Architecture and usability of OntoKeeper, an ontology evaluation tool

BACKGROUND: The existing community-wide bodies of biomedical ontologies are known to contain quality and content problems. Past research has revealed various errors related to their semantics and logical structure. Automated tools may help to ease the ontology construction, maintenance, assessment a...

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Autores principales: Amith, Muhammad, Manion, Frank, Liang, Chen, Harris, Marcelline, Wang, Dennis, He, Yongqun, Tao, Cui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Research
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686219/
https://www.ncbi.nlm.nih.gov/pubmed/31391056
http://dx.doi.org/10.1186/s12911-019-0859-z
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author Amith, Muhammad
Manion, Frank
Liang, Chen
Harris, Marcelline
Wang, Dennis
He, Yongqun
Tao, Cui
author_facet Amith, Muhammad
Manion, Frank
Liang, Chen
Harris, Marcelline
Wang, Dennis
He, Yongqun
Tao, Cui
author_sort Amith, Muhammad
collection PubMed
description BACKGROUND: The existing community-wide bodies of biomedical ontologies are known to contain quality and content problems. Past research has revealed various errors related to their semantics and logical structure. Automated tools may help to ease the ontology construction, maintenance, assessment and quality assurance processes. However, there are relatively few tools that exist that can provide this support to knowledge engineers. METHOD: We introduce OntoKeeper as a web-based tool that can automate quality scoring for ontology developers. We enlisted 5 experienced ontologists to test the tool and then administered the System Usability Scale to measure their assessment. RESULTS: In this paper, we present usability results from 5 ontologists revealing high system usability of OntoKeeper, and use-cases that demonstrate its capabilities in previous published biomedical ontology research. CONCLUSION: To the best of our knowledge, OntoKeeper is the first of a few ontology evaluation tools that can help provide ontology evaluation functionality for knowledge engineers with good usability.
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spelling pubmed-66862192019-08-12 Architecture and usability of OntoKeeper, an ontology evaluation tool Amith, Muhammad Manion, Frank Liang, Chen Harris, Marcelline Wang, Dennis He, Yongqun Tao, Cui BMC Med Inform Decis Mak Research BACKGROUND: The existing community-wide bodies of biomedical ontologies are known to contain quality and content problems. Past research has revealed various errors related to their semantics and logical structure. Automated tools may help to ease the ontology construction, maintenance, assessment and quality assurance processes. However, there are relatively few tools that exist that can provide this support to knowledge engineers. METHOD: We introduce OntoKeeper as a web-based tool that can automate quality scoring for ontology developers. We enlisted 5 experienced ontologists to test the tool and then administered the System Usability Scale to measure their assessment. RESULTS: In this paper, we present usability results from 5 ontologists revealing high system usability of OntoKeeper, and use-cases that demonstrate its capabilities in previous published biomedical ontology research. CONCLUSION: To the best of our knowledge, OntoKeeper is the first of a few ontology evaluation tools that can help provide ontology evaluation functionality for knowledge engineers with good usability. BioMed Central 2019-08-08 /pmc/articles/PMC6686219/ /pubmed/31391056 http://dx.doi.org/10.1186/s12911-019-0859-z Text en © The Author(s) 2019 Open Access This 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
Amith, Muhammad
Manion, Frank
Liang, Chen
Harris, Marcelline
Wang, Dennis
He, Yongqun
Tao, Cui
Architecture and usability of OntoKeeper, an ontology evaluation tool
title Architecture and usability of OntoKeeper, an ontology evaluation tool
title_full Architecture and usability of OntoKeeper, an ontology evaluation tool
title_fullStr Architecture and usability of OntoKeeper, an ontology evaluation tool
title_full_unstemmed Architecture and usability of OntoKeeper, an ontology evaluation tool
title_short Architecture and usability of OntoKeeper, an ontology evaluation tool
title_sort architecture and usability of ontokeeper, an ontology evaluation tool
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686219/
https://www.ncbi.nlm.nih.gov/pubmed/31391056
http://dx.doi.org/10.1186/s12911-019-0859-z
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