Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm
Autor(a) principal: | |
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Data de Publicação: | 2019 |
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/1822/60755 |
Resumo: | Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such tasks relied on the comparison of automatically generated results against a so-called Gold Standard dataset of manually labelled textual data, regardless of efficiency and robustness of the underlying implementations. Due to the rapid growth of unstructured data collections, including patent databases and particularly the scientific literature, there is a pressing need to generate, assess and expose robust big data text mining solutions to semantically enrich documents in real time. To address this pressing need, a novel track called ``Technical interoperability and performance of annotation servers'' was launched under the umbrella of the BioCreative text mining evaluation effort. The aim of this track was to enable the continuous assessment of technical aspects of text annotation web servers, specifically of online biomedical named entity recognition systems of interest for medicinal chemistry applications. |
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Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalmNamed entity recognitionShared taskREST-APITIPSBeCalm metaserverPatent miningAnnotation serverContinuous evaluationBioCreativeText miningScience & TechnologyShared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such tasks relied on the comparison of automatically generated results against a so-called Gold Standard dataset of manually labelled textual data, regardless of efficiency and robustness of the underlying implementations. Due to the rapid growth of unstructured data collections, including patent databases and particularly the scientific literature, there is a pressing need to generate, assess and expose robust big data text mining solutions to semantically enrich documents in real time. To address this pressing need, a novel track called ``Technical interoperability and performance of annotation servers'' was launched under the umbrella of the BioCreative text mining evaluation effort. The aim of this track was to enable the continuous assessment of technical aspects of text annotation web servers, specifically of online biomedical named entity recognition systems of interest for medicinal chemistry applications.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 654021 (OpenMinTeD), and the Encomienda MINETAD‑CNIO as part of the Plan for the Advancement of Language Technology for funding. This work was partially supported by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia), under the scope of the strategic funding of ED431C2018/55‑GRC Competitive Reference Group, and 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‑01‑0145‑FEDER‑006684).info:eu-repo/semantics/publishedVersionSpringerOpenUniversidade do MinhoPérez-Pérez, MartinPérez-Rodríguez, GaelBlanco-Míguez, AitorFdez-Riverola, FlorentinoValencia, AlfonsoKrallinger, MartinLourenço, Anália2019-122019-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/60755engPérez-Pérez, Martin; Pérez-Rodríguez, Gael; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália, Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. Journal of Cheminformatics, 11(42), 20191758-294610.1186/s13321-019-0363-6https://jcheminf.biomedcentral.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:RCAAP2023-07-21T12:28:51Zoai:repositorium.sdum.uminho.pt:1822/60755Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:23:44.281833Repositório 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 |
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm |
title |
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm |
spellingShingle |
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm Pérez-Pérez, Martin Named entity recognition Shared task REST-API TIPS BeCalm metaserver Patent mining Annotation server Continuous evaluation BioCreative Text mining Science & Technology |
title_short |
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm |
title_full |
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm |
title_fullStr |
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm |
title_full_unstemmed |
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm |
title_sort |
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm |
author |
Pérez-Pérez, Martin |
author_facet |
Pérez-Pérez, Martin Pérez-Rodríguez, Gael Blanco-Míguez, Aitor Fdez-Riverola, Florentino Valencia, Alfonso Krallinger, Martin Lourenço, Anália |
author_role |
author |
author2 |
Pérez-Rodríguez, Gael Blanco-Míguez, Aitor Fdez-Riverola, Florentino Valencia, Alfonso Krallinger, Martin Lourenço, Anália |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Pérez-Pérez, Martin Pérez-Rodríguez, Gael Blanco-Míguez, Aitor Fdez-Riverola, Florentino Valencia, Alfonso Krallinger, Martin Lourenço, Anália |
dc.subject.por.fl_str_mv |
Named entity recognition Shared task REST-API TIPS BeCalm metaserver Patent mining Annotation server Continuous evaluation BioCreative Text mining Science & Technology |
topic |
Named entity recognition Shared task REST-API TIPS BeCalm metaserver Patent mining Annotation server Continuous evaluation BioCreative Text mining Science & Technology |
description |
Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such tasks relied on the comparison of automatically generated results against a so-called Gold Standard dataset of manually labelled textual data, regardless of efficiency and robustness of the underlying implementations. Due to the rapid growth of unstructured data collections, including patent databases and particularly the scientific literature, there is a pressing need to generate, assess and expose robust big data text mining solutions to semantically enrich documents in real time. To address this pressing need, a novel track called ``Technical interoperability and performance of annotation servers'' was launched under the umbrella of the BioCreative text mining evaluation effort. The aim of this track was to enable the continuous assessment of technical aspects of text annotation web servers, specifically of online biomedical named entity recognition systems of interest for medicinal chemistry applications. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-12 2019-12-01T00:00:00Z |
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/1822/60755 |
url |
http://hdl.handle.net/1822/60755 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália, Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. Journal of Cheminformatics, 11(42), 2019 1758-2946 10.1186/s13321-019-0363-6 https://jcheminf.biomedcentral.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 |
SpringerOpen |
publisher.none.fl_str_mv |
SpringerOpen |
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 |
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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 |
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