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Title: TaxonWorks: Character state matrices and identification tools
TaxonWorks is an integrated web-based application for practicing taxonomists and biodiversity specialists. It is focused on promoting collaboration between researchers and developers. TaxonWorks has a modular structure that enables various components of the application to target specific needs and requirements of different groups of users. Specific areas of interest may include nomenclature-related tasks (Yoder and Dmitriev 2021) designed to help assemble and validate scientific name checklists of a target group of organisms; and collection management tasks, including interfaces to create, filter, and edit collecting events, collection objects, and loans. This presentation focuses on matrix-related tools integrated into TaxonWorks. A matrix, which could either be used for phylogenetic analysis or to build an identification key, is structured as a table where columns represent numerous characters that could be used to describe a set of entities, taxa or specimens (presented as rows of the table). Each cell of the table may contain observations for specific character/entity combinations. TaxonWorks does not generate a table for each a particular matrix—all observations are stored as graphs. This structure allows building of a matrix of an unlimited size as well as reuse of individual observations in multiple matrices. For matrix columns, TaxonWorks supports a variety of more » different kinds of characters or descriptors: qualitative, presence/absence, quantitative, sample, gene, free text, and media. Each character may have specific properties, for example a qualitative descriptor may have numerous characters states, and a quantitative descriptor may have a measurement unit defined. For an entity in a matrix row, TaxonWorks supports either collection objects (specimens) or taxa as Operational Taxonomic Units (OTU). OTUs could either be linked to nomenclature or be stand alone entities (e.g., representing undescribed species). The matrix, once built, could serve several purposes. A matrix based on qualitative and quantitative characters could be used to build an interactive key (Fig. 1), construct standardized natural language descriptions for each entity, and determine a diagnosis (a minimal set of characters that separate one entity from all others). It could also be exported and used for phylogenetic analysis or to build an interactive key in an external application. TaxonWorks supports export files in several formats, including Nexus, TNT, NeXML. Application Programming Interfaces (API) are also available. A matrix based on media descriptors could be used as a pictorial identification tool (Fig. 2). « less
Authors:
;
Award ID(s):
1639601
Publication Date:
NSF-PAR ID:
10312517
Journal Name:
Biodiversity Information Science and Standards
Volume:
5
ISSN:
2535-0897
Sponsoring Org:
National Science Foundation
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We have completed two usability studies on Character Recorder. a web-based application, Character Recorder (http://chrecorder.lusites.xyz/login), to faciliate the use and addition of ontology terms by Carex systematist authors while building their matrices, and a mobile application, Conflict Resolver (Android, https://tinyurl.com/5cfatrz8), to identify potential conflicts among the terms added by the authors and facilitate the resolution of the conflicts. We have completed two usability studies on Character Recorder. 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Nearly all of the students found Character Recorder was more useful for recording clear and consistent data and all students agreed that participating in this study raised their awareness of data variation issues. The expert group consisted of 3, 2, 1, 3 experts in age ranges 20-49, 50-59, 60-69, and >69, respectively. They each recorded over 100 characters for two or more samples. Detailed analysis of their characters is pending, but we have noticed color characters have more variations than other characters (Fig. 4). All experts reported that they learned to use Character Recorder quickly, and 6 out of 8 believed they would not need a tutorial the next time they used it. One out of 8 experts somewhat disliked the feature of reusing others' values ("Use This" in Fig. 2) as it may undermine the objectivity and independence of an author. All experts used Recommended Set of Characters and they liked the term suggestion and illustration features shown in Figs 2, 3. 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