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Computable Species Descriptions and Nanopublications: Applying Ontology-based Technologies to Dung Beetles (Coleoptera: Scarabaeinae)

Authors: Montanaro, Giulio; Balhoff, James; Girón, Jennifer; Söderholm, Max; Tarasov, Sergei; Montanaro, Giulio; Balhoff, James; +48 Authors

Computable Species Descriptions and Nanopublications: Applying Ontology-based Technologies to Dung Beetles (Coleoptera: Scarabaeinae)

Abstract

Taxonomy has long struggled with analyzing vast amounts of phenotypic data due to computational and accessibility challenges. Ontology-based technologies provide a framework for modeling semantic phenotypes that are understandable by computers and compliant with FAIR principles. In this paper, we explore the use of Phenoscript, an emerging language designed for creating semantic phenotypes, to produce computable species descriptions. Our case study centers on the application of this approach to dung beetles (Coleoptera: Scarabaeinae). We illustrate the effectiveness of Phenoscript for creating semantic phenotypes. We also demonstrate the ability of the Phenospy python package to automatically translate Phenoscript descriptions into natural language (NL), which eliminates the need for writing traditional NL descriptions. We introduce a computational pipeline that streamlines the generation of semantic descriptions and their conversion to NL. To demonstrate the power of the semantic approach, we apply simple semantic queries to the generated phenotypic descriptions. This paper addresses the current challenges in crafting semantic species descriptions and outlines the path towards future improvements. Furthermore, we discuss the promising integration of semantic phenotypes and nanopublications, as emerging methods for sharing scientific information. Overall, our study highlights the pivotal role of ontology-based technologies in modernizing taxonomy and aligning it with the evolving landscape of big data analysis and FAIR principles.

Countries
United States, Finland
Keywords

Grebennikovius, microCT, characters, QH301-705.5, Higher Education and Teaching, 590, Higher Education, Phenoscript, Education, taxonomy, Taxonomy & Inventories, Ecology, evolutionary biology, phenotypic t, Other Education, morphology, Teacher Education and Professional Development, phenotypic traits, Biology (General), semantic data

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    influence
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
1
Average
Average
Average
Green
gold
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