PhD Thesis

PhD Thesis

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The development of " omic" technologies and its applications into biological sciences has increased the need for an integrated view of bio-related information. The flood of information as well as the technological availability has made it necessary for researchers to share resources and join efforts more than ever in order to understand the function of genes, proteins and biological systems in general. Integrating biological information has been addressed mainly from a syntactical perspective. However, as we enter into the post-genomic era integration has acquired a meaning more related to the capacity of inference (finding hidden information) and sharebility in large web-based information systems. Ontologies play a central role when addressing both syntactic and semantic aspects of information integration. The purpose of this research has been to investigate how the biological community could develop those highly needed ontologies in a way that ensures both, maintainability and usability. Although the need for ontologies, as well as the benefits of having them, is obvious; it has proven to be difficult for the biological community not only to develop but also to effectively use them. Why? How should they be developed in such a way that they are maintainable and usable by existing and novel information systems? A feasible methodology elucidated from the careful study whilst developing biological ontologies is proposed. Methodological extensions gathered from the acquired experience are also presented. Throughout the chapters of this thesis diverse integrative approaches have also been analysed from different perspectives; a workflow-based solution to the integration of analytical tools was consequently proposed. This made it possible to better understand the need for welldefined semantics in biological information systems as well as the importance of a thoughtful understanding of the relationship between the semantic structure and the syntactic scaffold that should ultimately host the former. The role of communities in the construction of biological ontologies as well as the argumentative structure that takes place during the development and maintenance of them have been extensively studied in this thesis. What is the role of the domain expert when developing ontologies within the biological domain? Different scenarios in which ontologies were developed have been studied in order to answer this question. The relationship between domain experts and knowledge engineers was analyzed during the development of loosely centralised ontologies. As a consequence of those direct experiences developing ontologies a viable use for concept maps supporting collaboration and annotation was anticipated; consequent software developments are also part of this investigation. From this investigation several conclusions have been drawn, one of them with a particular significance is the relevance of collaboration between two asymmetric, yet not antagonist, communities; computer scientists and biologists may work and achieve results in different ways, nevertheless both communities hold valuable information that could be of mutual benefit. Within the context of biological ontologies " Romeo and Juliet" proved to be an apt metaphor that illustrates not only the importance of the collaboration, but also how we may avoid heading towards " A hundred years of solitude" .


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