Configurable web-services for biomedical document annotation
Abstract The need to efficiently find and extract information from the continuously growing biomedical literature has led to the development of various annotation tools aimed at identifying mentions of entities and relations. Many of these tools have been integrated in user-friendly applications fac...
Main Author: | |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2018-12-01
|
Series: | Journal of Cheminformatics |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s13321-018-0317-4 |
id |
doaj-bde28c9e2f9d4188a5fccc752a7c917d |
---|---|
record_format |
Article |
spelling |
doaj-bde28c9e2f9d4188a5fccc752a7c917d2020-11-25T01:16:35ZengBMCJournal of Cheminformatics1758-29462018-12-011011910.1186/s13321-018-0317-4Configurable web-services for biomedical document annotationSérgio Matos0DETI/IEETA, University of AveiroAbstract The need to efficiently find and extract information from the continuously growing biomedical literature has led to the development of various annotation tools aimed at identifying mentions of entities and relations. Many of these tools have been integrated in user-friendly applications facilitating their use by non-expert text miners and database curators. In this paper we describe the latest version of Neji, a web-services ready text processing and annotation framework. The modular and flexible architecture facilitates adaptation to different annotation requirements, while the built-in web services allow its integration in external tools and text mining pipelines. The evaluation of the web annotation server on the technical interoperability and performance of annotation servers track of BioCreative V.5 further illustrates the flexibility and applicability of this framework.http://link.springer.com/article/10.1186/s13321-018-0317-4Named entity recognitionBiomedical text miningWeb-services |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Sérgio Matos |
spellingShingle |
Sérgio Matos Configurable web-services for biomedical document annotation Journal of Cheminformatics Named entity recognition Biomedical text mining Web-services |
author_facet |
Sérgio Matos |
author_sort |
Sérgio Matos |
title |
Configurable web-services for biomedical document annotation |
title_short |
Configurable web-services for biomedical document annotation |
title_full |
Configurable web-services for biomedical document annotation |
title_fullStr |
Configurable web-services for biomedical document annotation |
title_full_unstemmed |
Configurable web-services for biomedical document annotation |
title_sort |
configurable web-services for biomedical document annotation |
publisher |
BMC |
series |
Journal of Cheminformatics |
issn |
1758-2946 |
publishDate |
2018-12-01 |
description |
Abstract The need to efficiently find and extract information from the continuously growing biomedical literature has led to the development of various annotation tools aimed at identifying mentions of entities and relations. Many of these tools have been integrated in user-friendly applications facilitating their use by non-expert text miners and database curators. In this paper we describe the latest version of Neji, a web-services ready text processing and annotation framework. The modular and flexible architecture facilitates adaptation to different annotation requirements, while the built-in web services allow its integration in external tools and text mining pipelines. The evaluation of the web annotation server on the technical interoperability and performance of annotation servers track of BioCreative V.5 further illustrates the flexibility and applicability of this framework. |
topic |
Named entity recognition Biomedical text mining Web-services |
url |
http://link.springer.com/article/10.1186/s13321-018-0317-4 |
work_keys_str_mv |
AT sergiomatos configurablewebservicesforbiomedicaldocumentannotation |
_version_ |
1725149250582478848 |