Genepi: a blackboard framework for genome annotation.

Full Abstract

BACKGROUND:
Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data) or methodological (new methods) knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a system

RESULTS:
We have implemented a blackboard framework (called Genepi) for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allen's temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures.

CONCLUSION:
In the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied) and opportunistic (the flow of execution depends on the state of our knowledge) aspects of the annotation process.

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Author information

Author/s: Descorps-Declère, Stéphane (S); Ziébelin, Danielle (D); Rechenmann, François (F); Viari, Alain (A);

Affiliation: GENOME express, Meylan, France. Stephane.Descorps-declere(-atsign-)inrialpes.fr

Journal and publication information

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal: BMC bioinformatics (BMC Bioinformatics), published in England. (Language: eng)

Reference: 2006-; vol 7 (issue ) : pp 450

Dates: Created 2006/10/30; Completed 2006/11/27; Revised 2008/11/20;

PMID: 17038181, status: MEDLINE (last retrieval date: 12/26/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Algorithms
Base Sequence
Chromosome Mapping - methods
Databases, Genetic
Genome - genetics

Information Storage and Retrieval - methods
Molecular Sequence Data
Sequence Analysis, DNA - methods
Software
User-Computer Interface

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