Chemical and Metabolic Pathway Semantic Similarity

Detalhes bibliográficos
Autor(a) principal: Grego, Tiago
Data de Publicação: 2010
Outros Autores: Ferreira, Joao D, Pesquita, Catia, Bastos, Hugo, Vila Viçosa, Diogo, Freire, João, Couto, Francisco M
Tipo de documento: Relatório
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/14249
Resumo: Reviewed by André Falcão
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spelling Chemical and Metabolic Pathway Semantic SimilaritywebtoolMetabolic pathwaySemantic similarityChemical compoundReviewed by André FalcãoBackground: 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.Work supported by FCT’s Multiannual Funding Programme and PhD grants SFRH/BD/36015/2007, SFRH/BD/42481/2007 and SFRH/BD/48035/2008.Repositório da Universidade de LisboaGrego, TiagoFerreira, Joao DPesquita, CatiaBastos, HugoVila Viçosa, DiogoFreire, JoãoCouto, Francisco M2010-03-05T17:28:57Z2010-03-05T17:28:57Z2010-03-05info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/reportapplication/pdfhttp://hdl.handle.net/10451/14249enginfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T15:59:56Zoai:repositorio.ul.pt:10451/14249Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T21:36:04.148531Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Chemical and Metabolic Pathway Semantic Similarity
title Chemical and Metabolic Pathway Semantic Similarity
spellingShingle Chemical and Metabolic Pathway Semantic Similarity
Grego, Tiago
webtool
Metabolic pathway
Semantic similarity
Chemical compound
title_short Chemical and Metabolic Pathway Semantic Similarity
title_full Chemical and Metabolic Pathway Semantic Similarity
title_fullStr Chemical and Metabolic Pathway Semantic Similarity
title_full_unstemmed Chemical and Metabolic Pathway Semantic Similarity
title_sort Chemical and Metabolic Pathway Semantic Similarity
author Grego, Tiago
author_facet Grego, Tiago
Ferreira, Joao D
Pesquita, Catia
Bastos, Hugo
Vila Viçosa, Diogo
Freire, João
Couto, Francisco M
author_role author
author2 Ferreira, Joao D
Pesquita, Catia
Bastos, Hugo
Vila Viçosa, Diogo
Freire, João
Couto, Francisco M
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Grego, Tiago
Ferreira, Joao D
Pesquita, Catia
Bastos, Hugo
Vila Viçosa, Diogo
Freire, João
Couto, Francisco M
dc.subject.por.fl_str_mv webtool
Metabolic pathway
Semantic similarity
Chemical compound
topic webtool
Metabolic pathway
Semantic similarity
Chemical compound
description Reviewed by André Falcão
publishDate 2010
dc.date.none.fl_str_mv 2010-03-05T17:28:57Z
2010-03-05T17:28:57Z
2010-03-05
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/report
format report
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/14249
url http://hdl.handle.net/10451/14249
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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