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

BMC Bioinformatics

Research Article

Jonas S Almeida¹  Helena F Deus²  Wolfgang Maass³ 

[1] Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd Houston, 77030, TX, USA;Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd Houston, 77030, TX, USA;Institute of Chemical and Biological Technology, Universidade Nova de Lisboa, Oeiras, Portugal;Research Center for Intelligent Media, Furtwangen University, Furtwangen, Germany;

关键词: Resource Description Framework;    Core Model;    Finite State Automaton;    Resource Description Framework Triple;    Finite State Automaton;   

DOI  :  10.1186/1471-2105-11-387

 received in 2010-06-17, accepted in 2010-07-20,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundBiomedical 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.ResultsA 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Almeida et al; licensee BioMed Central Ltd. 2010