BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines

Detalhes bibliográficos
Autor(a) principal: Jácome, Alberto G.
Data de Publicação: 2016
Outros Autores: Fdez-Riverola, Florentino, Lourenço, Anália
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/41302
Resumo: The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef
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spelling BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search enginessearch engine frameworkbiomedical literaturevertical enginetext miningweb applicationScience & TechnologyThe Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsefBackground and Objectives: Text mining and semantic analysis approaches can be applied to the construction of biomedical domain-specific search engines and provide an attractive alternative to create personalized and enhanced search experiences. Therefore, this work introduces the new open-source BIOMedical Search Engine Framework for the fast and lightweight development of domain-specific search engines. The rationale behind this framework is to incorporate core features typically available in search engine frameworks with flexible and extensible technologies to retrieve biomedical documents, annotate meaningful domain concepts, and develop highly customized Web search interfaces. Methods: The BIOMedical Search Engine Framework integrates taggers for major biomedical concepts, such as diseases, drugs, genes, proteins, compounds and organisms, and enables the use of domain-specific controlled vocabulary. Technologies from the Typesafe Reactive Platform, the AngularJS JavaScript framework and the Bootstrap HTML/CSS framework support the customization of the domain-oriented search application. Moreover, the RESTful API of the BIOMedical Search Engine Framework allows the integration of the search engine into existing systems or a complete web interface personalization. Results The construction of the Smart Drug Search is described as proof-of-concept of the BIOMedical Search Engine Framework. This public search engine catalogs scientific literature about antimicrobial resistance, microbial virulence and topics alike. The keyword-based queries of the users are transformed into concepts and search results are presented and ranked accordingly. The semantic graph view portraits all the concepts found in the results and the researcher may look into the relevance of different concepts, the strength of direct relations, and non-trivial, indirect relations. The number of occurrences of the concept shows its importance to the query, and the frequency of concept co-occurrence is indicative of biological relations meaningful to that particular scope of research. Conversely, indirect concept associations, i.e. concepts related by other intermediary concepts, can be useful to integrate information from different studies and look into non-trivial relations. Conclusions The BIOMedical Search Engine Framework supports the development of domain-specific search engines. The key strengths of the framework are modularity and extensibility in terms of software design, the use of open-source consolidated Web technologies, and the ability to integrate any number of biomedical text mining tools and information resources. Currently, the Smart Drug Search keeps over 1,186,000 documents, containing more than 11,854,000 annotations for 77,200 different concepts.This work was partially funded by the [14VI05] ContractProgramme from the University ofVigo and theAgrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa(2012/273).The research leading to these results has also received funding from the European Union Seventh Framework Programme FP7/REGPOT-2012-2013.1 under grant agreement n° 316265,BIOCAPS.This document reflects only the author’s views, and the European Union is not liable for any use that may be made of the information contained hereinElsevierUniversidade do MinhoJácome, Alberto G.Fdez-Riverola, FlorentinoLourenço, Anália2016-072016-07-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/41302engJácome, Alberto G.; Fdez-Riverola, Florentino; Lourenço, Anália, BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines. Computer Methods and Programs in Biomedicine, 131, 63-77, 20160169-260710.1016/j.cmpb.2016.03.03027265049http://www.cmpbjournal.com/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:RCAAP2023-07-21T12:15:37Zoai:repositorium.sdum.uminho.pt:1822/41302Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:08:05.098025Repositório 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 BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
title BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
spellingShingle BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
Jácome, Alberto G.
search engine framework
biomedical literature
vertical engine
text mining
web application
Science & Technology
title_short BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
title_full BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
title_fullStr BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
title_full_unstemmed BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
title_sort BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
author Jácome, Alberto G.
author_facet Jácome, Alberto G.
Fdez-Riverola, Florentino
Lourenço, Anália
author_role author
author2 Fdez-Riverola, Florentino
Lourenço, Anália
author2_role author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Jácome, Alberto G.
Fdez-Riverola, Florentino
Lourenço, Anália
dc.subject.por.fl_str_mv search engine framework
biomedical literature
vertical engine
text mining
web application
Science & Technology
topic search engine framework
biomedical literature
vertical engine
text mining
web application
Science & Technology
description The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef
publishDate 2016
dc.date.none.fl_str_mv 2016-07
2016-07-01T00:00:00Z
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/1822/41302
url http://hdl.handle.net/1822/41302
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Jácome, Alberto G.; Fdez-Riverola, Florentino; Lourenço, Anália, BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines. Computer Methods and Programs in Biomedicine, 131, 63-77, 2016
0169-2607
10.1016/j.cmpb.2016.03.030
27265049
http://www.cmpbjournal.com/
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 Elsevier
publisher.none.fl_str_mv Elsevier
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
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution 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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