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Updated: Jun 9, 2026

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

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

Published on: September 23, 2014

The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data.

Hyunseok P Kang1, Charles D Borromeo, Jules J Berman

  • 1Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo 14263, NY, USA.

Journal of Pathology Informatics
|September 1, 2010
PubMed
Summary
This summary is machine-generated.

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This study introduces an OWL schema to standardize tissue microarray (TMA) data, enabling efficient data sharing and integration for translational research. This approach overcomes limitations of localized XML formats, promoting collaborative scientific discovery.

Area of Science:

  • Bioinformatics
  • Translational Research
  • Data Science

Background:

  • Tissue microarrays (TMAs) are vital for translational research but face data sharing challenges due to incompatible database systems.
  • Current data exchange methods lack global scope, hindering efficient collaboration and data integration.
  • Resource Description Framework (RDF) and Uniform Resource Identifiers (URIs) offer a flexible, globally accessible data representation method.

Purpose of the Study:

  • To develop a standardized Web Ontology Language (OWL) schema for tissue microarray (TMA) data.
  • To facilitate seamless data sharing and integration across different research institutions.
  • To enhance the utility of TMAs in translational research.

Main Methods:

  • Designed a minimal OWL schema focusing on TMA experiment-specific concepts.
Keywords:
OWLOntologytissue microarray

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Manual Construction of a Tissue Microarray using the Tape Method and a Handheld Microarrayer
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A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies
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Manual Construction of a Tissue Microarray using the Tape Method and a Handheld Microarrayer
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Manual Construction of a Tissue Microarray using the Tape Method and a Handheld Microarrayer

Published on: June 10, 2022

  • Integrated general data elements from established ontologies like the NCI thesaurus.
  • Assigned URIs using the Linked Data format for global identification.

    • Main Results:

    • Presented example files demonstrating the application of the new OWL schema.
    • Showcased the conversion of Extensible Markup Language (XML) data to OWL format.
    • Validated the schema's capability to represent TMA data in a globally accessible manner.

    Conclusions:

    • The proposed OWL schema addresses limitations of localized XML by using predefined ontologies and global unique identifiers.
    • This standardization enhances the utilization of tissue resources for collaborative translational research.
    • Facilitates improved data integration and sharing, accelerating scientific discovery.