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The tissue micro-array data exchange specification: a web based experience browsing imported data.

David G Nohle1, Barbara A Hackman, 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
|August 10, 2005
PubMed
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Researchers can now easily access and navigate HIV/AIDS tissue microarray (TMA) data online. The BrowseTMA tool links virtual slides and clinical details, improving access to valuable research specimens.

Area of Science:

  • Pathology Informatics
  • Biomedical Data Management
  • Cancer Research Informatics

Background:

  • The AIDS and Cancer Specifer Resource (ACSR) provides HIV-infected and control tissue samples, including tissue microarrays (TMAs), with clinical data to researchers.
  • Efficiently viewing and navigating TMA materials, including digital images and associated clinical data, is crucial for researchers.
  • The Association for Pathology Informatics (API) extensible markup language (XML) TMA data exchange specification (TMA DES) offers a standardized format for TMA data.

Purpose of the Study:

  • To develop an efficient method for researchers to view and navigate TMA materials and associated clinical data.
  • To implement the API TMA DES for organizing, navigating, and publishing TMA data.
  • To create a web-based tool for accessing and cross-referencing TMA information.

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Main Methods:

  • Developed the BrowseTMA tool, a website that organizes and cross-references TMA lists, virtual slide images, TMA DES export data, legends, and clinical details.
  • Utilized Microsoft Excel and Word to convert tabular clinical data into XML files conforming to the TMA DES format.
  • Employed Extensible Stylesheet Language Transformations (XSLT) scripts within BrowseTMA to convert XML data into navigable HTML web pages.

Main Results:

  • Made TMA data, including virtual slide images and clinical details for 14 blocks (1623 cores), available on the ACSR website.
  • Processed TMA data from three additional institutions using the BrowseTMA tool, exporting data in the TMA DES format.
  • Enabled researchers to download TMA clinical data in the TMA DES format and provided access to virtual microscope functionality for viewing and annotating images.

Conclusions:

  • The BrowseTMA tool enables researchers to view virtual TMAs with clinical data online, facilitating review of TMA information.
  • The implemented approach successfully organizes, sorts, navigates, and publishes TMA information, enhancing its value.
  • Proposed and implemented enhancements to the API TMA DES based on practical experience, improving data standardization and validation.