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Zhang L, Starr J, Ford B, Reznicek A, Zhou Y, Léveillé-Bourret É, Lacroix-Carignan É, Cayouette J, Smith TW, Sutherland D, Catling P, Saarela JM, Cui H, Macklin J. Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype. Database (Oxford) 2025; 2025:baae097. [PMID: 39879563 PMCID: PMC11928229 DOI: 10.1093/database/baae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/01/2024] [Accepted: 08/28/2024] [Indexed: 01/31/2025]
Abstract
It is well-known that the use of vocabulary in phenotype treatments is often inconsistent. An earlier survey of biologists who create or use phenotypic characters revealed that this lack of standardization leads to ambiguities, frustrating both the consumers and producers of phenotypic data. Such ambiguities are challenging for biologists, and more so for Artificial Intelligence, to resolve. That survey also indicated a strong interest in a new authoring workflow supported by ontologies to ensure published phenotype data are FAIR (Findable, Accessible, Interoperable, and Reusable) and suitable for large-scale computational analyses. In this article, we introduce a prototype software system designed for authors to produce computational phenotype data. This platform includes a web-based, ontology-enhanced editor for taxonomic characters (Character Recorder), an Ontology Backend holding standardized vocabulary (the Cared Ontology), and a mobile application for resolving ontological conflicts (Conflict Resolver). We present two formal user evaluations of Character Recorder, the main interface authors would interact with to produce FAIR data. The evaluations were conducted with undergraduate biology students and Carex experts. We evaluated Character Recorder against Microsoft Excel on their effectiveness, efficiency, and the cognitive demands of the users in producing computable taxon-by-character matrices. The evaluations showed that Character Recorder is quickly learnable for both student and professional participants, with its cognitive demand comparable to Excel's. Participants agreed that the quality of the data Character Recorder yielded was superior. Students praised Character Recorder's educational value, while Carex experts were keen to recommend it and help evolve it from a prototype into a comprehensive tool. Feature improvements recommended by expert participants have been implemented after the evaluation.
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Affiliation(s)
- Limin Zhang
- School of Information, University of Arizona, 1103 E. 2nd Street, Tucson, AZ 85719, USA
- School of Fine Arts, Huaiyin Normal University, 71 Jiaotong Road, Huaian, Jiangsu 223001, China
| | - Julian Starr
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Bruce Ford
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Anton Reznicek
- University Herbarium, University of Michigan, 3600 Varsity Drive, Ann Arbor, MI 48108, US
| | - Yuxuan Zhou
- School of Information, University of Arizona, 1103 E. 2nd Street, Tucson, AZ 85719, USA
| | - Étienne Léveillé-Bourret
- Department of Biological Sciences, Université de Montréal, 1375 Avenue Thérèse-Lavoie-Roux, Montréal, QC H3A 2B3, Canada
| | - Étienne Lacroix-Carignan
- Department of Biological Sciences, Université de Montréal, 1375 Avenue Thérèse-Lavoie-Roux, Montréal, QC H3A 2B3, Canada
| | - Jacques Cayouette
- Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON CA K1A 0C6, Canada
| | - Tyler W Smith
- Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON CA K1A 0C6, Canada
| | - Donald Sutherland
- Natural Heritage Information Centre, Ontario Ministry of Natural Resources, P.O. Box 7000, Peterborough, Ontario K9J 8M5, Canada
| | - Paul Catling
- Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON CA K1A 0C6, Canada
| | - Jeffery M Saarela
- Research and Collections, Canadian Museum of Nature, 240 McLeod St, Ottawa, ON K1P 6P4, Canada
| | - Hong Cui
- School of Information, University of Arizona, 1103 E. 2nd Street, Tucson, AZ 85719, USA
| | - James Macklin
- Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON CA K1A 0C6, Canada
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