EN ISO 21393:2021
(Main)Genomics informatics - Omics Markup Language (OML) (ISO 21393:2021)
Genomics informatics - Omics Markup Language (OML) (ISO 21393:2021)
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.
Genomik-Informatik - Omics Auszeichnungssprache (OML) (ISO 21393:2021)
Informatique génomique - Langage de balisage Omics (OML) (ISO 21393:2021)
Le présent document est applicable au format d'échange de données qui est conçu pour faciliter l'échange de données omiques dans le monde entier sans imposer le moindre changement de schéma de base de données.
Le présent document spécifie les caractéristiques de l'OML selon les perspectives suivantes.
D'un point de vue informatique, OML définit le format d'échange de données basé sur XML. Le présent document établit des lignes directrices pour la spécification du format d'échange de données, mais il exclut le schéma de base de données proprement dit.
Du point de vue moléculaire, le présent document est applicable à toutes les sortes de données omiques bien qu'il exclue les détails relatifs aux molécules (par exemple, les détails des variations de la séquence génomique ou la séquence génomique complète). Le présent document est également applicable aux annotations moléculaires, y compris les questions cliniques et les relations avec les autres questions omiques.
Du point de vue de l'application, le présent document est applicable à la santé humaine, y compris les pratiques cliniques, la médecine préventive, la recherche translationnelle et la recherche clinique, notamment la découverte de médicaments. Le présent document ne s'applique pas à la recherche fondamentale et aux autres domaines scientifiques.
Du point de vue des espèces biologiques, le présent document est applicable aux espèces associées à la santé humaine telles que l'homme, les animaux en préclinique et les lignées cellulaires. Le présent document ne s'applique pas aux autres espèces biologiques.
Zdravstvena informatika - Označevalski jezik OMICS (OML) (ISO 21393:2021)
General Information
Standards Content (Sample)
SLOVENSKI STANDARD
01-oktober-2021
Zdravstvena informatika - Označevalski jezik OMICS (OML) (ISO 21393:2021)
Health informatics - Omics Markup Language (OML) (ISO 21393:2021)
Medizinische Informatik - OMICS Auszeichnungssprache (OML) (ISO 21393:2021)
Informatique de santé — Langage de balisage Omics (OML) (ISO 21393:2021)
Ta slovenski standard je istoveten z: EN ISO 21393:2021
ICS:
35.060 Jeziki, ki se uporabljajo v Languages used in
informacijski tehniki in information technology
tehnologiji
35.240.80 Uporabniške rešitve IT v IT applications in health care
zdravstveni tehniki technology
2003-01.Slovenski inštitut za standardizacijo. Razmnoževanje celote ali delov tega standarda ni dovoljeno.
EN ISO 21393
EUROPEAN STANDARD
NORME EUROPÉENNE
August 2021
EUROPÄISCHE NORM
ICS 35.240.80
English Version
Genomics informatics - Omics Markup Language (OML)
(ISO 21393:2021)
Informatique génomique - Langage de balisage Omics Medizinische Informatik - OMICS
(OML) (ISO 21393:2021) Auszeichnungssprache (OML) (ISO 21393:2021)
This European Standard was approved by CEN on 29 September 2020.
CEN members are bound to comply with the CEN/CENELEC Internal Regulations which stipulate the conditions for giving this
European Standard the status of a national standard without any alteration. Up-to-date lists and bibliographical references
concerning such national standards may be obtained on application to the CEN-CENELEC Management Centre or to any CEN
member.
This European Standard exists in three official versions (English, French, German). A version in any other language made by
translation under the responsibility of a CEN member into its own language and notified to the CEN-CENELEC Management
Centre has the same status as the official versions.
CEN members are the national standards bodies of Austria, Belgium, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia,
Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Norway,
Poland, Portugal, Republic of North Macedonia, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Turkey and
United Kingdom.
EUROPEAN COMMITTEE FOR STANDARDIZATION
COMITÉ EUROPÉEN DE NORMALISATION
EUROPÄISCHES KOMITEE FÜR NORMUNG
CEN-CENELEC Management Centre: Rue de la Science 23, B-1040 Brussels
© 2021 CEN All rights of exploitation in any form and by any means reserved Ref. No. EN ISO 21393:2021 E
worldwide for CEN national Members.
Contents Page
European foreword . 3
European foreword
This document (EN ISO 21393:2021) has been prepared by Technical Committee ISO/TC 215 "Health
informatics" in collaboration with Technical Committee CEN/TC 251 “Health informatics” the
secretariat of which is held by NEN.
This European Standard shall be given the status of a national standard, either by publication of an
identical text or by endorsement, at the latest by February 2022, and conflicting national standards
shall be withdrawn at the latest by February 2022.
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. CEN shall not be held responsible for identifying any or all such patent rights.
Any feedback and questions on this document should be directed to the users’ national standards
body/national committee. A complete listing of these bodies can be found on the CEN websites.
According to the CEN-CENELEC Internal Regulations, the national standards organizations of the
following countries are bound to implement this European Standard: Austria, Belgium, Bulgaria,
Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Iceland,
Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Norway, Poland, Portugal, Republic of
North Macedonia, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Turkey and the
United Kingdom.
Endorsement notice
The text of ISO 21393:2021 has been approved by CEN as EN ISO 21393:2021 without any modification.
INTERNATIONAL ISO
STANDARD 21393
First edition
2021-07
Genomics informatics — Omics
Markup Language (OML)
Informatique génomique — Langage de balisage Omics (OML)
Reference number
ISO 21393:2021(E)
©
ISO 2021
ISO 21393:2021(E)
© ISO 2021
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.
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Phone: +41 22 749 01 11
Email: copyright@iso.org
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Published in Switzerland
ii © ISO 2021 – All rights reserved
ISO 21393:2021(E)
Contents Page
Foreword .iv
Introduction .v
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 OML specification . 6
4.1 Specification requirements and OML positioning . 6
4.2 OML Structure . 6
4.3 OML DTD and XML Schema. 7
5 OML development process . 7
6 Figures . 8
Annex A (informative) Reference works .28
Bibliography .45
ISO 21393:2021(E)
Foreword
ISO (the International Organization for Standardization) is a worldwide federation of national standards
bodies (ISO member bodies). The work of preparing International Standards is normally carried out
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work.
ISO collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.
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 ISO documents 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 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).
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 Technical Committee ISO/TC 215, Health informatics, Subcommittee
SC 1, Genomics informatics, in collaboration with the European Committee for Standardization (CEN)
Technical Committee CEN/TC 251, Health informatics, in accordance with the Agreement on technical
cooperation between ISO and CEN (Vienna Agreement).
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 2021 – All rights reserved
ISO 21393:2021(E)
Introduction
In this post genomic era, the management of health-related data is becoming increasingly important
[1]
to both omics research and omics-based medicine. Informational approaches to the management of
clinical, image and omics data are beginning to have as much worth as basic, bench top research. In the
current electronic world, there are multiple different types of data for healthcare as shown in Figure 1.
Besides, nowadays there are many kinds of omics data around the world awaiting effective utilization
for human health. The development of data format and message standards to support the interchange
of clinical omics data is necessary. Omics data includes omics sequence, sequence variation and other
expression data, proteomics data, molecular network, etc. As an entry point, this document focuses on
the data exchange.
In the present circumstances, omics is expected to be a key to understand human response to external
[2]
stimuli such as any kinds of alien invasions, therapies, and the environmental interactions. Bacterial
infection is an example of alien invasion, and the responses to the infections are different among the
individuals. According to the therapy, the side effects to a drug are different among the patients. These
responses are also different in various environments. As a result of recent explosive amount of these
omics researches, the huge amounts of experimental data have been accumulating in many databases
in various types of data formats. These data are waiting to be used in drug discovery, clinical diagnosis,
and clinical researches.
The Markup Language is a set of symbols and rules for their use when doing a markup of a document.
[3] [4]
The first standardized markup language was ISO 8879 onGeneralized Markup Language (SGML)
which has strong similarities with troff and nroff text layout languages supplied with Unix systems.
[5]
Hypertext Markup Language (HTML) is based on SGML. Extensible Markup Language (XML) is
[6]
a pared-down version of SGML, designed especially for Web documents. XML acts as the basis for
[7] [8]
Extensible HTML (XHTML) and Wireless Markup Language (WML) and for standardized definitions
[9]
of system interaction such as Simple Object Access Protocol (SOAP). By contrast, text layout or
semantics are often defined in a purely machine-interpretable form, as in most word processor file
[10]
formats .
Markup Language for the biomedical field, based on XML, has been in development for several
decades to enhance the exchange data among researchers. Bioinformatic Sequence Markup Language
[11] [12] [13]
(BSML), Systems Biology Markup Language (SBML), Cell Markup Language (Cell ML), and
[14]
Neuro Markup Language (Neuro-ML) are examples of markup languages. Polymorphism Mining
[15]
and Annotation Programs (PolyMAPr) is centric on SNP and tries to achieve mining, annotation,
[16] [17] [18]
and functional analysis of public database as dbSNP, CGAP, and JSNP through programming.
ISO 25720 Genomic Sequence Variation Markup Language (GSVML) is the first standardized ML for
clinical genomic sequence variation data exchange.
The purpose of Omics Markup Language (OML) is to provide a standardized data exchange format for
omics in human health.
The recent expansion in omics research has produced large quantities of data held in many databases
with different formats. Standardization of data exchange is necessary for managing, analysing and
utilizing these data. Considering that omics, especially transcriptomics, proteomics, signalomics and
metabolomics, ha
...
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