taxonbytes at TDWG 2013 – two papers on Answer Set Programming as a tool for taxonomic reasoning
At this year’s TDWG 2013 Annual Conference held from October 28 to November 01, in Florence, Italy, Nico Franz will present two talks on Answer Set Programming and name/taxon concept representation and reasoning. Both papers form part of the Semantics for Biodiversity Symposium, and specifically the Session “Ontologies and Formal Models” convened by Ramona Walls of iPlant and Nico Franz. Here are the abstracts; the actual presentation slides will be shared on taxonbytes.
Paper 1: A Toolkit for Reconciling Multiple Taxonomic Perspectives: Euler/X and the Perelleschus Use Case
Nico Franz, Mingmin Chen, Shizhuo Yu, Shawn Bowers and Bertram Ludäscher
We will demonstrate the features of Euler/X, a toolkit in development for logic-based multi-taxonomy integration. The Euler project (see http://euler.cs.ucdavis.edu/; software code available at https://bitbucket.org/eulerx/euler-project) utilizes the taxonomic concept approach to represent perceived taxonomic entities in two or more related yet distinct classifications. Euler/X will read in these taxonomies together with an initial set of expert-made concept relationship assessments, or articulations. The latter are based on Region Connection Calculus (RCC-5) relations; specifically congruence (=), proper inclusion (>), inverse proper inclusion (<), overlap (><), and exclusion (!). Experts can encode uncertainty in their assessments using disjunctions (e.g., “A = B or A > B”). Given the input and additional taxonomic covering constraints, Euler/X provides an interactive workflow for detecting, explaining, and repairing any inconsistencies in the expert alignment. Throughout, the workflow employs a suite of reasoning approaches including First-Order Logic (FOL) and Answer Set Programming (ASP). Once the inconsistencies are resolved, the toolkit infers a set of maximally informative relations (MIRs), and one or more “possible worlds”, representing different ways to merge the input taxonomies, are visualized. Upon viewing the possible worlds the expert user has follow-up opportunities to revisit articulations that are responsible for ambiguities in the merge, thereby reducing the number of possible world solutions. We demonstrate the Euler/X workflow and related considerations and challenges using the example of a Perelleschus concept history published by Franz & Cardona-Duque, 2013 . This weevil genus was revised in 2001 and again in 2013, resulting in two distinct taxonomic and phylogenetic perspectives that can be aligned and merged with the toolkit. Euler/X implements innovative concepts and logic representation technologies that advance the task of tracking classification and phylogeny provenance in systematics, with implications for biodiversity data annotation and integration.
 Franz, N.M. & J. Cardona-Duque. 2013. Description of two new species and phylogenetic reassessment of Perelleschus Wibmer & O’Brien, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013. Systematics and Biodiversity 11: 209–236.
Paper 2: Using Answer Set Programming to Simulate the Interplay of Taxonomic and Nomenclatural Change
Nico Franz and Joohyung Lee
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 the 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.