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

BMC Bioinformatics
Jonas S AlmeidaWolfgang 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. The emergence of the "web as a computer" requires a formal model for the different functionalities involved in reading and wri...Continue Reading

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Citations

Apr 19, 2013·Bioinformatics·David E RobbinsJonas S Almeida
Oct 28, 2010·BMC Medical Informatics and Decision Making·Miria C CorreaJonas S Almeida
Dec 19, 2012·Journal of Biomedical Semantics·Pedro Lopes, José Luís Oliveira
Nov 8, 2013·Briefings in Bioinformatics·Catia M MachadoFrancisco M Couto
Jan 31, 2015·Pediatric and Developmental Pathology : the Official Journal of the Society for Pediatric Pathology and the Paediatric Pathology Society·Matthew D CainOna Marie Faye-Petersen

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Software Mentioned

JSON
s3db
varchar
SPARQL
Google Wave
S3QL
javascript
MATLAB
migrate

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