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A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies
09:32

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Published on: September 23, 2014

Using XML to encode TMA DES metadata.

Oliver Lyttleton1, Alexander Wright, Darren Treanor

  • 1Institute of Life Science, School of Medicine, Swansea University, SA2 8PP, U.K.

Journal of Pathology Informatics
|October 5, 2011
PubMed
Summary
This summary is machine-generated.

This study demonstrates how to encode all Tissue Microarray Data Exchange Specification (TMA DES) data in XML, simplifying processing. Using XML Schema and RDF enhances data validation and error checking for TMA DES.

Keywords:
CDEsDTDTMA DESXMLstatistical analysistissue microarray

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Area of Science:

  • Bioinformatics
  • Data Standards
  • Computational Biology

Background:

  • Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for TMA experiment data.
  • Current TMA DES uses DTD for syntax/structure and ISO 11179 for semantics.
  • Encoding all TMA DES data and metadata in XML can simplify program development and data validation.

Purpose of the Study:

  • To develop an XML Schema version of the TMA DES DTD.
  • To convert ISO 11179 semantic definitions to RDF encoded in XML.
  • To enable comprehensive XML encoding of TMA DES data and metadata.

Main Methods:

  • Created an XML Schema replacement for the TMA DES DTD.
  • Developed a converter for ISO 11179 to RDF (XML-encoded).
  • Converted TMA DES ISO 11179 definitions to RDF using the developed program.

Main Results:

  • Successfully validated a sample TMA DES XML file using the new XML Schema.
  • Validated the generated RDF data with the W3C RDF validation service.
  • Demonstrated feasibility of full XML encoding for TMA DES.

Conclusions:

  • All TMA DES data can be encoded using XML, streamlining processing.
  • XML Schema offers superior data type and constraint specification over DTDs.
  • Enhanced error checking is possible with XML Schema for Common Data Elements (CDEs).