DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline

Corvi, Javier Omar; McKitrick, Austin; Fernández González, José María; Fuenteslópez, Carla V.; Gelpí Buchaca, Josep Lluís; Ginebra Molins, Maria Pau|||0000-0002-4700-5621; Capella Gutiérrez, Salvador|||0000-0002-0309-604X; Hakimi, Osnat|||0000-0002-8839-4846

DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline

Biomaterials research output has experienced an exponential increase over the last three decades. The majority of research is published in the form of scientific articles and is therefore available as unstructured text, making it a challenging input for computational processing. Computational tools...

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Autores:	Corvi, Javier Omar, McKitrick, Austin, Fernández González, José María, Fuenteslópez, Carla V., Gelpí Buchaca, Josep Lluís, Ginebra Molins, Maria Pau\|\|\|0000-0002-4700-5621, Capella Gutiérrez, Salvador\|\|\|0000-0002-0309-604X, Hakimi, Osnat\|\|\|0000-0002-8839-4846
Tipo de recurso:	artículo
Fecha de publicación:	2023
País:	España
Institución:	Universitat Politècnica de Catalunya (UPC)
Repositorio:	UPCommons. Portal del coneixement obert de la UPC
Idioma:	inglés
OAI Identifier:	oai:upcommons.upc.edu:2117/398001
Acceso en línea:	https://hdl.handle.net/2117/398001 https://dx.doi.org/10.1002/adhm.202300150
Access Level:	acceso abierto
Palabra clave:	Biomedical materials Databases Data mining Materials biomèdics Bases de dades Mineria de dades Àrees temàtiques de la UPC::Enginyeria biomèdica::Biomaterials

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spelling	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipelineCorvi, Javier OmarMcKitrick, AustinFernández González, José MaríaFuenteslópez, Carla V.Gelpí Buchaca, Josep LluísGinebra Molins, Maria Pau\|\|\|0000-0002-4700-5621Capella Gutiérrez, Salvador\|\|\|0000-0002-0309-604XHakimi, Osnat\|\|\|0000-0002-8839-4846Biomedical materialsDatabasesData miningMaterials biomèdicsBases de dadesMineria de dadesÀrees temàtiques de la UPC::Enginyeria biomèdica::BiomaterialsBiomaterials research output has experienced an exponential increase over the last three decades. The majority of research is published in the form of scientific articles and is therefore available as unstructured text, making it a challenging input for computational processing. Computational tools are becoming essential to overcome this information overload. Among them, text mining systems present an attractive option for the automated extraction of information from text documents into structured datasets. This work presents the first automated system for biomaterial related information extraction from the National Library of Medicine's premier bibliographic database (MEDLINE) research abstracts into a searchable database. The system is a text mining pipeline that periodically retrieves abstracts from PubMed and identifies research and clinical studies of biomaterials. Thereafter, the pipeline identifies sixteen concept types of interest in the abstract using the Biomaterials Annotator, a tool for biomaterials Named Entity Recognition (NER). These concepts of interest, along with the abstract and relevant metadata are then deposited in DEBBIE, the Database of Experimental Biomaterials and their Biological Effect. DEBBIE is accessible through a web application that provides keyword searches and displays results in an intuitive and meaningful manner, aiming to facilitate an efficient mapping and organization of biomaterials information.Peer ReviewedJohn Wiley & sons20232023-10-0620232023-12-14journal articlehttp://purl.org/coar/resource_type/c_6501AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/398001https://dx.doi.org/10.1002/adhm.202300150reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3980012026-05-27T15:37:01Z
dc.title.none.fl_str_mv	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline
title	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline
spellingShingle	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline Corvi, Javier Omar Biomedical materials Databases Data mining Materials biomèdics Bases de dades Mineria de dades Àrees temàtiques de la UPC::Enginyeria biomèdica::Biomaterials
title_short	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline
title_full	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline
title_fullStr	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline
title_full_unstemmed	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline
title_sort	DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline
dc.creator.none.fl_str_mv	Corvi, Javier Omar McKitrick, Austin Fernández González, José María Fuenteslópez, Carla V. Gelpí Buchaca, Josep Lluís Ginebra Molins, Maria Pau\|\|\|0000-0002-4700-5621 Capella Gutiérrez, Salvador\|\|\|0000-0002-0309-604X Hakimi, Osnat\|\|\|0000-0002-8839-4846
author	Corvi, Javier Omar
author_facet	Corvi, Javier Omar McKitrick, Austin Fernández González, José María Fuenteslópez, Carla V. Gelpí Buchaca, Josep Lluís Ginebra Molins, Maria Pau\|\|\|0000-0002-4700-5621 Capella Gutiérrez, Salvador\|\|\|0000-0002-0309-604X Hakimi, Osnat\|\|\|0000-0002-8839-4846
author_role	author
author2	McKitrick, Austin Fernández González, José María Fuenteslópez, Carla V. Gelpí Buchaca, Josep Lluís Ginebra Molins, Maria Pau\|\|\|0000-0002-4700-5621 Capella Gutiérrez, Salvador\|\|\|0000-0002-0309-604X Hakimi, Osnat\|\|\|0000-0002-8839-4846
author2_role	author author author author author author author
dc.subject.none.fl_str_mv	Biomedical materials Databases Data mining Materials biomèdics Bases de dades Mineria de dades Àrees temàtiques de la UPC::Enginyeria biomèdica::Biomaterials
topic	Biomedical materials Databases Data mining Materials biomèdics Bases de dades Mineria de dades Àrees temàtiques de la UPC::Enginyeria biomèdica::Biomaterials
description	Biomaterials research output has experienced an exponential increase over the last three decades. The majority of research is published in the form of scientific articles and is therefore available as unstructured text, making it a challenging input for computational processing. Computational tools are becoming essential to overcome this information overload. Among them, text mining systems present an attractive option for the automated extraction of information from text documents into structured datasets. This work presents the first automated system for biomaterial related information extraction from the National Library of Medicine's premier bibliographic database (MEDLINE) research abstracts into a searchable database. The system is a text mining pipeline that periodically retrieves abstracts from PubMed and identifies research and clinical studies of biomaterials. Thereafter, the pipeline identifies sixteen concept types of interest in the abstract using the Biomaterials Annotator, a tool for biomaterials Named Entity Recognition (NER). These concepts of interest, along with the abstract and relevant metadata are then deposited in DEBBIE, the Database of Experimental Biomaterials and their Biological Effect. DEBBIE is accessible through a web application that provides keyword searches and displays results in an intuitive and meaningful manner, aiming to facilitate an efficient mapping and organization of biomaterials information.
publishDate	2023
dc.date.none.fl_str_mv	2023 2023-10-06 2023 2023-12-14
dc.type.none.fl_str_mv	journal article http://purl.org/coar/resource_type/c_6501 AM http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv	info:eu-repo/semantics/article
format	article
dc.identifier.none.fl_str_mv	https://hdl.handle.net/2117/398001 https://dx.doi.org/10.1002/adhm.202300150
url	https://hdl.handle.net/2117/398001 https://dx.doi.org/10.1002/adhm.202300150
dc.language.none.fl_str_mv	Inglés eng
language_invalid_str_mv	Inglés
language	eng
dc.rights.none.fl_str_mv	open access http://purl.org/coar/access_right/c_abf2 Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/
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-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv	openAccess
dc.format.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	John Wiley & sons
publisher.none.fl_str_mv	John Wiley & sons
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
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score	15.300724

DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline

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