BS ISO 25720-2009 Health informatics - Genomic sequence variation markup language (GSVML)《卫生信息学 基因组序列变异标记语言(GSVML)》.pdf
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1、BS ISO25720:2009ICS 35.240.80NO COPYING WITHOUT BSI PERMISSION EXCEPT AS PERMITTED BY COPYRIGHT LAWBRITISH STANDARDHealth informatics Genomic SequenceVariation MarkupLanguage (GSVML)This British Standardwas published under theauthority of the StandardsPolicy and StrategyCommittee on 31 October2009 B
2、SI 2009ISBN 978 0 580 57423 8Amendments/corrigenda issued since publicationDate CommentsBS ISO 25720:2009National forewordThis British Standard is the UK implementation of ISO 25720:2009.The UK participation in its preparation was entrusted to TechnicalCommittee IST/35, Health informatics.A list of
3、organizations represented on this committee can be obtained onrequest to its secretary.This publication does not purport to include all the necessary provisionsof a contract. Users are responsible for its correct application.Compliance with a British Standard cannot confer immunityfrom legal obligat
4、ions.BS ISO 25720:2009Reference numberISO 25720:2009(E)ISO 2009INTERNATIONAL STANDARD ISO25720First edition2009-08-15Health informatics Genomic Sequence Variation Markup Language (GSVML) Informatique de sant Langage de balisage de la variation de squence gnomique BS ISO 25720:2009ISO 25720:2009(E) P
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8、HT PROTECTED DOCUMENT ISO 2009 All rights reserved. Unless otherwise specified, no part of this publication may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying and microfilm, without permission in writing from either ISO at the address below or
9、 ISOs member body in the country of the requester. ISO copyright office Case postale 56 CH-1211 Geneva 20 Tel. + 41 22 749 01 11 Fax + 41 22 749 09 47 E-mail copyrightiso.org Web www.iso.org Published in Switzerland ii ISO 2009 All rights reservedBS ISO 25720:2009ISO 25720:2009(E) ISO 2009 All right
10、s reserved iiiContents Page Foreword iv Introduction.v 1 Scope1 2 Conformance .1 2.1 Purpose 1 2.2 Needs and general requirements.1 3 Normative references2 4 Terms and definitions .2 5 GSVML specification.5 5.1 Specification requirements and GSVML positioning 5 5.2 GSVML structure .5 5.3 GSVML DTD a
11、nd XML schema.5 6 GSVML development process5 Annex A (normative) DTD of GSVML 22 Annex B (normative) XML schema of GSVML .46 Annex C (informative) Basic reference works105 Bibliography131 BS ISO 25720:2009ISO 25720:2009(E) iv ISO 2009 All rights reservedForeword ISO (the International Organization f
12、or 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 th
13、e 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. Internat
14、ional Standards are drafted in accordance with the rules given in the ISO/IEC Directives, Part 2. The main task of technical committees is to prepare International Standards. Draft International Standards adopted by the technical committees are circulated to the member bodies for voting. Publication
15、 as an International Standard requires approval by at least 75 % of the member bodies casting a vote. 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.
16、 ISO 25720 was prepared by Technical Committee ISO/TC 215, Health informatics. BS ISO 25720:2009ISO 25720:2009(E) ISO 2009 All rights reserved vIntroduction In the current electronic world, there are multiple different types of data for healthcare, as shown in Figure 1. Besides clinical data and ima
17、ge data, as we move into this post genomic era, we are creating, internationally, overwhelming amounts of genomic data. The International Standards developing organizations are developing standards for these data; Health Level Seven develops standards for clinical data, DICOM and JPEG develop standa
18、rds for image data. Genomic Sequence Variation Markup Language (GSVML) defines a standard for genomic data, especially human-related DNA variation data. The core target for the GSVML is the Single Nucleotide Polymorphism (SNP). HL7Clinical dataHL7Clinical dataGenomic dataGSVMLDICOM,JPEGImage dataHL7
19、CG Figure 1 Major data types of health care In this post genomic era, the management of health-related data is becoming increasingly important to both genomic research and genome-based medicine (see reference 1). Informational approaches to the management of clinical, image and genomic data are begi
20、nning to have as much worth as basic, bench top research. Nowadays there are many kinds of -omics data around the world awaiting effective utilization for human health. The hurdle that must be overcome to achieve this goal is the development of data format and message standards to support the interc
21、hange of -omics data. Genomic data include genome sequence, DNA sequence variation and other genome-based data such as expression data, proteomics data, molecular network, etc. As an entry point, this International Standard focuses on the DNA sequence variation. Among the DNA sequence variation, the
22、 SNP is selected as the core object because of the following three reasons. a) SNP is the most researched sequence variation for human health. b) In the current context, vast amounts of SNP data exist around the world in various types of data formats. As a result of the recent explosion in SNP resea
23、rch, the vast amounts of experimental data have been BS ISO 25720:2009ISO 25720:2009(E) vi ISO 2009 All rights reservedaccumulating in many databases in various types of data formats. These data await utilization in drug discovery, clinical diagnosis and clinical research. c) SNP data already have a
24、 great impact for human applications such as gene-based medicine and pharmacogenomics. With a view to this context, the international community requires an interoperable format for the interchange of SNP data. Prior to the standardization development, we elucidated the need for data exchange among t
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