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Biotea: semantics for Pubmed Central

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized...

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Detalles Bibliográficos
Autores principales: Garcia, Alexander, Lopez, Federico, Garcia, Leyla, Giraldo, Olga, Bucheli, Victor, Dumontier, Michel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755483/
https://www.ncbi.nlm.nih.gov/pubmed/29312824
http://dx.doi.org/10.7717/peerj.4201
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author Garcia, Alexander
Lopez, Federico
Garcia, Leyla
Giraldo, Olga
Bucheli, Victor
Dumontier, Michel
author_facet Garcia, Alexander
Lopez, Federico
Garcia, Leyla
Giraldo, Olga
Bucheli, Victor
Dumontier, Michel
author_sort Garcia, Alexander
collection PubMed
description A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.
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spelling pubmed-57554832018-01-08 Biotea: semantics for Pubmed Central Garcia, Alexander Lopez, Federico Garcia, Leyla Giraldo, Olga Bucheli, Victor Dumontier, Michel PeerJ Bioinformatics A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io. PeerJ Inc. 2018-01-02 /pmc/articles/PMC5755483/ /pubmed/29312824 http://dx.doi.org/10.7717/peerj.4201 Text en ©2018 Garcia et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Garcia, Alexander
Lopez, Federico
Garcia, Leyla
Giraldo, Olga
Bucheli, Victor
Dumontier, Michel
Biotea: semantics for Pubmed Central
title Biotea: semantics for Pubmed Central
title_full Biotea: semantics for Pubmed Central
title_fullStr Biotea: semantics for Pubmed Central
title_full_unstemmed Biotea: semantics for Pubmed Central
title_short Biotea: semantics for Pubmed Central
title_sort biotea: semantics for pubmed central
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755483/
https://www.ncbi.nlm.nih.gov/pubmed/29312824
http://dx.doi.org/10.7717/peerj.4201
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