The Tissue Microarray OWL Schema: An Open-source Tool for Sharing Tissue Microarray Data

Overview

Journal J Pathol Inform

Specialty Medical Informatics

Date 2010 Sep 1

PMID 20805954

Citations 3

Authors

Hyunseok P Kang

Charles D Borromeo

Jules J Berman

Michael J Becich

Affiliations

Soon will be listed here.

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.

Citing Articles

REDCap and the National Mesothelioma Virtual Bank-a scalable and sustainable model for rare disease biorepositories.

Rashid R, Copelli S, Silverstein J, Becich M J Am Med Inform Assoc. 2023; 30(10):1634-1644.

PMID: 37487555 PMC: 10531116. DOI: 10.1093/jamia/ocad132.

Using XML to encode TMA DES metadata.

Lyttleton O, Wright A, Treanor D, Lewis P J Pathol Inform. 2011; 2:40.

PMID: 21969921 PMC: 3169921. DOI: 10.4103/2153-3539.84233.

Extending the tissue microarray data exchange specification for inclusion of data analysis results.

Lyttleton O, Wright A, Treanor D, Quirke P, Lewis P J Pathol Inform. 2011; 2:17.

PMID: 21572505 PMC: 3073064. DOI: 10.4103/2153-3539.78263.

References

Kajdacsy-Balla A, Geynisman J, Macias V, Setty S, Nanaji N, Berman J . Practical aspects of planning, building, and interpreting tissue microarrays: the Cooperative Prostate Cancer Tissue Resource experience. J Mol Histol. 2007; 38(2):113-21. DOI: 10.1007/s10735-006-9054-5. View

Mohanty S, Mistry A, Amin W, Parwani A, Pople A, Schmandt L . 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: 2329649. DOI: 10.1186/1471-2407-8-91. View

Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S . Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med. 1998; 4(7):844-7. DOI: 10.1038/nm0798-844. View

Amin W, Parwani A, Schmandt L, Mohanty S, Farhat G, Pople A . National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research. BMC Cancer. 2008; 8:236. PMC: 2533341. DOI: 10.1186/1471-2407-8-236. View

Berman J, Edgerton M, Friedman B . The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data. BMC Med Inform Decis Mak. 2003; 3:5. PMC: 165444. DOI: 10.1186/1472-6947-3-5. View

Whetzel P, Parkinson H, Causton H, Fan L, Fostel J, Fragoso G . The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006; 22(7):866-73. DOI: 10.1093/bioinformatics/btl005. View

Han H, Bearss D, Browne L, Calaluce R, Nagle R, Von Hoff D . Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. Cancer Res. 2002; 62(10):2890-6. View

Berman J, Datta M, Kajdacsy-Balla A, Melamed J, Orenstein J, Dobbin K . The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. BMC Bioinformatics. 2004; 5:19. PMC: 373442. DOI: 10.1186/1471-2105-5-19. View

Lee H, Park Y, Sim J, Park R, Kim W, Kim J . The tissue microarray object model: a data model for storage, analysis, and exchange of tissue microarray experimental data. Arch Pathol Lab Med. 2006; 130(7):1004-13. DOI: 10.5858/2006-130-1004-TTMOMA. View

10.

Yu Y, Landsittel D, Jing L, Nelson J, Ren B, Liu L . Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J Clin Oncol. 2004; 22(14):2790-9. DOI: 10.1200/JCO.2004.05.158. View

11.

Becich M . The role of the pathologist as tissue refiner and data miner: the impact of functional genomics on the modern pathology laboratory and the critical roles of pathology informatics and bioinformatics. Mol Diagn. 2001; 5(4):287-99. DOI: 10.1007/BF03262090. View

12.

Mousses S, Bubendorf L, Wagner U, Hostetter G, Kononen J, Cornelison R . Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarrays. Cancer Res. 2002; 62(5):1256-60. View

13.

Nohle D, Hackman B, Ayers L . The tissue micro-array data exchange specification: a web based experience browsing imported data. BMC Med Inform Decis Mak. 2005; 5:25. PMC: 1208890. DOI: 10.1186/1472-6947-5-25. View

14.

Song Y, Lee H, Park Y, Kim D, Sim J, Kang H . TMA-TAB: a spreadsheet-based document for exchange of tissue microarray data based on the tissue microarray-object model. J Biomed Inform. 2009; 43(3):435-41. DOI: 10.1016/j.jbi.2009.10.001. View

15.

Noy N, Shah N, Whetzel P, Dai B, Dorf M, Griffith N . BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009; 37(Web Server issue):W170-3. PMC: 2703982. DOI: 10.1093/nar/gkp440. View

16.

Nohle D, Ayers L . The tissue microarray data exchange specification: a document type definition to validate and enhance XML data. BMC Med Inform Decis Mak. 2005; 5:12. PMC: 1183103. DOI: 10.1186/1472-6947-5-12. View

17.

Patel A, Kajdacsy-Balla A, Berman J, Bosland M, Datta M, Dhir R . 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: 1236914. DOI: 10.1186/1471-2407-5-108. View