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.
figure1
SUPPLEMENTARY 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.
figure3
SUPPLEMENTARY 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.
figure4
SUPPLEMENTARY 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.
figure5
SUPPLEMENTARY 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.
figure6
SUPPLEMENTARY 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.
figure7
SUPPLEMENTARY 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.
figureS3-1
SUPPLEMENTARY 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.
figureS3-2
SUPPLEMENTARY 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.
figureS3-3
SUPPLEMENTARY 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.
figureS3-4
SUPPLEMENTARY 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.
figureS3-5
SUPPLEMENTARY 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.
figureS3-6
SUPPLEMENTARY 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.
figureS3-7
SUPPLEMENTARY 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.
figureS3-8
SUPPLEMENTARY 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.
figureS3-9
SUPPLEMENTARY 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.
figureS3-10
SUPPLEMENTARY 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.
figureS3-11
SUPPLEMENTARY 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.
figureS3-12
SUPPLEMENTARY 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.
figureS3-13
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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_mir
SUPPLEMENTARY 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-mir
SUPPLEMENTARY 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-S3
SUPPLEMENTARY 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-S4
SUPPLEMENTARY MATERIALS S4. – List of 24 newly recognized, acquisition-contingent species-level concepts sec. Groves (2005).