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An expert study on hierarchy comparison methods applied to biological taxonomies curation

Comparison of hierarchies aims at identifying differences and similarities between two or more hierarchical structures. In the biological taxonomy domain, comparison is indispensable for the reconciliation of alternative versions of a taxonomic classification. Biological taxonomies are knowledge str...

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Detalles Bibliográficos
Autores principales: Sancho-Chavarria, Lilliana, Beck, Fabian, Mata-Montero, Erick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924413/
https://www.ncbi.nlm.nih.gov/pubmed/33816928
http://dx.doi.org/10.7717/peerj-cs.277
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author Sancho-Chavarria, Lilliana
Beck, Fabian
Mata-Montero, Erick
author_facet Sancho-Chavarria, Lilliana
Beck, Fabian
Mata-Montero, Erick
author_sort Sancho-Chavarria, Lilliana
collection PubMed
description Comparison of hierarchies aims at identifying differences and similarities between two or more hierarchical structures. In the biological taxonomy domain, comparison is indispensable for the reconciliation of alternative versions of a taxonomic classification. Biological taxonomies are knowledge structures that may include large amounts of nodes (taxa), which are typically maintained manually. We present the results of a user study with taxonomy experts that evaluates four well-known methods for the comparison of two hierarchies, namely, edge drawing, matrix representation, animation and agglomeration. Each of these methods is evaluated with respect to seven typical biological taxonomy curation tasks. To this end, we designed an interactive software environment through which expert taxonomists performed exercises representative of the considered tasks. We evaluated participants’ effectiveness and level of satisfaction from both quantitative and qualitative perspectives. Overall quantitative results evidence that participants were less effective with agglomeration whereas they were more satisfied with edge drawing. Qualitative findings reveal a greater preference among participants for the edge drawing method. In addition, from the qualitative analysis, we obtained insights that contribute to explain the differences between the methods and provide directions for future research.
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spelling pubmed-79244132021-04-02 An expert study on hierarchy comparison methods applied to biological taxonomies curation Sancho-Chavarria, Lilliana Beck, Fabian Mata-Montero, Erick PeerJ Comput Sci Bioinformatics Comparison of hierarchies aims at identifying differences and similarities between two or more hierarchical structures. In the biological taxonomy domain, comparison is indispensable for the reconciliation of alternative versions of a taxonomic classification. Biological taxonomies are knowledge structures that may include large amounts of nodes (taxa), which are typically maintained manually. We present the results of a user study with taxonomy experts that evaluates four well-known methods for the comparison of two hierarchies, namely, edge drawing, matrix representation, animation and agglomeration. Each of these methods is evaluated with respect to seven typical biological taxonomy curation tasks. To this end, we designed an interactive software environment through which expert taxonomists performed exercises representative of the considered tasks. We evaluated participants’ effectiveness and level of satisfaction from both quantitative and qualitative perspectives. Overall quantitative results evidence that participants were less effective with agglomeration whereas they were more satisfied with edge drawing. Qualitative findings reveal a greater preference among participants for the edge drawing method. In addition, from the qualitative analysis, we obtained insights that contribute to explain the differences between the methods and provide directions for future research. PeerJ Inc. 2020-06-29 /pmc/articles/PMC7924413/ /pubmed/33816928 http://dx.doi.org/10.7717/peerj-cs.277 Text en © 2020 Sancho-Chavarria et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://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 Computer Science) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Sancho-Chavarria, Lilliana
Beck, Fabian
Mata-Montero, Erick
An expert study on hierarchy comparison methods applied to biological taxonomies curation
title An expert study on hierarchy comparison methods applied to biological taxonomies curation
title_full An expert study on hierarchy comparison methods applied to biological taxonomies curation
title_fullStr An expert study on hierarchy comparison methods applied to biological taxonomies curation
title_full_unstemmed An expert study on hierarchy comparison methods applied to biological taxonomies curation
title_short An expert study on hierarchy comparison methods applied to biological taxonomies curation
title_sort expert study on hierarchy comparison methods applied to biological taxonomies curation
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924413/
https://www.ncbi.nlm.nih.gov/pubmed/33816928
http://dx.doi.org/10.7717/peerj-cs.277
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