Conference Paper

Fact and Task Oriented System for Genome Assembly and Annotation.

DOI: 10.1007/11532323_32 In proceeding of: Proceedings of the 2005 Brazilian conference on Advances in Bioinformatics and Computational Biology
Source: DBLP

ABSTRACT We present a preliminary description and results of a system to help the curation of genome assembly and annotation. Standard
tools are used for these tasks, and our methodology focuses on user guidance, data visualization and integration, and data
browsing aspects.

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    ABSTRACT: Bioinformatics activities are growing all over the world, following a proliferation of data and tools. This brings new challenges, such as how to understand and organize these resources, how to exchange and reuse successful experimental procedures (tools and data), and how to provide interoperability among data and tools across different sites, and used for users with distinct profiles. This thesis proposes a computational infrastructure to solve these problems. The infrastructure allows to design, reuse, annotate, validate, share and document bioinformatics experiments. Scientific workflows are the mechanisms used to represent these experiments. Combining research on databases, scientific workflows, artificial intelligence and semantic Web, the infrastructure takes advantage of ontologies to support the specification and annotation of bioinformatics workflows and, to serve as basis for traceability mechanisms. Moreover, it uses artificial intelligence planning techniques to support automatic, iterative and supervised composition of tasks to satisfy the needs of the different kinds of user. The data integration and interoperability aspects are solved combining the use of ontologies, structure mapping and interface matching algorithms. The infrastructure was implemented in a prototype and validated on real bioinformatics data.
    08/2007, Degree: PhD in Computer Science, Supervisor: João Carlos Setubal, Claudia Bauzer Medeiros

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