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
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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)