of other syntax elements. The parsing process for this data type is
specified by the return value of the function read_bits( n ) interpreted as a binary representation of
an unsigned integer with most significant bit written first.
— st(v): null-terminated string encoded as universal coded character set (UCS) transmission format-8
(UTF-8) characters as specified in ISO/IEC 10646. The parsing process is specified as follows:
st(v) reads and returns a series of bytes from the bitstream, beginning at the current position and
continuing up to but not including the next byte that is equal to 0x00, and advances the bitstream
pointer by ( stringLength + 1 ) * 8 bit positions, where stringLength is equal to the number of bytes
returned. The maximum value of stringLength is 16384.
— c(n): sequence of n ASCII characters as specified in ISO/IEC 10646.
6.3 Syntax for representation
KLV (Key Length Value) format is used for all the data structures listed in Table 4 but the block, block_
header, offset, packet and packet_header.
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The KLV syntax is defined as follows:
struct gen_info
{
c(4)     Key;
u(64)     Length;
u(8)     Value[];
}
The Length field specifi
...