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Semantic annotation in biomedicine: the current landscape

The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advan...

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Detalles Bibliográficos
Autores principales: Jovanović, Jelena, Bagheri, Ebrahim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610427/
https://www.ncbi.nlm.nih.gov/pubmed/28938912
http://dx.doi.org/10.1186/s13326-017-0153-x
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author Jovanović, Jelena
Bagheri, Ebrahim
author_facet Jovanović, Jelena
Bagheri, Ebrahim
author_sort Jovanović, Jelena
collection PubMed
description The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing. This process is widely known as semantic annotation, and the tools that perform it are known as semantic annotators. Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology. Aiming to establish grounds for further developments in this area, we review a selected set of state of the art biomedical semantic annotators, focusing particularly on general purpose annotators, that is, semantic annotation tools that can be customized to work with texts from any area of biomedicine. We also examine potential directions for further improvements of today’s annotators which could make them even more capable of meeting the needs of real-world applications. To motivate and encourage further developments in this area, along the suggested and/or related directions, we review existing and potential practical applications and benefits of semantic annotators.
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spelling pubmed-56104272017-10-10 Semantic annotation in biomedicine: the current landscape Jovanović, Jelena Bagheri, Ebrahim J Biomed Semantics Review The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing. This process is widely known as semantic annotation, and the tools that perform it are known as semantic annotators. Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology. Aiming to establish grounds for further developments in this area, we review a selected set of state of the art biomedical semantic annotators, focusing particularly on general purpose annotators, that is, semantic annotation tools that can be customized to work with texts from any area of biomedicine. We also examine potential directions for further improvements of today’s annotators which could make them even more capable of meeting the needs of real-world applications. To motivate and encourage further developments in this area, along the suggested and/or related directions, we review existing and potential practical applications and benefits of semantic annotators. BioMed Central 2017-09-22 /pmc/articles/PMC5610427/ /pubmed/28938912 http://dx.doi.org/10.1186/s13326-017-0153-x Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Review
Jovanović, Jelena
Bagheri, Ebrahim
Semantic annotation in biomedicine: the current landscape
title Semantic annotation in biomedicine: the current landscape
title_full Semantic annotation in biomedicine: the current landscape
title_fullStr Semantic annotation in biomedicine: the current landscape
title_full_unstemmed Semantic annotation in biomedicine: the current landscape
title_short Semantic annotation in biomedicine: the current landscape
title_sort semantic annotation in biomedicine: the current landscape
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610427/
https://www.ncbi.nlm.nih.gov/pubmed/28938912
http://dx.doi.org/10.1186/s13326-017-0153-x
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