ISO/IEC 23092-3:2020
(Main)Information technology — Genomic information representation — Part 3: Metadata and application programming interfaces (APIs)
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)
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INTERNATIONAL ISO/IEC
STANDARD 23092-3
First edition
2020-03
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 23092-3:2020(E)
©
ISO/IEC 2020
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ISO/IEC 23092-3:2020(E)
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ISO/IEC 23092-3:2020(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 Syntax functions and data types . 2
5.3 Graphic notations . 3
6 Information metadata . 4
6.1 General . 4
6.2 Dataset group metadata . 4
6.3 Reference metadata . 4
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 .17
7.3.1 General.17
7.3.2 Example of use of privacy rules .18
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.19
7.4.4 Signatures carried in access unit protection .21
7.4.5 Signatures carried in descriptor stream protection .21
8 Access unit information .22
8.1 General .22
8.2 genAuxRecord .22
8.3 genAux .23
8.4 genTag .23
9 Decoding process for metadata.24
9.1 General .24
9.2 Initialization of parameters .26
9.2.1 General.26
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ISO/IEC 23092-3:2020(E)
9.2.2 Properties .26
9.2.3 Parameters .26
9.2.4 Constants .27
9.2.5 Process .28
9.3 Macros .29
9.4 Decoding process .31
10 Application programming interfaces (APIs) .38
10.1 General .38
10.2 Structure of the API .38
10.3 Detailed specification of the API .38
10.3.1 Data types .38
10.3.2 Return codes .39
10.3.3 Metadata fields .39
10.3.4 Output structures .40
10.3.5 Filters .47
10.3.6 Genomic information .52
10.3.7 Metadata .56
10.3.8 Protection .58
10.3.9 Reference .59
10.3.10 Statistics .60
Annex A (normative) XML schemas corresponding to metadata information and protection
elements .63
Annex B (informative) XML schemas and XML-based data .64
Annex C (informative) SAM interoperability .77
Annex D (informative) Example of key transport .84
Bibliography .88
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ISO/IEC 23092-3:2020(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).
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.
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.
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ISO/IEC 23092-3:2020(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 23092-3:2020(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 23092-3:2020(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 23092-3:2020(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 23092-3:2020(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, Information technology — Genomic information representation — Part 1: Transport and
storage of genomic information
ISO/IEC 23092-2, Information technology — Genomic information representation — Part 2: Coding of
genomic information
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
IETF, PKCS #1: RSA Cryptography Specifications Version 2.2, November 2016, Available: https:// tools
.ietf .org/ html/ rfc8017
IETF, PKCS #5: Password-Based Cryptography Specification Version 2.1, January 2017, Available:
https:// tools .ietf .org/ html/ rfc2898https:// tools .ietf .org/ html/ rfc8018
IETF, Advanced Encryption Standard (AES) Key Wrap Algorithm, September 2002, Available: https://
tools .ietf .org/ html/ rfc3394
W3C, XML Path Language (XPath), Version 1.0, 16 November 1999, Available: https:// www .w3 .org/ TR/
xpath -10/
IEEE, 754-2008, IEEE Standard for Floating-Point Arithmetic, August 2008, Available: https:// ieeexplore
.ieee .org/ document/ 4610935
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ISO/IEC 23092-3:2020(E)
3 Terms and definitions
For the purposes of this document, the terms and definitions in ISO/IEC 23092-1 and ISO/IEC 23092-2
and the following 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
BAM
compressed binary version of SAM
3.2
dataset group
collection of one or more datasets
Note 1 to entry: Which information is represented varies depending on the genomic information representation.
4 Abbreviated terms
AU access unit
AUC access unit contiguity
DSC descriptor stream contiguity
EBI European Bioinformatics Institute
EGA European Genome Archive
ENA European Nucleotide Archive
LSB least significant bit
NCBI National Center for Biotechnology Information
SRA sequence read archive
URN uniform resource name
5 Conventions
5.1 Character encoding
...
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