Biblio-MetReS: A bibliometric network reconstruction application and server

Background: Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools al...

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Detalles Bibliográficos
Autores: Usié Chimenos, Anabel, Karathia, Hiren, Teixidó Torrelles, Ivan, Valls Marsal, Joan, Faus i Torà, Xavier, Alves, Rui, Solsona Tehàs, Francesc
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2011
País:España
Institución:Universitat de Lleida (UdL)
Repositorio:Repositori Obert UdL
OAI Identifier:oai:repositori.udl.cat:10459.1/45586
Acceso en línea:https://doi.org/10.1186/1471-2105-12-387
http://hdl.handle.net/10459.1/45586
Access Level:acceso abierto
Palabra clave:Mineria de dades
Bases de dades
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spelling Biblio-MetReS: A bibliometric network reconstruction application and serverUsié Chimenos, AnabelKarathia, HirenTeixidó Torrelles, IvanValls Marsal, JoanFaus i Torà, XavierAlves, RuiSolsona Tehàs, FrancescMineria de dadesBases de dadesBackground: Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools allow expert users to elaborate and analyze the full content of a corpus of scientific documents. However, to our knowledge, no user friendly tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available. Results: This article presents such a tool, Biblio-MetReS, and compares its functioning and results to those of other user-friendly applications (iHOP, STRING) that are widely used. Under similar conditions, Biblio-MetReS creates networks that are comparable to those of other user friendly tools. Furthermore, analysis of full text documents provides more complete reconstructions than those that result from using only the abstract of the document. Conclusions: Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio- MetReS is an application that can be downloaded from http://metres.udl.cat/. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents.RA was partially supported by the Ministerio de Ciencia e Innovación (MICINN, Spain through grants BFU2007-62772/BMC and BFU2010-17704), and by the FLAD foundation. FS was partially funded by the MICINN, with grants TIN2008-05913 and CSD-2007-00050. The authors are members of the research groups 2009SGR809 and 2009SGR145, funded by the "Generalitat de Catalunya". HK is funded by a Generalitat de Catalunya (AGAUR) Ph. D. fellowship. AU is funded by a Universitat de Lleida Ph. D. fellowship. We thank David Terés for assistance in programming parts of the application. We also thank two anonymous reviewers for suggestion and criticism that made this work better.BioMed Central2011info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://doi.org/10.1186/1471-2105-12-387http://hdl.handle.net/10459.1/45586reponame:Repositori Obert UdL instname:Universitat de Lleida (UdL)InglésMIECI/PN2004-2007/BFU2007-62772/BMCMICINN/PN2008-2011/BFU2010-17704MICINN/PN2008-2011/TIN2008-05913MIECI/PN2004-2007/CSD-2007-00050Reproducció del document publicat a https://doi.org/10.1186/1471-2105-12-387BMC Bioinformatics, 2011, vol. 12, núm. 387, p. 1-10cc-by, (c) Usié et al., 2011info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/2.0/es/deed.caoai:repositori.udl.cat:10459.1/455862026-06-24T12:42:17Z
dc.title.none.fl_str_mv Biblio-MetReS: A bibliometric network reconstruction application and server
title Biblio-MetReS: A bibliometric network reconstruction application and server
spellingShingle Biblio-MetReS: A bibliometric network reconstruction application and server
Usié Chimenos, Anabel
Mineria de dades
Bases de dades
title_short Biblio-MetReS: A bibliometric network reconstruction application and server
title_full Biblio-MetReS: A bibliometric network reconstruction application and server
title_fullStr Biblio-MetReS: A bibliometric network reconstruction application and server
title_full_unstemmed Biblio-MetReS: A bibliometric network reconstruction application and server
title_sort Biblio-MetReS: A bibliometric network reconstruction application and server
dc.creator.none.fl_str_mv Usié Chimenos, Anabel
Karathia, Hiren
Teixidó Torrelles, Ivan
Valls Marsal, Joan
Faus i Torà, Xavier
Alves, Rui
Solsona Tehàs, Francesc
author Usié Chimenos, Anabel
author_facet Usié Chimenos, Anabel
Karathia, Hiren
Teixidó Torrelles, Ivan
Valls Marsal, Joan
Faus i Torà, Xavier
Alves, Rui
Solsona Tehàs, Francesc
author_role author
author2 Karathia, Hiren
Teixidó Torrelles, Ivan
Valls Marsal, Joan
Faus i Torà, Xavier
Alves, Rui
Solsona Tehàs, Francesc
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Mineria de dades
Bases de dades
topic Mineria de dades
Bases de dades
description Background: Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools allow expert users to elaborate and analyze the full content of a corpus of scientific documents. However, to our knowledge, no user friendly tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available. Results: This article presents such a tool, Biblio-MetReS, and compares its functioning and results to those of other user-friendly applications (iHOP, STRING) that are widely used. Under similar conditions, Biblio-MetReS creates networks that are comparable to those of other user friendly tools. Furthermore, analysis of full text documents provides more complete reconstructions than those that result from using only the abstract of the document. Conclusions: Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio- MetReS is an application that can be downloaded from http://metres.udl.cat/. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents.
publishDate 2011
dc.date.none.fl_str_mv 2011
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.1186/1471-2105-12-387
http://hdl.handle.net/10459.1/45586
url https://doi.org/10.1186/1471-2105-12-387
http://hdl.handle.net/10459.1/45586
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv MIECI/PN2004-2007/BFU2007-62772/BMC
MICINN/PN2008-2011/BFU2010-17704
MICINN/PN2008-2011/TIN2008-05913
MIECI/PN2004-2007/CSD-2007-00050
Reproducció del document publicat a https://doi.org/10.1186/1471-2105-12-387
BMC Bioinformatics, 2011, vol. 12, núm. 387, p. 1-10
dc.rights.none.fl_str_mv cc-by, (c) Usié et al., 2011
info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/2.0/es/deed.ca
rights_invalid_str_mv cc-by, (c) Usié et al., 2011
http://creativecommons.org/licenses/by/2.0/es/deed.ca
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositori Obert UdL
instname:Universitat de Lleida (UdL)
instname_str Universitat de Lleida (UdL)
reponame_str Repositori Obert UdL
collection Repositori Obert UdL
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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