DOI: 10.5061/dryad.cd13v
title: Data from: A logic approach to modeling nomenclatural change

description: We utilize an Answer Set Programming (ASP) approach to show that the
 principles of nomenclature are tractable in computational logic. To this
 end we design a hypothetical, 20 nomenclatural taxon use case with
 starting conditions that embody several overarching principles of the
 International Code of Zoological Nomenclature; including Binomial
 Nomenclature, Priority, Coordination, Homonymy, Typification, and the
 structural requirement of Gender Agreement. The use case ending conditions
 are triggered by the reinterpretation of the diagnostic features of one of
 12 type specimens anchoring the corresponding species-level epithets.
 Permutations of this child-to-parent reassignment action lead to 36
 alternative scenarios, where each scenario requires a set of 1–14
 logically contingent nomenclatural emendations. We show that an ASP
 transition system approach can correctly infer the Code-mandated changes
 for each scenario, and visually output the ending conditions. The results
 provide a foundation for further developing logic-based nomenclatural
 change optimization and validation services, which could be applied in
 global nomenclatural registries. More generally, logic explorations of
 nomenclatural and taxonomic change scenarios provide a novel means of
 assessing design biases inherent in the principles of nomenclature, and
 thus may inform the design of future, big data-compatible identifier
 solutions that recognize and mitigate these constraints.
description: FranzEtAl-2017-SupplementaryMaterials-S1SUPPLEMENTARY MATERIALS S1. – Answer Set Programming code (.txt), with extensive comments, to perform the 20 nomenclatural taxon use case in conjunction with the Potassco solver clingo. See also Table 1.FranzEtAl-2017-SupplementaryMaterials-S2SUPPLEMENTARY MATERIALS S2. – Data file (.txt) with installation instructions and command line interface operations to run the ASP code and obtain the related reasoning and visualization outputs.FranzEtAl-2017-SupplementaryMaterials-S3SUPPLEMENTARY MATERIALS S3. – Data file (.txt) with the complete textual clingo solver output for the 20 nomenclatural taxon use case. This output is used to produce the GraphViz visualizations.FranzEtAl-2017-SupplementaryMaterials-S4SUPPLEMENTARY MATERIALS S4. – Java Archive file (.jar) needed to translate the clingo solver output into the corresponding GraphViz visualizations.FranzEtAl-2017-SupplementaryMaterials-S5SUPPLEMENTARY MATERIALS S5. – Collated set of GraphViz visualizations (transformed into .pdf) for the 20 nomenclatural taxon use case.FranzEtAl-2017-SupplementaryMaterials-S6SUPPLEMENTARY MATERIALS S6. – Set of 36 Euler/X input data files for the respective alignments (summarized in Table 3). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and input/output visualizations. The corresponding Euler/X .pdf input visualizations are also provided.FranzEtAl-2017-SupplementaryMaterials-S7SUPPLEMENTARY MATERIALS S7. – Set of 36 Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S6. Each output file is saved in .csv format.FranzEtAl-2017-SupplementaryMaterials-S8SUPPLEMENTARY MATERIALS S8. – Set of 36 Euler/X output alignment visualizations (.pdf) for the input data files provided in the Supplementary Materials S6.