Automatic assignment of prokaryotic genes to functional categories using literature profiling.

Detalhes bibliográficos
Autor(a) principal: Torrieri, Raul
Data de Publicação: 2012
Outros Autores: Oliveira, Francislon Silva de, Oliveira, Guilherme Corrêa de, Coimbra, Roney Santos
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/7868
Resumo: Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, Brasil
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spelling Torrieri, RaulOliveira, Francislon Silva deOliveira, Guilherme Corrêa deCoimbra, Roney Santos2014-07-04T14:29:41Z2014-07-04T14:29:41Z2012TORRIERI, Raul et al. Automatic assignment of prokaryotic genes to functional categories using literature profiling. Plos One. 2012, vol.7, pp. e474361932-6203https://www.arca.fiocruz.br/handle/icict/786810.1371/journal.pone.0047436engPublic Library of ScienceAutomatic assignment of prokaryotic genes to functional categories using literature profiling.info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, BrasilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, BrasilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, BrasilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, Brasil/Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Grupo de Biologia Genômica e Computacional. Belo Horizonte, MG, BrasilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, Brasil/Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Grupo de Biologia Genômica e Computacional. Belo Horizonte, MG, BrasilIn the last years, there was an exponential increase in the number of publicly available genomes. Once finished, most genome projects lack financial support to review annotations. A few of these gene annotations are based on a combination of bioinformatics evidence, however, in most cases, annotations are based solely on sequence similarity to a previously known gene, which was most probably annotated in the same way. As a result, a large number of predicted genes remain unassigned to any functional category despite the fact that there is enough evidence in the literature to predict their function. We developed a classifier trained with term-frequency vectors automatically disclosed from text corpora of an ensemble of genes representative of each functional category of the J. Craig Venter Institute Comprehensive Microbial Resource (JCVI-CMR) ontology. The classifier achieved up to 84% precision with 68% recall (for confidence≥0.4), F-measure 0.76 (recall and precision equally weighted) in an independent set of 2,220 genes, from 13 bacterial species, previously classified by JCVI-CMR into unambiguous categories of its ontology. Finally, the classifier assigned (confidence≥0.7) to functional categories a total of 5,235 out of the ~24 thousand genes previously in categories “Unknown function” or “Unclassified” for which there is literature in MEDLINE. Two biologists reviewed the literature of 100 of these genes, randomly picket, and assigned them to the same functional categories predicted by the automatic classifier. Our results confirmed the hypothesis that it is possible to confidently assign genes of a real world repository to functional categories, based exclusively on the automatic profiling of its associated literature.Gene ontologiesGene ontology annotationsGene ontology annotationsGenomic databasesMetabolic processesOntologiesProkaryotic cellsinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINALAutomatic assignment of prokaryotic genes to functional categories using literature profiling.pdfAutomatic assignment of prokaryotic genes to functional categories using literature profiling.pdfapplication/pdf1400414https://www.arca.fiocruz.br/bitstream/icict/7868/1/Automatic%20assignment%20of%20prokaryotic%20genes%20to%20functional%20categories%20using%20literature%20profiling.pdf2cd0fca991716d620965797b9e8d55f4MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81914https://www.arca.fiocruz.br/bitstream/icict/7868/2/license.txt7d48279ffeed55da8dfe2f8e81f3b81fMD52TEXTAutomatic assignment of prokaryotic genes to functional categories using literature profiling.pdf.txtAutomatic assignment of prokaryotic genes to functional categories using literature profiling.pdf.txtExtracted texttext/plain7https://www.arca.fiocruz.br/bitstream/icict/7868/3/Automatic%20assignment%20of%20prokaryotic%20genes%20to%20functional%20categories%20using%20literature%20profiling.pdf.txt212b0306580d4f0044d18f9a3edcc832MD53icict/78682018-04-06 08:43:56.975oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352018-04-06T11:43:56Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv Automatic assignment of prokaryotic genes to functional categories using literature profiling.
title Automatic assignment of prokaryotic genes to functional categories using literature profiling.
spellingShingle Automatic assignment of prokaryotic genes to functional categories using literature profiling.
Torrieri, Raul
Gene ontologies
Gene ontology annotations
Gene ontology annotations
Genomic databases
Metabolic processes
Ontologies
Prokaryotic cells
title_short Automatic assignment of prokaryotic genes to functional categories using literature profiling.
title_full Automatic assignment of prokaryotic genes to functional categories using literature profiling.
title_fullStr Automatic assignment of prokaryotic genes to functional categories using literature profiling.
title_full_unstemmed Automatic assignment of prokaryotic genes to functional categories using literature profiling.
title_sort Automatic assignment of prokaryotic genes to functional categories using literature profiling.
author Torrieri, Raul
author_facet Torrieri, Raul
Oliveira, Francislon Silva de
Oliveira, Guilherme Corrêa de
Coimbra, Roney Santos
author_role author
author2 Oliveira, Francislon Silva de
Oliveira, Guilherme Corrêa de
Coimbra, Roney Santos
author2_role author
author
author
dc.contributor.author.fl_str_mv Torrieri, Raul
Oliveira, Francislon Silva de
Oliveira, Guilherme Corrêa de
Coimbra, Roney Santos
dc.subject.en.pt_BR.fl_str_mv Gene ontologies
Gene ontology annotations
Gene ontology annotations
Genomic databases
Metabolic processes
Ontologies
Prokaryotic cells
topic Gene ontologies
Gene ontology annotations
Gene ontology annotations
Genomic databases
Metabolic processes
Ontologies
Prokaryotic cells
description Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, Brasil
publishDate 2012
dc.date.issued.fl_str_mv 2012
dc.date.accessioned.fl_str_mv 2014-07-04T14:29:41Z
dc.date.available.fl_str_mv 2014-07-04T14:29:41Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv TORRIERI, Raul et al. Automatic assignment of prokaryotic genes to functional categories using literature profiling. Plos One. 2012, vol.7, pp. e47436
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/7868
dc.identifier.issn.none.fl_str_mv 1932-6203
dc.identifier.doi.none.fl_str_mv 10.1371/journal.pone.0047436
identifier_str_mv TORRIERI, Raul et al. Automatic assignment of prokaryotic genes to functional categories using literature profiling. Plos One. 2012, vol.7, pp. e47436
1932-6203
10.1371/journal.pone.0047436
url https://www.arca.fiocruz.br/handle/icict/7868
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.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
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instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
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