Publicação
Chemical and Metabolic Pathway Semantic Similarity
| dc.contributor.author | Grego, Tiago | por |
| dc.contributor.author | Ferreira, Joao D | por |
| dc.contributor.author | Pesquita, Catia | por |
| dc.contributor.author | Bastos, Hugo | por |
| dc.contributor.author | Vila Viçosa, Diogo | por |
| dc.contributor.author | Freire, João | por |
| dc.contributor.author | Couto, Francisco M | por |
| dc.date.accessioned | 2010-03-05T17:28:57Z | por |
| dc.date.accessioned | 2014-11-14T16:24:12Z | |
| dc.date.available | 2010-03-05T17:28:57Z | por |
| dc.date.available | 2014-11-14T16:24:12Z | |
| dc.date.issued | 2010-03-05T17:28:57Z | por |
| dc.description | Reviewed by André Falcão | por |
| dc.description.abstract | 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. | por |
| dc.description.sponsorship | Work supported by FCT’s Multiannual Funding Programme and PhD grants SFRH/BD/36015/2007, SFRH/BD/42481/2007 and SFRH/BD/48035/2008. | por |
| dc.identifier.uri | http://hdl.handle.net/10451/14249 | por |
| dc.identifier.uri | http://repositorio.ul.pt/handle/10455/3335 | por |
| dc.language.iso | eng | por |
| dc.relation.ispartofseries | 2010;1 | por |
| dc.subject | webtool | por |
| dc.subject | Metabolic pathway | por |
| dc.subject | Semantic similarity | por |
| dc.subject | Chemical compound | por |
| dc.title | Chemical and Metabolic Pathway Semantic Similarity | por |
| dc.type | report | |
| dspace.entity.type | Publication | |
| rcaap.rights | openAccess | por |
| rcaap.type | report | por |