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J Biomed Inform. 2010 Jun;43(3):435-41. doi: 10.1016/j.jbi.2009.10.001. Epub 2009 Oct 14.

TMA-TAB: a spreadsheet-based document for exchange of tissue microarray data based on the tissue microarray-object model.

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1
Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Republic of Korea.

Abstract

The importance of tissue microarrays (TMA) as clinical validation tools for cDNA microarray results is increasing, whereas researchers are still suffering from TMA data management issues. After we developed a comprehensive data model for TMA data storage, exchange and analysis, TMA-OM, we focused our attention on the development of a user-friendly exchange format with high expressivity in order to promote data communication of TMA results and TMA-OM supportive database applications. We developed TMA-TAB, a spreadsheet-based data format for TMA data submission to the TMA-OM supportive TMA database system. TMA-TAB was developed by simplifying, modifying and reorganizing classes, attributes and templates of TMA-OM into five entities: experiment, block, slide, core_in_block, and core_in_slide. Five tab-delimited formats (investigation design format, block description format, slide description format, core clinicohistopathological data format, and core result data format) were made, each representing the entities of experiment, block, slide, core_in_block, and core_in_slide. We implemented TMA-TAB import and export modules on Xperanto-TMA, a TMA-OM supportive database application, to facilitate data submission. Development and implementation of TMA-TAB and TMA-OM provide a strong infrastructure for powerful and user-friendly TMA data management.

PMID:
19835983
DOI:
10.1016/j.jbi.2009.10.001
[Indexed for MEDLINE]
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