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Related Experiment Videos

The tissue microarray data exchange specification: a document type definition to validate and enhance XML data.

David G Nohle1, Leona W Ayers

  • 1The Mid-Region AIDS and Cancer Specimen Resource (ACSR), Department of Pathology, The Ohio State University, Columbus, OH, USA. nohle-1@medctr.osu.edu

BMC Medical Informatics and Decision Making
|May 6, 2005
PubMed
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The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) Tissue Microarray Data Exchange Specification (TMA DES) enables standardized sharing of tissue microarray data. Implementation by the AIDS and Cancer Specimen Resource (ACSR) validated its utility and informed enhancements for improved data management and interoperability.

Area of Science:

  • Pathology Informatics
  • Bioinformatics
  • Data Standards

Background:

  • The Association for Pathology Informatics (API) developed the Extensible Mark-up Language (XML) Tissue Microarray Data Exchange Specification (TMA DES) for standardized sharing of tissue microarray (TMA) data.
  • The AIDS and Cancer Specimen Resource (ACSR), a National Cancer Institute (NCI) consortium, provides HIV-related tissues in TMAs with clinical data for research.
  • Exporting ACSR TMA data to the TMA DES format allows for practical evaluation of the specification's utility and potential enhancements.

Purpose of the Study:

  • To evaluate the utility of the API TMA DES specification in a real-world setting.
  • To develop and apply a Document Type Definition (DTD) for validating TMA DES XML data.
  • To identify potential enhancements for the TMA DES specification based on implementation experience.

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Main Methods:

  • Developed and implemented a DTD to govern common data elements (CDEs) for TMA DES export XML files.
  • Utilized the DTD for routine data validation within the ACSR TMA data management application.
  • Documented implementation experiences and suggested improvements for the TMA DES specification.

Main Results:

  • A functional DTD was created, tested, and is in routine use by the ACSR for validating TMA DES export files.
  • The ACSR implementation demonstrated the practical utility of the TMA DES specification.
  • The process identified areas for improvement in the TMA DES, including clearer identifiers and hierarchical relationships.

Conclusions:

  • ACSR's implementation confirmed the TMA DES's utility and the effectiveness of using a DTD for data validation.
  • The experience highlighted the need for enhancements to the TMA DES to reduce ambiguity and improve data interoperability.
  • Proposed enhancements, including better identifiers and hierarchical structures, can facilitate automated data processing and strengthen data validation.