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Extending the tissue microarray data exchange specification for inclusion of data analysis results

Paul Lewis

Journal of Pathology Informatics, Volume: 2, Issue: 17

Swansea University Author: Paul Lewis

Abstract

Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an eXtensible Markup Language (XML) specification for encoding TMA experiment data in a machine-readable format that is also human readable. TMA DES defines Common Data Elements (CDEs) that form a basic vocabulary for describ...

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Published in: Journal of Pathology Informatics
Published: 2011
URI: https://cronfa.swan.ac.uk/Record/cronfa12676
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fullrecord <?xml version="1.0"?><rfc1807><datestamp>2011-10-01T00:00:00.0000000</datestamp><bib-version>v2</bib-version><id>12676</id><entry>2012-09-12</entry><title>Extending the tissue microarray data exchange specification for inclusion of data analysis results</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>SGMGT</deptcode><abstract>Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an eXtensible Markup Language (XML) specification for encoding TMA experiment data in a machine-readable format that is also human readable. TMA DES defines Common Data Elements (CDEs) that form a basic vocabulary for describing TMA data. TMA data are routinely subjected to univariate and multivariate statistical analysis to determine differences or similarities between pathologically distinct groups of tumors for one or more markers or between markers for different groups. Such statistical analysis tests include the t-test, ANOVA, Chi-square, Mann-Whitney U, and Kruskal-Wallis tests. All these generate output that needs to be recorded and stored with TMA data. Materials and Methods: We propose extending the TMA DES to include syntactic and semantic definitions of CDEs for describing the results of statistical analyses performed upon TMA DES data. These CDEs are described in this paper and it is illustrated how they can be added to the TMA DES. We created a Document Type Definition (DTD) file defining the syntax for these CDEs, and a set of ISO 11179 entries providing semantic definitions for them. We describe how we wrote a program in R that read TMA DES data from an XML file, performed statistical analyses on that data, and created a new XML file containing both the original XML data and CDEs representing the results of our analyses. This XML file was submitted to XML parsers in order to confirm that they conformed to the syntax defined in our extended DTD file. TMA DES XML files with deliberately introduced errors were also parsed in order to verify that our new DTD file could perform error checking. Finally, we also validated an existing TMA DES XML file against our DTD file in order to demonstrate the backward compatibility of our DTD. Results: Our experiments demonstrated the encoding of analysis results using our proposed CDEs. We used XML parsers to confirm that these XML data were syntactically correct and conformed to the rules specified in our extended TMA DES DTD. We also demonstrated that this extended DTD was capable of being used to successfully perform error checking, and was backward compatible with pre-existing TMA DES data which did not use our new CDEs. Conclusions: The TMA DES allows Tissue Microarray data to be shared. A variety of statistical tests are used to analyze such data. We have proposed a set of CDEs as an extension to the TMA DES which can be used to annotate TMA DES data with the results of statistical analyses performed on that data. We performed experiments which demonstrated the usage of TMA DES data containing our proposed CDEs.</abstract><type>Journal Article</type><journal>Journal of Pathology Informatics</journal><volume>2</volume><journalNumber>17</journalNumber><paginationStart/><paginationEnd/><publisher/><placeOfPublication/><issnPrint/><issnElectronic/><keywords>CDEs, DTD, statistical analysis, tissue microarray, TMA Data Exchange Specification, XML</keywords><publishedDay>16</publishedDay><publishedMonth>2</publishedMonth><publishedYear>2011</publishedYear><publishedDate>2011-02-16</publishedDate><doi/><url/><notes/><college>COLLEGE NANME</college><department>School of Management - School</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>SGMGT</DepartmentCode><institution>Swansea University</institution><apcterm/><lastEdited>2011-10-01T00:00:00.0000000</lastEdited><Created>2012-09-12T23:57:04.9134331</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 12676 2012-09-12 Extending the tissue microarray data exchange specification for inclusion of data analysis results 46dfc22d7468f247c390ba0c6cd8fba6 Paul Lewis Paul Lewis true false 2012-09-12 SGMGT Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an eXtensible Markup Language (XML) specification for encoding TMA experiment data in a machine-readable format that is also human readable. TMA DES defines Common Data Elements (CDEs) that form a basic vocabulary for describing TMA data. TMA data are routinely subjected to univariate and multivariate statistical analysis to determine differences or similarities between pathologically distinct groups of tumors for one or more markers or between markers for different groups. Such statistical analysis tests include the t-test, ANOVA, Chi-square, Mann-Whitney U, and Kruskal-Wallis tests. All these generate output that needs to be recorded and stored with TMA data. Materials and Methods: We propose extending the TMA DES to include syntactic and semantic definitions of CDEs for describing the results of statistical analyses performed upon TMA DES data. These CDEs are described in this paper and it is illustrated how they can be added to the TMA DES. We created a Document Type Definition (DTD) file defining the syntax for these CDEs, and a set of ISO 11179 entries providing semantic definitions for them. We describe how we wrote a program in R that read TMA DES data from an XML file, performed statistical analyses on that data, and created a new XML file containing both the original XML data and CDEs representing the results of our analyses. This XML file was submitted to XML parsers in order to confirm that they conformed to the syntax defined in our extended DTD file. TMA DES XML files with deliberately introduced errors were also parsed in order to verify that our new DTD file could perform error checking. Finally, we also validated an existing TMA DES XML file against our DTD file in order to demonstrate the backward compatibility of our DTD. Results: Our experiments demonstrated the encoding of analysis results using our proposed CDEs. We used XML parsers to confirm that these XML data were syntactically correct and conformed to the rules specified in our extended TMA DES DTD. We also demonstrated that this extended DTD was capable of being used to successfully perform error checking, and was backward compatible with pre-existing TMA DES data which did not use our new CDEs. Conclusions: The TMA DES allows Tissue Microarray data to be shared. A variety of statistical tests are used to analyze such data. We have proposed a set of CDEs as an extension to the TMA DES which can be used to annotate TMA DES data with the results of statistical analyses performed on that data. We performed experiments which demonstrated the usage of TMA DES data containing our proposed CDEs. Journal Article Journal of Pathology Informatics 2 17 CDEs, DTD, statistical analysis, tissue microarray, TMA Data Exchange Specification, XML 16 2 2011 2011-02-16 COLLEGE NANME School of Management - School COLLEGE CODE SGMGT Swansea University 2011-10-01T00:00:00.0000000 2012-09-12T23:57:04.9134331 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Paul Lewis 1
title Extending the tissue microarray data exchange specification for inclusion of data analysis results
spellingShingle Extending the tissue microarray data exchange specification for inclusion of data analysis results
Paul Lewis
title_short Extending the tissue microarray data exchange specification for inclusion of data analysis results
title_full Extending the tissue microarray data exchange specification for inclusion of data analysis results
title_fullStr Extending the tissue microarray data exchange specification for inclusion of data analysis results
title_full_unstemmed Extending the tissue microarray data exchange specification for inclusion of data analysis results
title_sort Extending the tissue microarray data exchange specification for inclusion of data analysis results
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 17
publishDate 2011
institution Swansea University
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
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
document_store_str 0
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description Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an eXtensible Markup Language (XML) specification for encoding TMA experiment data in a machine-readable format that is also human readable. TMA DES defines Common Data Elements (CDEs) that form a basic vocabulary for describing TMA data. TMA data are routinely subjected to univariate and multivariate statistical analysis to determine differences or similarities between pathologically distinct groups of tumors for one or more markers or between markers for different groups. Such statistical analysis tests include the t-test, ANOVA, Chi-square, Mann-Whitney U, and Kruskal-Wallis tests. All these generate output that needs to be recorded and stored with TMA data. Materials and Methods: We propose extending the TMA DES to include syntactic and semantic definitions of CDEs for describing the results of statistical analyses performed upon TMA DES data. These CDEs are described in this paper and it is illustrated how they can be added to the TMA DES. We created a Document Type Definition (DTD) file defining the syntax for these CDEs, and a set of ISO 11179 entries providing semantic definitions for them. We describe how we wrote a program in R that read TMA DES data from an XML file, performed statistical analyses on that data, and created a new XML file containing both the original XML data and CDEs representing the results of our analyses. This XML file was submitted to XML parsers in order to confirm that they conformed to the syntax defined in our extended DTD file. TMA DES XML files with deliberately introduced errors were also parsed in order to verify that our new DTD file could perform error checking. Finally, we also validated an existing TMA DES XML file against our DTD file in order to demonstrate the backward compatibility of our DTD. Results: Our experiments demonstrated the encoding of analysis results using our proposed CDEs. We used XML parsers to confirm that these XML data were syntactically correct and conformed to the rules specified in our extended TMA DES DTD. We also demonstrated that this extended DTD was capable of being used to successfully perform error checking, and was backward compatible with pre-existing TMA DES data which did not use our new CDEs. Conclusions: The TMA DES allows Tissue Microarray data to be shared. A variety of statistical tests are used to analyze such data. We have proposed a set of CDEs as an extension to the TMA DES which can be used to annotate TMA DES data with the results of statistical analyses performed on that data. We performed experiments which demonstrated the usage of TMA DES data containing our proposed CDEs.
published_date 2011-02-16T03:14:35Z
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