Biological taxon names are descriptive names

Brzozowski, Jerzy André

doi:10.1007/s40656-020-00322-1

Cited by 3 publications

(1 citation statement)

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“…First, repurposed Linnaean names define taxon concepts by means of a type specimen and description (Brzozowski 2020). However, whenever the type is missing from the phylogeny--which is typically the case--there are no agreed rules for mapping type specimens to clades.…”

Section: Linnaean Names Make Data Discovery Difficult To Reproducementioning

confidence: 99%

Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts

Cellinese

Conix

Lapp

2022

Philosophy, Theory, and Practice in Biology

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Evolutionary and organismal biology have become inundated with data. At the same rate, we are experiencing a surge in broader evolutionary and ecological syntheses for which tree-thinking is the staple for a variety of post-tree analyses. To fully take advantage of this wealth of data to discover and understand large-scale evolutionary and ecological patterns, computational data integration, i.e., the use of machines to link data at large scale, is crucial. The most common shared entity by which evolutionary and ecological data need to be linked is the taxon to which they belong. We propose a set of requirements that a system for defining such taxa should meet for computational data science: taxon definitions should maintain conceptual consistency, be reproducible via a known algorithm, be computationally automatable, and be applicable across the Tree of Life. We argue that Linnaean names, the most prevalent means of linking data to taxa, fail to meet these requirements due to fundamental theoretical and practical shortfalls. We argue that for the purposes of data-integration we should instead use phylogenetic definitions transformed into formal logic expressions. We call such expressions phyloreferences, and argue that, unlike Linnaean names, they meet all requirements for effective data-integration.

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Section: Linnaean Names Make Data Discovery Difficult To Reproducementioning

confidence: 99%