Using XML to encode TMA DES metadata
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2011-01-01
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| Series: | Journal of Pathology Informatics |
| Subjects: | |
| Online Access: | http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2011;volume=2;issue=1;spage=40;epage=40;aulast=Lyttleton |
| _version_ | 1811231392415088640 |
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| author | Oliver Lyttleton Alexander Wright Darren Treanor Paul Lewis |
| author_facet | Oliver Lyttleton Alexander Wright Darren Treanor Paul Lewis |
| author_sort | Oliver Lyttleton |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-12T10:44:32Z |
| format | Article |
| id | doaj.art-4f85273f09f1435ca45a31f714f67abe |
| institution | Directory Open Access Journal |
| issn | 2153-3539 2153-3539 |
| language | English |
| last_indexed | 2024-04-12T10:44:32Z |
| publishDate | 2011-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Pathology Informatics |
| spelling | doaj.art-4f85273f09f1435ca45a31f714f67abe2022-12-22T03:36:29ZengElsevierJournal of Pathology Informatics2153-35392153-35392011-01-0121404010.4103/2153-3539.84233Using XML to encode TMA DES metadataOliver LyttletonAlexander WrightDarren TreanorPaul LewisBackground: 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.http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2011;volume=2;issue=1;spage=40;epage=40;aulast=LyttletonCDEsDTDstatistical analysistissue microarrayTMA DESXML |
| spellingShingle | Oliver Lyttleton Alexander Wright Darren Treanor Paul Lewis Using XML to encode TMA DES metadata Journal of Pathology Informatics CDEs DTD statistical analysis tissue microarray TMA DES XML |
| title | 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_short | Using XML to encode TMA DES metadata |
| title_sort | using xml to encode tma des metadata |
| topic | CDEs DTD statistical analysis tissue microarray TMA DES XML |
| url | http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2011;volume=2;issue=1;spage=40;epage=40;aulast=Lyttleton |
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