Integration of prostate cancer clinical data using an ontology

It is increasingly important for investigators to efficiently and effectively access, interpret, and analyze the data from diverse biological, literature, and annotation sources in a unified way. The heterogeneity of biomedical data and the lack of metadata are the primary sources of the difficulty...

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Bibliographic Details
Published in:Journal of biomedical informatics 2009-12, Vol.42 (6), p.1035-1045
Main Authors: Min, Hua, Manion, Frank J., Goralczyk, Elizabeth, Wong, Yu-Ning, Ross, Eric, Beck, J. Robert
Format: Article
Language:English
Subjects:
Computational Biology - methods
Data integration
Database Management Systems
Databases, Factual
Humans
Information Storage and Retrieval - methods
Knowledge sharing
Male
Ontology
Prostatic Neoplasms
Semantic heterogeneity
Semantics
Terminology as Topic
User-Computer Interface
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Summary:It is increasingly important for investigators to efficiently and effectively access, interpret, and analyze the data from diverse biological, literature, and annotation sources in a unified way. The heterogeneity of biomedical data and the lack of metadata are the primary sources of the difficulty for integration, presenting major challenges to effective search and retrieval of the information. As a proof of concept, the Prostate Cancer Ontology (PCO) is created for the development of the Prostate Cancer Information System (PCIS). PCIS is applied to demonstrate how the ontology is utilized to solve the semantic heterogeneity problem from the integration of two prostate cancer related database systems at the Fox Chase Cancer Center. As the results of the integration process, the semantic query language SPARQL is applied to perform the integrated queries across the two database systems based on PCO.
ISSN:1532-0464
1532-0480
DOI:10.1016/j.jbi.2009.05.007