JPhyloRef: a tool for testing and resolving phyloreferences
Author:
Publisher
The Open Journal
Link
https://joss.theoj.org/papers/10.21105/joss.03374.pdf
Reference9 articles.
1. Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts, Cellinese, Nico and Conix, Stijn and Lapp, Hilmar, Evolutionary and organismal biology, similar to other fields in 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 by shared entities, is crucial. The most common shared entity by which evolutionary and ecological data need to be linked is the taxon to which they belong. In this paper, 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 based in Linnaean taxonomy, by far 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 clade 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., Philosophy, Theory and Practice in Biology, 2021, Accepted. Preprint available on EcoEvoRxiv at https://doi.org/10.32942/osf.io/57yjs
2. Phylogenetic Taxonomy
3. Phylogenetic definitions and taxonomic philosophy
4. Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names
5. The Incredible ELK
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1. A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx);PeerJ;2022-02-15
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