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Merge taxonomies with the Euler/ASP toolkit – the Andropogon use case

We have a new manuscript ready for submission that uses the Euler/ASP toolkit to reason over taxonomic change in the Andropogon (glomeratus-virginicus) ‘complex’ – an illuminating use case assembled by the visionary Alan Weakley. More on this toolkit soon; it is ready for application to larger and more complex use cases.

Nico M. Franz, Mingmin Chen, Shizhuo Yu, Shawn Bowers &  Bertram Ludäscher

Names Are Not Good Enough: Reasoning over Taxonomic Change in the Andropogon Complex

Abstract. The performance of taxonomic names and concepts to act as identifiers of changing taxonomic content is analyzed and visualized using a novel Answer Set Programming reasoning approach. The Euler/ASP toolkit is applied to a use case of eight succeeding classifications, ranging from 1889 to 2006, of a ‘complex’ of grasses in the genus Andropogon in the Carolinas and surrounding areas. Based on an input of 64 constituent concepts and 131 Region Connection Calculus articulations provided by an expert taxonomist, nine pairwise and logically consistent alignments are inferred and visualized as merge taxonomies that reflect the hierarchical relationships of congruent and non-congruent taxonomic concepts. The respectively valid names are integrated with these results, thus permitting quantitative assessments of name/concept resolution. Accordingly, 65.2% of 46 possible instances of congruence were realized in the alignments. Incongruent concepts were twice as common as their counterparts. Usages of different names failed to continuously identify congruent concepts in 66.7% of 30 cases, and the same names incorrectly identified incongruent concepts in 33.9% of 59 cases. Concept-level articulations can take into account both member- and property-based information when identifying similarities and differences between succeeding taxonomic perspectives. Names and nomenclatural relationships, in turn, are limited to establishing ‘identity’ based on subsets of ostensively designated (type) members. Using names-based identifiers to represent and reason over changing taxonomic content in the Semantic Web domain will be similarly limited.

Keywords. answer set programming, biological nomenclature, data integration, knowledge representation and reasoning, provenance, region connection calculus, taxonomic concepts, visualization

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