Semantic similarity in biomedical ontologies.

In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degre...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Catia Pesquita, Daniel Faria, André O Falcão, Phillip Lord, Francisco M Couto
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/84a7f00e12144713b8e4373bca187744
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:84a7f00e12144713b8e4373bca187744
record_format	dspace
spelling	oai:doaj.org-article:84a7f00e12144713b8e4373bca1877442021-11-25T05:42:16ZSemantic similarity in biomedical ontologies.1553-734X1553-735810.1371/journal.pcbi.1000443https://doaj.org/article/84a7f00e12144713b8e4373bca1877442009-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19649320/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies.Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research.Catia PesquitaDaniel FariaAndré O FalcãoPhillip LordFrancisco M CoutoPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 7, p e1000443 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Catia Pesquita Daniel Faria André O Falcão Phillip Lord Francisco M Couto Semantic similarity in biomedical ontologies.
description	In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies.Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research.
format	article
author	Catia Pesquita Daniel Faria André O Falcão Phillip Lord Francisco M Couto
author_facet	Catia Pesquita Daniel Faria André O Falcão Phillip Lord Francisco M Couto
author_sort	Catia Pesquita
title	Semantic similarity in biomedical ontologies.
title_short	Semantic similarity in biomedical ontologies.
title_full	Semantic similarity in biomedical ontologies.
title_fullStr	Semantic similarity in biomedical ontologies.
title_full_unstemmed	Semantic similarity in biomedical ontologies.
title_sort	semantic similarity in biomedical ontologies.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/84a7f00e12144713b8e4373bca187744
work_keys_str_mv	AT catiapesquita semanticsimilarityinbiomedicalontologies AT danielfaria semanticsimilarityinbiomedicalontologies AT andreofalcao semanticsimilarityinbiomedicalontologies AT philliplord semanticsimilarityinbiomedicalontologies AT franciscomcouto semanticsimilarityinbiomedicalontologies
_version_	1718414527161171968

Semantic similarity in biomedical ontologies.

Ejemplares similares