Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/44741 |
Resumo: | Considerable research efforts are being invested in the development of novel antimicrobial therapies effective against the growing number of multi-drug resistant (MDR) pathogens. Notably, the combination of different agents is increasingly explored as means to exploit and improve individual agent actions while minimising microorganism resistance. Although there are several databases on antimicrobial agents, scientific literature is the primary source of information on experimental antimicrobial combination testing. This work presents a semi-automated database curation workflow that supports the mining of scientific literature and enables the reconstruction of recently documented antimicrobial combinations. Currently, the database contains data on antimicrobial combinations that have been experimentally tested against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Listeria monocytogenes and Candida albicans, which are prominent pathogenic organisms and are well-known for their wide and growing resistance to conventional antimicrobials. Researchers are able to explore the experimental results for a single organism or across organisms. Likewise, researchers may look into indirect network associations and identify new potential combinations to be tested. The database is available without charges. Database URL: http://sing.ei.uvigo.es/antimicrobialCombination/ |
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Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflowCombinatorial antimicrobial therapyAntimicrobial peptidesPathogenic organismsAntimicrobial resistanceDatabase curation workflowScience & TechnologyConsiderable research efforts are being invested in the development of novel antimicrobial therapies effective against the growing number of multi-drug resistant (MDR) pathogens. Notably, the combination of different agents is increasingly explored as means to exploit and improve individual agent actions while minimising microorganism resistance. Although there are several databases on antimicrobial agents, scientific literature is the primary source of information on experimental antimicrobial combination testing. This work presents a semi-automated database curation workflow that supports the mining of scientific literature and enables the reconstruction of recently documented antimicrobial combinations. Currently, the database contains data on antimicrobial combinations that have been experimentally tested against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Listeria monocytogenes and Candida albicans, which are prominent pathogenic organisms and are well-known for their wide and growing resistance to conventional antimicrobials. Researchers are able to explore the experimental results for a single organism or across organisms. Likewise, researchers may look into indirect network associations and identify new potential combinations to be tested. The database is available without charges. Database URL: http://sing.ei.uvigo.es/antimicrobialCombination/This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145FEDER-006684), and support by FCT and the European Community fund FEDER, through the Programme COMPETE, under the scope of the Projects AntiPep PTDC/SAU-SAP/113196/2009 (FCOMP-01-0124-FEDER-016012) and RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462). Authors acknowledge the PhD Grant of Paula Jorge, funded by FCT Ref. SFRH/BD/ 88192/2012, and the PhD grants of Martin Pérez-Pérez and Gael Pe´rez-Rodriguez, funded by the University of Vigo. Finally, this study was partially funded by the [15VI013] Contract-Programme from the University of Vigo and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273). This document reflects only the authors views and the European Union is not liable for any use that may be made of the information contained herein.Oxford University PressUniversidade do MinhoJorge, P.Pérez-Pérez, MartínRodríguez, Gael PérezFdez-Riverola, FlorentinoPereira, Maria OlíviaLourenço, Anália20162016-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/44741engJorge, P.; Pérez-Pérez, Martín; Rodríguez, Gael Pérez; Fdez-Riverola, Florentino; Pereira, Maria Olívia; Lourenço, Anália, Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow. Database - The Journal of Biological Databases and Curation, 2016(baw143), 20161758-04631758-046310.1093/database/baw14328025336http://database.oxfordjournals.org/info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:07:19Zoai:repositorium.sdum.uminho.pt:1822/44741Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:58:13.444163Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow |
title |
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow |
spellingShingle |
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow Jorge, P. Combinatorial antimicrobial therapy Antimicrobial peptides Pathogenic organisms Antimicrobial resistance Database curation workflow Science & Technology |
title_short |
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow |
title_full |
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow |
title_fullStr |
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow |
title_full_unstemmed |
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow |
title_sort |
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow |
author |
Jorge, P. |
author_facet |
Jorge, P. Pérez-Pérez, Martín Rodríguez, Gael Pérez Fdez-Riverola, Florentino Pereira, Maria Olívia Lourenço, Anália |
author_role |
author |
author2 |
Pérez-Pérez, Martín Rodríguez, Gael Pérez Fdez-Riverola, Florentino Pereira, Maria Olívia Lourenço, Anália |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Jorge, P. Pérez-Pérez, Martín Rodríguez, Gael Pérez Fdez-Riverola, Florentino Pereira, Maria Olívia Lourenço, Anália |
dc.subject.por.fl_str_mv |
Combinatorial antimicrobial therapy Antimicrobial peptides Pathogenic organisms Antimicrobial resistance Database curation workflow Science & Technology |
topic |
Combinatorial antimicrobial therapy Antimicrobial peptides Pathogenic organisms Antimicrobial resistance Database curation workflow Science & Technology |
description |
Considerable research efforts are being invested in the development of novel antimicrobial therapies effective against the growing number of multi-drug resistant (MDR) pathogens. Notably, the combination of different agents is increasingly explored as means to exploit and improve individual agent actions while minimising microorganism resistance. Although there are several databases on antimicrobial agents, scientific literature is the primary source of information on experimental antimicrobial combination testing. This work presents a semi-automated database curation workflow that supports the mining of scientific literature and enables the reconstruction of recently documented antimicrobial combinations. Currently, the database contains data on antimicrobial combinations that have been experimentally tested against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Listeria monocytogenes and Candida albicans, which are prominent pathogenic organisms and are well-known for their wide and growing resistance to conventional antimicrobials. Researchers are able to explore the experimental results for a single organism or across organisms. Likewise, researchers may look into indirect network associations and identify new potential combinations to be tested. The database is available without charges. Database URL: http://sing.ei.uvigo.es/antimicrobialCombination/ |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016 2016-01-01T00:00:00Z |
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.uri.fl_str_mv |
http://hdl.handle.net/1822/44741 |
url |
http://hdl.handle.net/1822/44741 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Jorge, P.; Pérez-Pérez, Martín; Rodríguez, Gael Pérez; Fdez-Riverola, Florentino; Pereira, Maria Olívia; Lourenço, Anália, Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow. Database - The Journal of Biological Databases and Curation, 2016(baw143), 2016 1758-0463 1758-0463 10.1093/database/baw143 28025336 http://database.oxfordjournals.org/ |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
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:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799132372381204480 |