Publicação
Development of a tool for partial automated annotation of metabolic reactions
| Resumo: | Metabolic network reconstructions provide the mathematical in-silico frame work for the study of metabolism through the simulation of generic or specific metabolic pathways. Polyphenols are niche dietary compounds with a growing field of interest in the scientific community. Modelling with these compounds is a step for ward in the completion of metabolic reconstructions. As polyphenols are metabolized by both the gut microbiome and the human host, it is essential to understand the organism-specific metabolic mechanism behind their degradation. Since information is spread out through several information sources and their metabolism is highly complex, it is extremely challenging and time-consuming to manually annotate their metabolism. The focus of the work here developed was thus the creation of a tool that could speed up the data collection process for posterior manual curation, with a focus on the addition of polyphenol metabolism into the largest and most comprehensive reconstruction of human metabolism, ”Recon”. This resulted in the creation of the Database Reaction Automatic eXtraction (DRAX) tool, a biological database web scraper. DRAX was initially targeted at polyphenols but it also allows the collection of reactions for other metabolites and drugs. DRAX allows the comprehensive extraction of metabolite reactions through metabolic pathway-based iterative web scraping. It will provide researchers with a starting point for metabolism reconstruction, allowing a more efficient addition of novel metabolic pathways. |
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| Autores principais: | Queirós, Pedro Miguel Teixeira |
| Assunto: | Ciências Naturais::Ciências Biológicas |
| Ano: | 2018 |
| 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: | Metabolic network reconstructions provide the mathematical in-silico frame work for the study of metabolism through the simulation of generic or specific metabolic pathways. Polyphenols are niche dietary compounds with a growing field of interest in the scientific community. Modelling with these compounds is a step for ward in the completion of metabolic reconstructions. As polyphenols are metabolized by both the gut microbiome and the human host, it is essential to understand the organism-specific metabolic mechanism behind their degradation. Since information is spread out through several information sources and their metabolism is highly complex, it is extremely challenging and time-consuming to manually annotate their metabolism. The focus of the work here developed was thus the creation of a tool that could speed up the data collection process for posterior manual curation, with a focus on the addition of polyphenol metabolism into the largest and most comprehensive reconstruction of human metabolism, ”Recon”. This resulted in the creation of the Database Reaction Automatic eXtraction (DRAX) tool, a biological database web scraper. DRAX was initially targeted at polyphenols but it also allows the collection of reactions for other metabolites and drugs. DRAX allows the comprehensive extraction of metabolite reactions through metabolic pathway-based iterative web scraping. It will provide researchers with a starting point for metabolism reconstruction, allowing a more efficient addition of novel metabolic pathways. |
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