LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely avail...

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Detalhes bibliográficos
Autores: Cañada, Andres, Capella-Gutierrez, Salvador, Rabal, Obdulia, Oyarzabal, Julen, Valencia, Alfonso|||0000-0002-8937-6789, Krallinger, Martin
Formato: artículo
Fecha de publicación:2017
País:España
Recursos:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/106762
Acesso em linha:https://hdl.handle.net/2117/106762
https://dx.doi.org/10.1093/nar/gkx462
Access Level:acceso abierto
Palavra-chave:Text Mining
Proteins--Analysis
Text mining
Literature Mining for Toxicology
Proteïnes--Investigació
Mineria de dades
Àrees temàtiques de la UPC::Enginyeria biomèdica
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spelling LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genesCañada, AndresCapella-Gutierrez, SalvadorRabal, ObduliaOyarzabal, JulenValencia, Alfonso|||0000-0002-8937-6789Krallinger, MartinText MiningProteins--AnalysisText miningLiterature Mining for ToxicologyProteïnes--InvestigacióMineria de dadesÀrees temàtiques de la UPC::Enginyeria biomèdicaA considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely available chemical text-mining/search engine technologies are currently accessible. Here we present LimTox (Literature Mining for Toxicology), a web-based online biomedical search tool with special focus on adverse hepatobiliary reactions. It integrates a range of text mining, named entity recognition and information extraction components. LimTox relies on machine-learning, rule-based, pattern-based and term lookup strategies. This system processes scientific abstracts, a set of full text articles and medical agency assessment reports. Although the main focus of LimTox is on adverse liver events, it enables also basic searches for other organ level toxicity associations (nephrotoxicity, cardiotoxicity, thyrotoxicity and phospholipidosis). This tool supports specialized search queries for: chemical compounds/drugs, genes (with additional emphasis on key enzymes in drug metabolism, namely P450 cytochromes—CYPs) and biochemical liver markers. The LimTox website is free and open to all users and there is no login requirement. LimTox can be accessed at: http://limtox.bioinfo.cnio.eseTOX project [IMI-115002]; European Commission H2020 project OpenMinted [654021]; Plan de Impulso de las Tecnologías del Lenguaje de la Agenda Digital (PITL) of the Secretary of State of Telecommunications of the Spanish Ministry of Energy, Tourism and the Digital Agenda; ISCIII and ERDF [PT13/0001/00]. Funding for open access charge: European Commission H2020 project Open-Minted [654021].Peer ReviewedOxford University Press20172017-05-2220172017-07-24journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/106762https://dx.doi.org/10.1093/nar/gkx46228531339reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengEuropean Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 654021 Open Mining INfrastructure for TExt and DataEuropean Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 115002 Integrating bioinformatics and chemoinformatics approaches for the development of expert systems allowing the in silico prediction of toxicitiesopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivs 4.0 Spainhttp://creativecommons.org/licenses/by-nc-nd/4.0/es/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/1067622026-05-27T15:37:01Z
dc.title.none.fl_str_mv LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
title LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
spellingShingle LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
Cañada, Andres
Text Mining
Proteins--Analysis
Text mining
Literature Mining for Toxicology
Proteïnes--Investigació
Mineria de dades
Àrees temàtiques de la UPC::Enginyeria biomèdica
title_short LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
title_full LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
title_fullStr LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
title_full_unstemmed LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
title_sort LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
dc.creator.none.fl_str_mv Cañada, Andres
Capella-Gutierrez, Salvador
Rabal, Obdulia
Oyarzabal, Julen
Valencia, Alfonso|||0000-0002-8937-6789
Krallinger, Martin
author Cañada, Andres
author_facet Cañada, Andres
Capella-Gutierrez, Salvador
Rabal, Obdulia
Oyarzabal, Julen
Valencia, Alfonso|||0000-0002-8937-6789
Krallinger, Martin
author_role author
author2 Capella-Gutierrez, Salvador
Rabal, Obdulia
Oyarzabal, Julen
Valencia, Alfonso|||0000-0002-8937-6789
Krallinger, Martin
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Text Mining
Proteins--Analysis
Text mining
Literature Mining for Toxicology
Proteïnes--Investigació
Mineria de dades
Àrees temàtiques de la UPC::Enginyeria biomèdica
topic Text Mining
Proteins--Analysis
Text mining
Literature Mining for Toxicology
Proteïnes--Investigació
Mineria de dades
Àrees temàtiques de la UPC::Enginyeria biomèdica
description A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely available chemical text-mining/search engine technologies are currently accessible. Here we present LimTox (Literature Mining for Toxicology), a web-based online biomedical search tool with special focus on adverse hepatobiliary reactions. It integrates a range of text mining, named entity recognition and information extraction components. LimTox relies on machine-learning, rule-based, pattern-based and term lookup strategies. This system processes scientific abstracts, a set of full text articles and medical agency assessment reports. Although the main focus of LimTox is on adverse liver events, it enables also basic searches for other organ level toxicity associations (nephrotoxicity, cardiotoxicity, thyrotoxicity and phospholipidosis). This tool supports specialized search queries for: chemical compounds/drugs, genes (with additional emphasis on key enzymes in drug metabolism, namely P450 cytochromes—CYPs) and biochemical liver markers. The LimTox website is free and open to all users and there is no login requirement. LimTox can be accessed at: http://limtox.bioinfo.cnio.es
publishDate 2017
dc.date.none.fl_str_mv 2017
2017-05-22
2017
2017-07-24
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/106762
https://dx.doi.org/10.1093/nar/gkx462
28531339
url https://hdl.handle.net/2117/106762
https://dx.doi.org/10.1093/nar/gkx462
identifier_str_mv 28531339
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv European Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 654021 Open Mining INfrastructure for TExt and Data
European Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 115002 Integrating bioinformatics and chemoinformatics approaches for the development of expert systems allowing the in silico prediction of toxicities
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 4.0 Spain
http://creativecommons.org/licenses/by-nc-nd/4.0/es/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 4.0 Spain
http://creativecommons.org/licenses/by-nc-nd/4.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869404600500486144
score 15,300724

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