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

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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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

25、he human health-related facilities that have various types of data formats. In the present circumstances, SNP is expected to be a key to understanding human response to external stimuli such as any kind of alien invasions, therapies, and the environmental interactions (see reference 2). Bacterial in

26、fection is an example of alien invasion, and the responses to the infections are different amongst individuals. According to the therapy, the side effects to a drug are different amongst the patients. These responses are also different in various environments. The Markup Language is a set of symbols

27、 and rules for their use when doing a markup of a document (see reference 3). The first standardized markup language was Standard Generalized Markup Language (SGML), 4 which has strong similarities with troff and nroff text layout languages supplied with Unix systems. Hypertext Markup Language (HTML

28、) is based on SGML 5. Extensible Markup Language (XML) is a pared-down version of SGML, designed especially for Web documents (see reference 6). XML acts as the basis for Extensible HTML (XHTML) 7and Wireless Markup Language (WML) (see reference 8) and for standardized definitions of system interact

29、ion such as Simple Object Access Protocol (SOAP) 9. By contrast, text layout or semantics are often defined in a purely machine-interpretable form, as in most word processor file formats (see reference 10). Markup Language for the biomedical field, based on XML, has been in development for several d

30、ecades to enhance the exchange data among researchers. Bioinformatic Sequence Markup Language (BSML) (see reference 11), Systems Biology Markup Language (SBML) 12, Cell Markup Language (Cell ML) 13, and Neuro Markup Language (Neuro-ML) 14are examples of markup languages. Polymorphism Mining and Anno

31、tation Programs (PolyMAPr) 15is centric on SNP and tries to achieve mining, annotation and functional analysis of public databases such as dbSNP 16, the Cancer Gene Anatomy Project (CGAP) (see reference 17), and Japanese single nucleotide polymorphisms (JSNP) (see reference 18) through programming.

32、To utilize the accumulated SNP data among many facilities around the world, standards for the interchange of SNP data must be defined. The required standards include defining a data format and exchange messages. Markup Language is the reasonable choice to address this need. As for genomic data messa

33、ge handling, Health Level Seven Clinical Genomics Special Interest Group 19has summarized clinical use cases for general genomic data. The GSVML project has contributed to these efforts. Additionally, this work incorporated use cases based on the Japanese Millennium Project 20. Based on these contex

34、ts and investigations, this International Standard elucidates the needs and the requirements for GSVML and then proposes the specification of GSVML for the international standardization. BS ISO 25720:2009INTERNATIONAL STANDARD ISO 25720:2009(E) ISO 2009 All rights reserved 1Health informatics Genomi

35、c Sequence Variation Markup Language (GSVML) IMPORTANT The electronic file of this document contains colours which are considered to be useful for the correct understanding of the document. Users should therefore consider printing this document using a colour printer. 1 Scope This International Stan

36、dard is applicable to the data exchange format that is designed to facilitate the exchange of the genomic sequence variation data around the world, without forcing change of any database schema. From an informatics perspective, GSVML defines the data exchange format based on XML. The scope of this I

37、nternational Standard is the data exchange format, but the database schema itself is outside the scope of this International Standard. From a biological point of view, all genetic sequence variations are taken into consideration and are within the scope of this International Standard, while polymorp

38、hisms, especially SNPs, are the main focus of this International Standard. In other words, the annotations of variation as clinical concerns and -omics concerns are within the scope of this International Standard. Though SNPs exist in various biological species, the scope of this International Stand

39、ard covers the human health associated species as human, cell line, and preclinical animals. The other biological species are outside the scope of this International Standard. The clinical field is within the scope of this International Standard, but the basic research fields and other scientific fi

40、elds are outside the scope of this International Standard. Here, clinical research, including drug discovery, is within the scope of this International Standard. As for supposed application fields, the main focus is in human health, including clinical practice, preventive medicine, translational res

41、earch and clinical researches. 2 Conformance 2.1 Purpose This International Standard provides a data exchange format for genomic sequence variation data in human health. This International Standard provides the GSVML specification mainly for the case of SNP and Short Tandem Repeat Polymorphism (STRP

42、). Considering that SNP and STRP are the major and simple polymorphisms in human health research, centering on them and expanding the specification to the other sequence variation data seems reasonable. This International Standard allows for the expandability of GSVML from SNP and STRP to other sequ

43、ence variation data. 2.2 Needs and general requirements The vast volume of experimental data from the recent explosion of genomic sequence variation research has produced an overwhelming amount of data stored in many databases with various types of format worldwide. Standardization of data exchange

44、is urgent for managing, analysing, and utilizing these data. Standardizing the interoperable format is necessary for easy and convenient genomic sequence variation data exchange. Considering that genomic sequence variation, especially SNP and STRP, has its significant meaning in the gene-based medic

45、ine and the pharmacogenomics for human health, the data exchange format is the key to enhancing the gene-based clinical research and the gene-based medicine. The management of genomic data is as critical as the basic research data in this new era. There are many kinds of -omics data around the world

46、, and the time has come to effectively use these genomic data for human health. In order to use these data effectively and efficiently, standards must be developed to permit the interoperable interchange of genomic data globally. These standards must define the data format as well as BS ISO 25720:20

47、09ISO 25720:2009(E) 2 ISO 2009 All rights reservedthe messages to be used to interchange and share this data globally. This International Standard addresses those requirements, using a Markup Language. 3 Normative references The following referenced documents are indispensable for the application of

48、 this document. For dated references, only the edition cited applies. For undated references, the latest edition of the referenced document (including any amendments) applies. EN 13606 (all parts), Health informatics Electronic healthcare record communication 4 Terms and definitions For the purposes

49、 of this document, the following terms and definitions apply. 4.1 actor something or someone who supplies a stimulus to the system NOTE Actors include both humans and other quasi-autonomous things, such as machines, computer tasks and systems. 4.2 Bioinformatic Sequence Markup Language BSML extensible language specification and container for bioinformatic data 4.3 Cell Markup Language Cell ML Extensible Markup Language to provide a standard method for representing and exchanging computer-based biologi