Publication: Arquitectura de un sistema multi-agente para el soporte de la anotación funcional
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2016-06-30
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Universidad Complutense de Madrid
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Abstract
Predecir la función biológica de secuencias de Ácido Desoxirribonucleico (ADN) es unos de los mayores desafíos a los que se enfrenta la Bioinformática. Esta tarea se denomina anotación funcional y es un proceso complejo, laborioso y que requiere mucho tiempo. Dado su impacto en investigaciones y anotaciones futuras, la anotación debe ser lo más able y precisa posible. Idealmente, las secuencias deberían ser estudiadas y anotadas manualmente por un experto, garantizando así resultados precisos y de calidad. Sin embargo, la anotación manual solo es factible para pequeños conjuntos de datos o genomas de referencia. Con la llegada de las nuevas tecnologías de secuenciación, el volumen de datos ha crecido signi cativamente, haciendo aún más crítica la necesidad de implementaciones automáticas del proceso. Por su parte, la anotación automática es capaz de manejar grandes cantidades de datos y producir un análisis consistente. Otra ventaja de esta aproximación es su rapidez y bajo coste en relación a la manual. Sin embargo, sus resultados son menos precisos que los manuales y, en general, deben ser revisados ( curados ) por un experto. Aunque los procesos colaborativos de la anotación en comunidad pueden ser utilizados para reducir este cuello de botella, los esfuerzos en esta línea no han tenido hasta ahora el éxito esperado. Además, el problema de la anotación, como muchos otros en el dominio de la Bioinformática, abarca información heterogénea, distribuida y en constante evolución. Una posible aproximación para superar estos problemas consiste en cambiar el foco del proceso de los expertos individuales a su comunidad, y diseñar las herramientas de manera que faciliten la gestión del conocimiento y los recursos. Este trabajo adopta esta línea y propone MASSA (Multi-Agent System to Support functional Annotation), una arquitectura de Sistema Multi-Agente (SMA) para Soportar la Anotación funcional...
Predicting the biological function of Deoxyribonucleic Acid (DNA) sequences is one of the many challenges faced by Bioinformatics. This task is called functional annotation, and it is a complex, labor-intensive, and time-consuming process. This annotation has to be as accurate and reliable as possible given its impact in further researches and annotations. In order to guarantee a high-quality outcome, each sequence should be manually studied and annotated by an expert. Although desirable, the manual annotation is only feasible for small datasets or reference genomes. As the volume of genomic data has been increasing, specially after the advent of Next Generation Sequencing techniques, automatic implementations of this process are a necessity. The automatic annotation can handle a huge amount of data and produce consistent analyses. Besides, it is faster and less expensive than the manual approach. However, its outcome is less precise than the one predicted manually and often has to be curated by an expert. Although collaborative processes of community annotation could address this expert bottleneck in automatic annotation, these e orts have failed until now. Moreover, the annotation problem, as many others in this domain, has to deal with heterogeneous information that is distributed and constantly evolving. A possible way to overcome these hurdles is with a shift in the focus of the process from individual experts to communities, and with a design of tools that facilitates the management of knowledge and resources. This work follows this approach proposing MASSA, an architecture for a Multi-Agent System (MAS) to Support functional Annotation...
Predicting the biological function of Deoxyribonucleic Acid (DNA) sequences is one of the many challenges faced by Bioinformatics. This task is called functional annotation, and it is a complex, labor-intensive, and time-consuming process. This annotation has to be as accurate and reliable as possible given its impact in further researches and annotations. In order to guarantee a high-quality outcome, each sequence should be manually studied and annotated by an expert. Although desirable, the manual annotation is only feasible for small datasets or reference genomes. As the volume of genomic data has been increasing, specially after the advent of Next Generation Sequencing techniques, automatic implementations of this process are a necessity. The automatic annotation can handle a huge amount of data and produce consistent analyses. Besides, it is faster and less expensive than the manual approach. However, its outcome is less precise than the one predicted manually and often has to be curated by an expert. Although collaborative processes of community annotation could address this expert bottleneck in automatic annotation, these e orts have failed until now. Moreover, the annotation problem, as many others in this domain, has to deal with heterogeneous information that is distributed and constantly evolving. A possible way to overcome these hurdles is with a shift in the focus of the process from individual experts to communities, and with a design of tools that facilitates the management of knowledge and resources. This work follows this approach proposing MASSA, an architecture for a Multi-Agent System (MAS) to Support functional Annotation...
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Tesis inédita de la Universidad Complutense de Madrid, Facultad de Informática, Departamento de Ingeniería del Software e Inteligencia Artificial, leída el 23-11-2015