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S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

Jonas S. Almeida, Helena F. Deus & Wolfgang Maass

abstract Biomedical research is set to greatly benefit from the use of semantic web technologies in the design of computational infrastructure. However, beyond well defined research initiatives, substantial issues of data heterogeneity, source distribution, and privacy currently stand in the way towards the personalization of Medicine.

A computational framework for bioinformatic infrastructure was designed to deal with the heterogeneous data sources and the sensitive mixture of public and private data that characterizes the biomedical domain. This framework consists of a logical model build with semantic web tools, coupled with a Markov process that propagates user operator states. An accompanying open source prototype was developed to meet a series of applications that range from collaborative multi-institution data acquisition efforts to data analysis applications that need to quickly traverse complex data structures. This report describes the two abstractions underlying the S3DB-based infrastructure, logical and numerical, and discusses its generality beyond the immediate confines of existing implementations.

Conclusions: The emergence of the "web as a computer" requires a formal model for the different functionalities involved in reading and writing to it. The S3DB core model proposed was found to address the design criteria of biomedical computational infrastructure, such as those supporting large scale multi-investigator research, clinical trials, and molecular epidemiology
   
type journal paper
   
keywords RFD, framework, S3DB, data integration, semantic web technologies
   
language English
kind of paper journal article
date of appearance 20-7-2010
journal BMC Bioinformatics
publisher BioMed Central (London)
ISSN (online) 1471-2105
DOI 10.1186/1471-2105-11-387
volume of journal 11
number of issue 387
page(s) 1-10
review double-blind review
   
citation Almeida, J. S., Deus, H. F., & Maass, W. (2010). S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics, 11(387), 1-10, DOI:10.1186/1471-2105-11-387.