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Journal article 1142 views

Using XML to encode TMA DES metadata

Paul Lewis

Journal of Pathology Informatics, Volume: 2, Issue: 40

Swansea University Author: Paul Lewis

Abstract

Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of...

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Published in: Journal of Pathology Informatics
Published: 2011
URI: https://cronfa.swan.ac.uk/Record/cronfa12677
first_indexed 2013-07-23T12:08:32Z
last_indexed 2018-02-09T04:42:52Z
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fullrecord <?xml version="1.0"?><rfc1807><datestamp>2011-10-01T00:00:00.0000000</datestamp><bib-version>v2</bib-version><id>12677</id><entry>2012-09-12</entry><title>Using XML to encode TMA DES metadata</title><swanseaauthors><author><sid>46dfc22d7468f247c390ba0c6cd8fba6</sid><firstname>Paul</firstname><surname>Lewis</surname><name>Paul Lewis</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2012-09-12</date><deptcode>CBAE</deptcode><abstract>Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.</abstract><type>Journal Article</type><journal>Journal of Pathology Informatics</journal><volume>2</volume><journalNumber>40</journalNumber><paginationStart/><paginationEnd/><publisher/><placeOfPublication/><issnPrint/><issnElectronic/><keywords>CDEs, DTD, statistical analysis, tissue microarray, TMA DES, XML</keywords><publishedDay>27</publishedDay><publishedMonth>6</publishedMonth><publishedYear>2011</publishedYear><publishedDate>2011-06-27</publishedDate><doi/><url/><notes/><college>COLLEGE NANME</college><department>Management School</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>CBAE</DepartmentCode><institution>Swansea University</institution><apcterm/><lastEdited>2011-10-01T00:00:00.0000000</lastEdited><Created>2012-09-12T23:59:30.0713507</Created><path><level id="1">Faculty of Medicine, Health and Life Sciences</level><level id="2">Swansea University Medical School - Medicine</level></path><authors><author><firstname>Paul</firstname><surname>Lewis</surname><order>1</order></author></authors><documents/><OutputDurs/></rfc1807>
spelling 2011-10-01T00:00:00.0000000 v2 12677 2012-09-12 Using XML to encode TMA DES metadata 46dfc22d7468f247c390ba0c6cd8fba6 Paul Lewis Paul Lewis true false 2012-09-12 CBAE Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs. Journal Article Journal of Pathology Informatics 2 40 CDEs, DTD, statistical analysis, tissue microarray, TMA DES, XML 27 6 2011 2011-06-27 COLLEGE NANME Management School COLLEGE CODE CBAE Swansea University 2011-10-01T00:00:00.0000000 2012-09-12T23:59:30.0713507 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Paul Lewis 1
title Using XML to encode TMA DES metadata
spellingShingle Using XML to encode TMA DES metadata
Paul Lewis
title_short Using XML to encode TMA DES metadata
title_full Using XML to encode TMA DES metadata
title_fullStr Using XML to encode TMA DES metadata
title_full_unstemmed Using XML to encode TMA DES metadata
title_sort Using XML to encode TMA DES metadata
author_id_str_mv 46dfc22d7468f247c390ba0c6cd8fba6
author_id_fullname_str_mv 46dfc22d7468f247c390ba0c6cd8fba6_***_Paul Lewis
author Paul Lewis
author2 Paul Lewis
format Journal article
container_title Journal of Pathology Informatics
container_volume 2
container_issue 40
publishDate 2011
institution Swansea University
college_str Faculty of Medicine, Health and Life Sciences
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hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
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description Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.
published_date 2011-06-27T03:24:13Z
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