Publicação

Chemical and Metabolic Pathway Semantic Similarity

Detalhes bibliográficos
Resumo:	Background: Similarity measures for the comparison of metabolic pathways can provide a better understanding of evolutionary relationships among species or strains and have an important biotechnological value for the pharmaceutical industry. Semantic similarity applied to enzymes has been used; here we show an approach using metabolites. While there is a number of methods to compare and align metabolic pathways based on metabolites, they are usually based only on their structural information neglecting their biological information. Results: In this work we present an alternative approach for measuring the semantic similarity between metabolic pathways by comparing their metabolites. This comparison is based on the Chemical Entities of Biological Interest ontology, and can be useful in toxicology and drug discovery for assessment of biological activity of chemical compounds. We implemented a software capable of measuring the similarity between metabolic pathways present in the Kyoto Encyclopedia of Genes and Genomes database and a preliminary analysis shows the effectiveness of the proposed approach. Conclusions: We have shown that semantic similarity can be applied to pathways whose chemical compounds are annotated in the Chemical Entities of Biological Interest ontology. This work resulted in the creation of a software, CMPSim, accessible as a web-tool at http://xldb.di.fc.ul.pt/biotools/cmpsim/. It can be used to obtain similarity measures between chemical compounds and metabolic pathways.
Autores principais:	Grego, Tiago
Outros Autores:	Ferreira, Joao D; Pesquita, Catia; Bastos, Hugo; Vila Viçosa, Diogo; Freire, João; Couto, Francisco M
Assunto:	webtool Metabolic pathway Semantic similarity Chemical compound
Ano:	2010
País:	Portugal
Tipo de documento:	relatório
Tipo de acesso:	acesso aberto
Instituição associada:	Universidade de Lisboa
Idioma:	inglês
Origem:	Repositório da Universidade de Lisboa

Descrição
Resumo:	Background: Similarity measures for the comparison of metabolic pathways can provide a better understanding of evolutionary relationships among species or strains and have an important biotechnological value for the pharmaceutical industry. Semantic similarity applied to enzymes has been used; here we show an approach using metabolites. While there is a number of methods to compare and align metabolic pathways based on metabolites, they are usually based only on their structural information neglecting their biological information. Results: In this work we present an alternative approach for measuring the semantic similarity between metabolic pathways by comparing their metabolites. This comparison is based on the Chemical Entities of Biological Interest ontology, and can be useful in toxicology and drug discovery for assessment of biological activity of chemical compounds. We implemented a software capable of measuring the similarity between metabolic pathways present in the Kyoto Encyclopedia of Genes and Genomes database and a preliminary analysis shows the effectiveness of the proposed approach. Conclusions: We have shown that semantic similarity can be applied to pathways whose chemical compounds are annotated in the Chemical Entities of Biological Interest ontology. This work resulted in the creation of a software, CMPSim, accessible as a web-tool at http://xldb.di.fc.ul.pt/biotools/cmpsim/. It can be used to obtain similarity measures between chemical compounds and metabolic pathways.