DOI: 10.5061/dryad.6jg71
title: Data from: Two influential primate classifications logically aligned

description: Classifications and phylogenies of perceived natural entities change in
 the light of new evidence. Taxonomic changes, translated into
 Code-compliant names, frequently lead to name:meaning dissociations across
 succeeding treatments. Classification standards such as the Mammal Species
 of the World (MSW) may experience significant levels of taxonomic change
 from one edition to the next, with potential costs to long-term,
 large-scale information integration. This circumstance challenges the
 biodiversity and phylogenetic data communities to express taxonomic
 congruence and incongruence in ways that both humans and machines can
 process, that is, to logically represent taxonomic alignments across
 multiple classifications. We demonstrate that such alignments are feasible
 for two classifications of primates corresponding to the second and third
 MSW editions. Our approach has three main components: (i) use of taxonomic
 concept labels, that is name sec. author (where sec. means according to),
 to assemble each concept hierarchy separately via parent/child
 relationships; (ii) articulation of select concepts across the two
 hierarchies with user-provided Region Connection Calculus (RCC-5)
 relationships; and (iii) the use of an Answer Set Programming toolkit to
 infer and visualize logically consistent alignments of these input
 constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317
 taxonomic concepts; 233 at the species level) and Primates sec. Groves
 (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402
 RCC-5 input articulations, the reasoning process yields a single,
 consistent alignment and 153,111 Maximally Informative Relations that
 constitute a comprehensive meaning resolution map for every concept pair
 in the Primates sec. MSW2/MSW3. The complete alignment, and various
 partitions thereof, facilitate quantitative analyses of name:meaning
 dissociation, revealing that nearly one in three taxonomic names are not
 reliable across treatments—in the sense of the same name identifying
 congruent taxonomic meanings. The RCC-5 alignment approach is potentially
 widely applicable in systematics and can achieve scalable, precise
 resolution of semantically evolving name usages in synthetic,
 next-generation biodiversity, and phylogeny data platforms.
description: figure1SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figure3SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figure4SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figure5SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figure6SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figure7SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-1SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-2SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-3SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-4SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-5SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-6SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-7SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-8SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-9SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-10SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-11SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-12SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figureS3-13SUPPLEMENTARY MATERIALS S1. – Set of Euler/X toolkit input data files for all alignments produced in the Prim-UC (Figs. 1, 3–7, S3 1–13). Each file is saved is saved in .txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the 19 corresponding figures.figure1_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figure3_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figure4_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figure5_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figure6_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figure7_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-1_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-2_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-3_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-4_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-5_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-6_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-7_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-8_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-9_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-10_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-11_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-12_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).figureS3-13_mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).primates-all-mirSUPPLEMENTARY MATERIALS S2. – Set of Euler/X toolkit output Maximally Informative Relations (MIR) for the input data files provided in the Supplementary Materials S1 and for the entire Prim-UC ("primates-all.csv"). Each output file is saved in .csv format. The MIR files form the basis for analyses of name:meaning relations (Tables 3–5).SupplementaryMaterials-S3SUPPLEMENTARY MATERIALS S3. – Visualizations for the primary set (3 partitions; Figs. S3 1–3) and secondary set (10 partitions; Figs. S3 4–13) of alignments for the Prim-UC. Each caption specifies the most inclusive concept sec. Groves (2005), aligned with the respective congruent and/or entailed concepts sec. Groves (1993). Fig. S3–1: 2005.Strepsirrhini (partition 3; see Table 2). Fig. S3–2: 2005.Haplorrhini, excluding 2005.Catarrhini (partition 4; see Table 2). Fig. S3–3: 2005.Catarrhini (partition 5; see Table 2). Fig. S3–4: 2005.Cheirogaleoidea. Fig. S3–5: 2005.Lemuroidea. Fig. S3–6: 2005.Lorisiformes. Fig. S3–7: 2005.Chiromyiformes. Fig. S3–8: 2005.Tarsiiformes. Fig. S3–9: 2005.Platyrrhini, excluding 2005.Callitrichinae. Fig. S3–10: 2005.Callitrichinae. Fig. S3–11: 2005.Cercopithecinae. Fig. S3–12: 2005.Colobinae. Fig. S3–13: 2005.Hominoidea (= Fig. 5). See also Supplementary Materials S1 and S2.SupplementaryMaterials-S4SUPPLEMENTARY MATERIALS S4. – List of 24 newly recognized, acquisition-contingent species-level concepts sec. Groves (2005).