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The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides

Paul Lewis

Journal of Pathology Informatics

Swansea University Author: Paul Lewis

Abstract

Background: Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exc...

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Published in: Journal of Pathology Informatics
Published: 2011
URI: https://cronfa.swan.ac.uk/Record/cronfa12675
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fullrecord <?xml version="1.0"?><rfc1807><datestamp>2011-10-01T00:00:00.0000000</datestamp><bib-version>v2</bib-version><id>12675</id><entry>2012-09-12</entry><title>The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides</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: Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exchange Specification (TMA DES) is a set of eXtensible Markup Language (XML)-based protocols for storing and sharing digitized Tissue Microarray data. XML data are enclosed by named tags which serve as identifiers. These tag names can be Common Data Elements (CDEs), which have a predefined meaning or semantics. By using this specification in a laboratory setting with increasing demands for digital pathology integration, we found that the data structure lacked the ability to cope with digital slide imaging in respect to web-enabled digital pathology systems and advanced scoring techniques. Materials and Methods: By employing user centric design, and observing behavior in relation to TMA scoring and associated data, the TMA DES format was extended to accommodate the current limitations. This was done with specific focus on developing a generic tool for handling any given scoring system, and utilizing data for multiple observations and observers. Results: DTDs were created to validate the extensions of the TMA DES protocol, and a test set of data containing scores for 6,708 TMA core images was generated. The XML was then read into an image processing algorithm to utilize the digital pathology data extensions, and scoring results were easily stored alongside the existing multiple pathologist scores. Conclusions: By extending the TMA DES format to include digital pathology data and customizable scoring systems for TMAs, the new system facilitates the collaboration between pathologists and organizations, and can be used in automatic or manual data analysis. This allows complying systems to effectively communicate complex and varied scoring data.</abstract><type>Journal Article</type><journal>Journal of Pathology Informatics</journal><volume></volume><journalNumber></journalNumber><paginationStart/><paginationEnd/><publisher/><placeOfPublication/><issnPrint/><issnElectronic/><keywords>CDEs, DTD, tissue microarray, TMA DES, virtual pathology, XML</keywords><publishedDay>15</publishedDay><publishedMonth>3</publishedMonth><publishedYear>2011</publishedYear><publishedDate>2011-03-15</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>2012-09-12T23:54:53.4640497</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 12675 2012-09-12 The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides 46dfc22d7468f247c390ba0c6cd8fba6 Paul Lewis Paul Lewis true false 2012-09-12 SGMGT Background: Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exchange Specification (TMA DES) is a set of eXtensible Markup Language (XML)-based protocols for storing and sharing digitized Tissue Microarray data. XML data are enclosed by named tags which serve as identifiers. These tag names can be Common Data Elements (CDEs), which have a predefined meaning or semantics. By using this specification in a laboratory setting with increasing demands for digital pathology integration, we found that the data structure lacked the ability to cope with digital slide imaging in respect to web-enabled digital pathology systems and advanced scoring techniques. Materials and Methods: By employing user centric design, and observing behavior in relation to TMA scoring and associated data, the TMA DES format was extended to accommodate the current limitations. This was done with specific focus on developing a generic tool for handling any given scoring system, and utilizing data for multiple observations and observers. Results: DTDs were created to validate the extensions of the TMA DES protocol, and a test set of data containing scores for 6,708 TMA core images was generated. The XML was then read into an image processing algorithm to utilize the digital pathology data extensions, and scoring results were easily stored alongside the existing multiple pathologist scores. Conclusions: By extending the TMA DES format to include digital pathology data and customizable scoring systems for TMAs, the new system facilitates the collaboration between pathologists and organizations, and can be used in automatic or manual data analysis. This allows complying systems to effectively communicate complex and varied scoring data. Journal Article Journal of Pathology Informatics CDEs, DTD, tissue microarray, TMA DES, virtual pathology, XML 15 3 2011 2011-03-15 COLLEGE NANME School of Management - School COLLEGE CODE SGMGT Swansea University 2011-10-01T00:00:00.0000000 2012-09-12T23:54:53.4640497 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Paul Lewis 1
title The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides
spellingShingle The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides
Paul Lewis
title_short The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides
title_full The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides
title_fullStr The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides
title_full_unstemmed The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides
title_sort The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides
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
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
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description Background: Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exchange Specification (TMA DES) is a set of eXtensible Markup Language (XML)-based protocols for storing and sharing digitized Tissue Microarray data. XML data are enclosed by named tags which serve as identifiers. These tag names can be Common Data Elements (CDEs), which have a predefined meaning or semantics. By using this specification in a laboratory setting with increasing demands for digital pathology integration, we found that the data structure lacked the ability to cope with digital slide imaging in respect to web-enabled digital pathology systems and advanced scoring techniques. Materials and Methods: By employing user centric design, and observing behavior in relation to TMA scoring and associated data, the TMA DES format was extended to accommodate the current limitations. This was done with specific focus on developing a generic tool for handling any given scoring system, and utilizing data for multiple observations and observers. Results: DTDs were created to validate the extensions of the TMA DES protocol, and a test set of data containing scores for 6,708 TMA core images was generated. The XML was then read into an image processing algorithm to utilize the digital pathology data extensions, and scoring results were easily stored alongside the existing multiple pathologist scores. Conclusions: By extending the TMA DES format to include digital pathology data and customizable scoring systems for TMAs, the new system facilitates the collaboration between pathologists and organizations, and can be used in automatic or manual data analysis. This allows complying systems to effectively communicate complex and varied scoring data.
published_date 2011-03-15T03:14:35Z
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score 11.016235

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