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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

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A logic approach to modelling nomenclatural change.

Nico M Franz¹, Chao Zhang², Joohyung Lee²

¹School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA.

Cladistics : the International Journal of the Willi Hennig Society

|October 14, 2021

Summary

Computational logic can handle nomenclature principles. Answer Set Programming (ASP) successfully inferred changes for 36 taxonomic scenarios, paving the way for optimized nomenclatural services.

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Area of Science:

Computational logic
Taxonomy
Bioinformatics

Background:

Nomenclature principles govern biological classification.
Current systems face challenges with large datasets and complex reclassifications.
Automating nomenclatural changes is crucial for taxonomic databases.

Purpose of the Study:

To demonstrate the tractability of nomenclature principles in computational logic.
To develop and test an Answer Set Programming (ASP) model for nomenclatural emendations.
To explore the implications of taxonomic reinterpretation on nomenclature.

Main Methods:

Designed a 20-taxon use case based on the International Code of Zoological Nomenclature.
Implemented an ASP transition system to model nomenclatural rules (Binomial Nomenclature, Priority, Homonymy, Typification, Gender Agreement).
Simulated 36 scenarios involving type specimen reinterpretation and analyzed required emendations.

Main Results:

The ASP system accurately inferred code-mandated nomenclatural changes for all simulated scenarios.
Each scenario required 1-14 logically contingent emendations.
The system visually outputted the resulting nomenclatural conditions.

Conclusions:

Answer Set Programming is a viable approach for computational nomenclature.
This work provides a foundation for logic-based services for nomenclatural optimization and validation.
Logic-based exploration can reveal design biases in nomenclature and inform future identifier systems.