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. 2010 Jul 13:1:9.
doi: 10.4103/2153-3539.65347.

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

Hyunseok P Kang  1 , Charles D Borromeo, Jules J Berman, Michael J Becich
Affiliations

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

Hyunseok P Kang et al. J Pathol Inform. .

Abstract

Background: Tissue microarrays (TMAs) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject-Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration.

Methods: A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format.

Results: We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES) to OWL.

Conclusion: By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.

Keywords: OWL; Ontology; tissue microarray.

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Figures

Figure 1
Figure 1
Example OWL file; this example uses the TMA OWL schema to describe the basic elements of a simplified TMA
Figure 2
Figure 2
MGED example; this example illustrates one way to connect a file describing a TMA to a data file using a different ontology
See this image and copyright information in PMC

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References

    1. Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S, et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med. 1998;4:844–7. - PubMed
    1. Han H, Bearss DJ, Browne LW, Calaluce R, Nagle RB, Von Hoff DD. Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. Cancer Res. 2002;62:2890–6. - PubMed
    1. Mousses S, Bubendorf L, Wagner U, Hostetter G, Kononen J, Cornelison R, et al. Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarrays. Cancer Res. 2002;62:1256–60. - PubMed
    1. Mohanty SK, Mistry AT, Amin W, Parwani AV, Pople AK, Schmandt L, et al. The development and deployment of Common Data Elements for tissue banks for translational research in cancer - an emerging standard based approach for the Mesothelioma Virtual Tissue Bank. BMC Cancer. 2008;8:91. - PMC - PubMed
    1. Patel AA, Kajdacsy-Balla A, Berman JJ, Bosland M, Datta MW, Dhir R, et al. The development of common data elements for a multi-institute prostate cancer tissue bank: The Cooperative Prostate Cancer Tissue Resource (CPCTR) experience. BMC Cancer. 2005;5:108. - PMC - PubMed