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TDWG 2013: Using ASP to simulate the interplay of taxonomic and nomenclatural change

Presentation slides are now posted for the TDWG 2013 ASP Taxonomy Nomenclature talk.

Franz Et Al. Using ASP to Simulate the Interplay of Taxonomic and Nomenclatural Change from taxonbytes

Using Answer Set Programming to Simulate the Interplay of Taxonomic and Nomenclatural Change

Nico Franz, Joohyung Lee & Chao Zhang

Date: 2013-11-01 10:03 AM – 10:11 AM


Answer Set Programming (ASP) is a declarative, stable model approach to logic programming with an under-realized potential for representing and reasoning over biological information. ASP is particularly suited to address reasoning challenges with complex starting conditions and rule sets. One such challenge is the interplay of taxonomic and nomenclatural change in biological taxonomy that often results when a taxonomy is revised based on a previously published perspective. Depending on the nature of the taxonomic changes to be undertaken, one or more Code-mandated principles will apply to regulate specific and concomitant name changes. In the case of the International Code of Zoological Nomenclature, two principles of significance include the Principles of Priority and Typification. Although the relationship between the number of taxonomic and nomenclatural adjustments under a given transition scenario is not linear, the application of the name-changing rules is usually unambiguous and therefore amenable to logic representation. Here we explore the modeling of the taxonomy/nomenclature interplay in ASP with a simple, abstract nine-taxon use case that contains four terminal species of which two are type-bearers for their respective genera. Four distinct one-taxon transfer scenarios are simulated through a transition system approach, requiring 1-7 concomitant nomenclatural changes depending (1) on the priority relationships among the terminal taxa being repositioned and (2) the type-bearing name dependencies of their higher-level parents. ASP can simulate these rules faithfully and thus reason over situations that range from a one-to-one match of taxonomic and nomenclatural changes to situations where they two kinds of change become increasingly disconnected (e.g., transfer of non-type genera among tribes without name change, or “transfer” [in reverse direction] of a single priority-carrying name/taxon into a larger yet junior entity with numerous required name changes). Our results, though very preliminary, illustrate how ASP logic approach may be utilized to perform optimizations at the taxonomy/nomenclature intersection, and generally represent a novel step towards translating Code-mandated naming rules into logic, with potential benefits for virtual taxonomic domains.

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