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. 2011:2:40.
doi: 10.4103/2153-3539.84233. Epub 2011 Aug 24.

Using XML to encode TMA DES metadata

Oliver Lyttleton  1 , Alexander Wright, Darren Treanor, Paul Lewis
Affiliations

Using XML to encode TMA DES metadata

Oliver Lyttleton et al. J Pathol Inform. 2011.

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.

Keywords: CDEs; DTD; TMA DES; XML; statistical analysis; tissue microarray.

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Figures

Figure 1
Figure 1
Extract from a modified TMA DES XML file[7]
Figure 2
Figure 2
DTD definition for the tma element
Figure 3
Figure 3
ISO 11179 description of the TMA DES “tma” CDE
Figure 4
Figure 4
TMA DES data requires separate parsers for XML, DTD, and ISO 11179 documents
Figure 5
Figure 5
CDEs from TMA DES XML data
Figure 6
Figure 6
XML Schema definition of a TMA DES CDE
Figure 7
Figure 7
XML Schema definition of the core_organism CDE
Figure 8
Figure 8
RDF description of the “histo” CDE
See this image and copyright information in PMC

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