Task-based assessment of visualization tools for the comparison of biological taxonomies

Research Ideas and Outcomes, Aug 2018

Maintenance and curation of large-sized biological taxonomies are complex and laborious activities. Information visualization systems use interactive visual interfaces to facilitate analytical reasoning on complex information. Several approaches such as treemaps, indented lists, cone trees, radial trees, and many others have been used to visualize and analyze a single taxonomy. In addition, methods such as edge drawing, animation, and matrix representations have been used for comparing trees. Visualizing similarities and differences between two or more large taxonomies is harder than the visualization of a single taxonomy. On one hand, less space is available on the screen to display each tree; on the other hand, differences should be highlighted. The comparison of two alternative taxonomies and the analysis of a taxonomy as it evolves over time provide fundamental information to taxonomists and global initiatives that promote standardization and integration of taxonomic databases to better document biodiversity and support its conservation. In this work we assess how ten user visualization tasks for the curation of biological taxonomies are supported by several visualization tools. Tasks include the identification of conditions such as congruent taxa, splits, merges, and new species added to a taxonomy. We consider tools that have gone beyond the prototype stage, that have been described in peer-reviewed publications, or are in current use. We conclude with the identification of challenges for future development of taxonomy comparison tools.

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Task-based assessment of visualization tools for the comparison of biological taxonomies

Task-based assessment of visualization tools for the comparison of biological taxonomies Lilliana Sancho-Chavarria 0 Fabian Beck 2 Daniel Weiskopf 1 Erick Mata-Montero 0 Fabian Beck () Erick Mata-Montero () 0 School of Computing, Costa Rica Institute of Technology , Cartago , Costa Rica 1 VISUS, University of Stuttgart , Stuttgart , Germany 2 Institute for Computer Science and Business Information Systems, University of Duisburg-Essen , Essen , Germany Maintenance and curation of large-sized biological taxonomies are complex and laborious activities. Information visualization systems use interactive visual interfaces to facilitate analytical reasoning on complex information. Several approaches such as treemaps, indented lists, cone trees, radial trees, and many others have been used to visualize and analyze a single taxonomy. In addition, methods such as edge drawing, animation, and matrix representations have been used for comparing trees. Visualizing similarities and differences between two or more large taxonomies is harder than the visualization of a single taxonomy. On one hand, less space is available on the screen to display each tree; on the other hand, differences should be highlighted. The comparison of two alternative taxonomies and the analysis of a taxonomy as it evolves over time provide fundamental information to taxonomists and global initiatives that promote standardization and integration of taxonomic databases to better document biodiversity and support its conservation. In this work we assess how ten user visualization tasks for the curation of biological taxonomies are supported by several visualization tools. Tasks include the identification of conditions such as congruent taxa, splits, merges, and new species added - Reviewable v1 © Sancho-Chavarria L et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. to a taxonomy. We consider tools that have gone beyond the prototype stage, that have been described in peer-reviewed publications, or are in current use. We conclude with the identification of challenges for future development of taxonomy comparison tools. Information visualization, biodiversity informatics, taxonomy, taxonomy comparison tools. 1. Introduction Biological taxonomies are hierarchical structures that represent classifications of living organisms. Taxonomists, herbaria, natural history museums, and biodiversity initiatives worldwide classify biodiversity according to literature and other sources of information available to them, and to a choice of criteria that they recognize as valid. Consequently, it is not surprising that different classifications emerge and that there is disagreement in the scientific community about which classification is correct. To resolve these conflicts, taxonomists perform studies―called revisions―that could lead to other variants of the classifications. Taxonomists and global initiatives eventually need to reconcile these multiplicity in order to properly document biodiversity. Therefore, differences and similarities between such alternative taxonomies have to be identified. Since taxonomies can be large and the number of changes substantial, the support of software tools to carry out this endeavor becomes indispensable. In this article we analyze information visualization tools designed to support comparison of biological taxonomies. We reviewed the tools and contrast them with ten user visualization tasks that we characterized in a previous work (Sancho-Chavarria et al. 2016). Section 2 presents a brief description of the reviewed tools and the list of ten user visualization tasks which we use as software requirements for the visual comparison of taxonomic changes. Section 3 describes the methodology used to assess the tools. Section 4 presents the assessment of the tools. Finally, Section 5 discusses future challenges and presents conclusions. 2. Background The comparison of alternative classifications has long been a research topic in information visualization (Graham and Kennedy 2010). In this work we are interested in assessing how tools for the comparison of biological taxonomies support previously characterized user tasks. A hierarchy comparison tool is expected to receive as input at least two hierarchies and facilitate the visualization of similarities and differences. These similarities and differences could be indicated manually by experts, inferred by the software itself, or both. We consider that the process for the comparison and curation of taxonomies involves three components as illustrated in Fig. 1. The purpose of the Inference component is to compute the differences and similarities between taxonomies. To do so, sometimes the software would require the taxonomic history of the species, that is, how a species has bee (...truncated)


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Lilliana Sancho-Chavarria, Fabian Beck, Daniel Weiskopf, Erick Mata-Montero. Task-based assessment of visualization tools for the comparison of biological taxonomies, Research Ideas and Outcomes, 2018, Issue 4, DOI: doi:10.3897/rio.4.e25742