PROVA Rule Based Java Scripting for a Bioinformatics Semantic Web 1st Edition by Alexander Kozlenkov, Michael Schroeder 9783540213000

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ISBN 13: 9783540213000

Author: Alexander Kozlenkov, Michael Schroeder

Transparent information integration across distributed and heterogeneous data sources and computational tools is a prime concern for bioinformatics. Recently, there have been proposals for a semantic web addressing these requirements. A promising approach for such a semantic web are the integration of rules to specify and implement workflows and object-orientation to cater for computational aspects.

We present PROVA, a Java-based rule-engine, which realises this integration. It enables one to separate a declarative description of information workflows from any implementation details and thus easily create and maintain code. We show how PROVA is used to compose an information and computation workflow involving

• rules for specifying the workflow,

• rules for reasoning over the data,

• rules for accessing flat files, databases, and other services, and

• rules involving heavy-duty computations.

The resulting code is very compact and re-usable.

We give a detailed account of PROVA and document its use with a example of a system, PSIMAP, which derives domain-domain interactions from multi-domain structures in the PDB using the SCOP domain and superfamily definitions. PSIMAP is a typical bioinformatics application in that it integrates disparate information resources in different formats (flat files (PDB) and database (SCOP)) requiring additional computations

PROVA Rule Based Java Scripting for a Bioinformatics Semantic Web 1st Table of contents:

1 Background

2 Motivation

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