Abstract
Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.
Highlights
The present contribution is a companion paper to [1] and offers a novel, use case-centered illustration of aligning multiple succeeding taxonomies through the interaction of human users and logic reasoners
Our broader intention is to promote the taxonomic concept approach [2,3,4] as a feasible solution to the challenge of provenance tracking in cases were name/circumscription relationships change across taxonomies as an outcome of scientific advancement
We recount the creation of input taxonomies and articulations in present tense
Summary
The present contribution is a companion paper to [1] and offers a novel, use case-centered illustration of aligning multiple succeeding taxonomies through the interaction of human users and logic reasoners. It is of a technical, detail-focused nature and most immediately directed at biodiversity scientists who wish to integrate taxonomically non-congruent classifications and phylogenies. Our broader intention is to promote the taxonomic concept approach [2,3,4] as a feasible solution to the challenge of provenance tracking in cases were name/circumscription relationships change across taxonomies as an outcome of scientific advancement. In aligning multiple input classifications or phylogenies, we ask not: “which names or circumscriptions are valid?" Instead we ask: “how can we logically represent, and perform reliable inferences over, the similarities and differences between multiple, independently published taxonomic perspectives?” We show here that this is feasible with an unprecedented degree of resolution
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
