Publicação
Development of a data integration pipeline for human metabolic models and databases
| Resumo: | Systems Biology aims to integrate experimental and computational approaches with the purpose of explaining and predicting the organisms' behavior. The development of mathematical models in silico gives us a better in-depth knowledge of their biological mechanism. Bioinformatics tools enabled the integration of a large amount of complex biological data into computer models, but also capable to perform computational simulations with these models, that can predict the organisms' phenotypic behavior in different conditions. Up to date, genome-scale metabolic models (GSMMs) include several metabolic components of an organism. These are related to the metabolic capabilities encoded in the genome. In recent years, multiple GSMMs have been built by several research groups. With the increase in number, of these models, important issues regarding the standardization have arisen, a common problem is the different nomenclatures used by each of the research groups. In this work, the major focus is to address these problems, specifically for the human GSSMs. Therefore, the two most recent human GSMMs were selected to go through a data integration process. Integration strategies of these models most important entities (metabolites and reactions), were defined based on an exhaustive analysis of the models. The broad knowledge of their attributes enabled the creation of effective and efficient integration methods, supported by a core database developed in the local research group. The final result of this work, is a unified repository of the human metabolism. It contains all the metabolites and reactions that were automatically integrated along with some manual curation. |
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| Autores principais: | Barbosa, Susana Raquel da Silva |
| Assunto: | Engenharia e Tecnologia::Engenharia Eletrotécnica, Eletrónica e Informática |
| Ano: | 2016 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | Systems Biology aims to integrate experimental and computational approaches with the purpose of explaining and predicting the organisms' behavior. The development of mathematical models in silico gives us a better in-depth knowledge of their biological mechanism. Bioinformatics tools enabled the integration of a large amount of complex biological data into computer models, but also capable to perform computational simulations with these models, that can predict the organisms' phenotypic behavior in different conditions. Up to date, genome-scale metabolic models (GSMMs) include several metabolic components of an organism. These are related to the metabolic capabilities encoded in the genome. In recent years, multiple GSMMs have been built by several research groups. With the increase in number, of these models, important issues regarding the standardization have arisen, a common problem is the different nomenclatures used by each of the research groups. In this work, the major focus is to address these problems, specifically for the human GSSMs. Therefore, the two most recent human GSMMs were selected to go through a data integration process. Integration strategies of these models most important entities (metabolites and reactions), were defined based on an exhaustive analysis of the models. The broad knowledge of their attributes enabled the creation of effective and efficient integration methods, supported by a core database developed in the local research group. The final result of this work, is a unified repository of the human metabolism. It contains all the metabolites and reactions that were automatically integrated along with some manual curation. |
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