SIA: a scalable interoperable annotation server for biomedical named entities

Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools into custo...

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Detalles Bibliográficos
Autores principales: Kirschnick, Johannes, Thomas, Philippe, Roller, Roland, Hennig, Leonhard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2018
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755617/
https://www.ncbi.nlm.nih.gov/pubmed/30552534
http://dx.doi.org/10.1186/s13321-018-0319-2
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author Kirschnick, Johannes
Thomas, Philippe
Roller, Roland
Hennig, Leonhard
author_facet Kirschnick, Johannes
Thomas, Philippe
Roller, Roland
Hennig, Leonhard
author_sort Kirschnick, Johannes
collection PubMed
description Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools into customized workflows is often cumbersome and difficult. We describe SIA (Scalable Interoperable Annotation Server), our contribution to the BeCalm-Technical interoperability and performance of annotation servers (BeCalm-TIPS) task, a scalable, extensible, and robust annotation service. The system currently covers six named entity types (i.e., chemicals, diseases, genes, miRNA, mutations, and organisms) and is freely available under Apache 2.0 license at https://github.com/Erechtheus/sia.
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spelling pubmed-67556172019-09-26 SIA: a scalable interoperable annotation server for biomedical named entities Kirschnick, Johannes Thomas, Philippe Roller, Roland Hennig, Leonhard J Cheminform Research Article Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools into customized workflows is often cumbersome and difficult. We describe SIA (Scalable Interoperable Annotation Server), our contribution to the BeCalm-Technical interoperability and performance of annotation servers (BeCalm-TIPS) task, a scalable, extensible, and robust annotation service. The system currently covers six named entity types (i.e., chemicals, diseases, genes, miRNA, mutations, and organisms) and is freely available under Apache 2.0 license at https://github.com/Erechtheus/sia. Springer International Publishing 2018-12-14 /pmc/articles/PMC6755617/ /pubmed/30552534 http://dx.doi.org/10.1186/s13321-018-0319-2 Text en © The Author(s) 2018 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 Research Article
Kirschnick, Johannes
Thomas, Philippe
Roller, Roland
Hennig, Leonhard
SIA: a scalable interoperable annotation server for biomedical named entities
title SIA: a scalable interoperable annotation server for biomedical named entities
title_full SIA: a scalable interoperable annotation server for biomedical named entities
title_fullStr SIA: a scalable interoperable annotation server for biomedical named entities
title_full_unstemmed SIA: a scalable interoperable annotation server for biomedical named entities
title_short SIA: a scalable interoperable annotation server for biomedical named entities
title_sort sia: a scalable interoperable annotation server for biomedical named entities
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755617/
https://www.ncbi.nlm.nih.gov/pubmed/30552534
http://dx.doi.org/10.1186/s13321-018-0319-2
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AT hennigleonhard siaascalableinteroperableannotationserverforbiomedicalnamedentities

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