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

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

  1. 1. Using Answer Set Programming to Simulate the Interplay of Taxonomic and Nomenclatural Change Nico Franz1, Joohyung Lee2 & Chao Zhang2 1 School of Life Sciences, Arizona State University 2 CIDSE Automated Reasoning Group, ASU TDWD 2013 Annual Conference, Florence, Italy Semantics for Biodiversity – Formal Models and Ontologies November 01, 2013 Slides @ http://taxonbytes.org/tdwg-2013-using-asp-to-simulate-the-interplay-of-taxonomic-and-nomenclatural-change
  2. 2. Question – are the rules of nomenclature logically tractable?
  3. 3. Core principles embodied in the Code of Zoological Nomenclature 1. Binominal Nomenclature • The scientific name of a species, and not of a taxon at any other rank, is a combination of two names. 2. Priority • The valid name of a taxon is the oldest available name applied to it. 3. Coordination • Within the [family, genus, species] group, a name established for a taxon at any rank is simultaneously established with the same author/date for taxa with the same name-bearing type at other ranks in the group. 4. First Reviser • The relative precedence of two or more names or nomenclatural acts published on the same date, or of different original spellings of the same name, is determined by the First Reviser. 5. Homonymy • The name of each taxon must be unique. 6. Typification • Each nominal taxon in the family group, genus group or species group has a name-bearing type fixed to provide the objective standard of reference by which the application of the name is determined. 7. [Gender Agreement] • Agreement in grammatical gender between a generic name and Latin or latinized adjectival or participial species-group names combined with it originally or subsequently. Source: Code On-Line: http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp
  4. 4. Core principles embodied in the Code of Zoological Nomenclature 1. Binominal Nomenclature • The scientific name of a species, and not… 2. Priority • The valid name of a taxon is the oldest…. Working hypothesis: All (6 + 1) Principles are representable in Stable Model Semantics and computable with ASP programs & solvers. 3. Coordination • Within the [family, genus, species] group, a name established for a taxon at any rank is simultaneously established with the same author/date for taxa with the same name-bearing type at other ranks in the group. 4. First Reviser • The relative precedence of two or more names or nomenclatural acts published on the same date, or of different original spellings of the same name, is determined by the First Reviser. 5. Homonymy • The name of each taxon must be unique. 6. Typification • Each nominal taxon in the family group, genus group or species group has a name-bearing type fixed to provide the objective standard of reference by which the application of the name is determined. 7. [Gender Agreement] • Agreement in grammatical gender between a generic name and Latin or latinized adjectival or participial species-group names combined with it originally or subsequently. Source: Code On-Line: http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp
  5. 5. Answer Set Programming reviewed in 10 bullet points • Relatively new programming paradigm, not widely used until late 1990s • A form of declarative programming based on Stable Model Semantics • Combines expressive representation language with efficient solving tools • Instead of proving truth/falsity, identifies solutions that satisfy conditions
  6. 6. Answer Set Programming reviewed in 10 bullet points • Relatively new programming paradigm, not widely used until late 1990s • A form of declarative programming based on Stable Model Semantics • Combines expressive representation language with efficient solving tools • Instead of proving truth/falsity, identifies solutions that satisfy conditions • Closed World Assumption – what is not known is false (unlike OWL-DL) • Can compute non-monotonic reasoning • Has the property of elaboration tolerance • Excels at modeling complex rules
  7. 7. Answer Set Programming reviewed in 10 bullet points • Relatively new programming paradigm, not widely used until late 1990s • A form of declarative programming based on Stable Model Semantics • Combines expressive representation language with efficient solving tools • Instead of proving truth/falsity, identifies solutions that satisfy conditions • Closed World Assumption – what is not known is false (unlike OWL-DL) • Can compute non-monotonic reasoning • Has the property of elaboration tolerance • Excels at modeling complex rules • Capable of default reasoning ("by default, X is true"), transition systems • Translatable (in part) into First-Order Logic (FOL), Description Logic (DL) • More information in the reference list appended to this presentation
  8. 8. ASP paradigm – set conditions, constraints, ground, identify SMs Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf
  9. 9. ASP paradigm – apply to taxonomy/nomenclature change scenario  Fully specified input taxonomy (t = 0); incl.: ranked names, priority/type relationships  At t = 1 (revision), effect a taxonomic change where 1 species is moved into another genus Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf
  10. 10. ASP paradigm – apply to taxonomy/nomenclature change scenario  Represent: input tree, names, years, ranks…  Encode: Principles of Nomenclature  Choice: Select a taxonomic change scenario Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf
  11. 11. ASP paradigm – apply to taxonomy/nomenclature change scenario  Grounding of all domains, variables and conditions at t = 0 (original) vs. t = 1 (revision) Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf
  12. 12. ASP paradigm – apply to taxonomy/nomenclature change scenario  Inference of Stable Models (taxonomies) and all concomitant nomenclatural emendations Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf
  13. 13. 9-taxon use case – transition model
  14. 14. Input (original) taxonomy at t = 0 ["9-name/taxon use case"] • All type bearing and non-type bearing epithets have different publication years t=0 * = type-bearing name  Transition: exactly 1 species will move to the other genus at t = 1.  Since there are 4 species, this yields 4 Stable Models.
  15. 15. Model 1: O. secundus moves into Agenus • Requires new higher-level synonymies, "cascading", new names, new types t=0 t=1  Required nomenclatural changes; O. secundus is a type bearer.
  16. 16. Model 2: A. tertius moves into Ogenus • Non-type bearer – 1 taxonomic change ↔ 1 new combination t=0 t=1
  17. 17. Model 3: O. quartus moves into Agenus • Non-type bearer – 1 taxonomic change ↔ 1 new combination t=0 t=1
  18. 18. Model 4: A. primus "moves" [Ogenus spp. ingress into Agenus] • Most dramatic nomenclatural adjustments – A. primus is globally oldest type t=0 t=1  Two species (names) – secundus & quartus – move into Agenus.
  19. 19. Modeling in ASP Does it work? It does.
  20. 20. Current ASP program properly resolves all 4 models* * Output optics notwithstanding; actual tree visualization in progress.
  21. 21. Conclusion – ASP can logically represent key rules of nomenclature 1. Binominal Nomenclature • The scientific name of a species, and not… 2. Priority = Principles currently modeled. • The valid name of a taxon is the oldest…. 3. Coordination • Within the [family, genus, species] group, a name established for a taxon at any rank is simultaneously established with the same author/date for taxa with the same name-bearing type at other ranks in the group. 4. First Reviser Extension of Priority. • The relative precedence of two or more names or nomenclatural acts published on the same date, or of different original spellings of the same name, is determined by the First Reviser. 5. Homonymy Likely feasible. • The name of each taxon must be unique. 6. Typification • Each nominal taxon in the family group, genus group or species group has a name-bearing type fixed to provide the objective standard of reference by which the application of the name is determined. 7. [Gender Agreement] Likely feasible. • Agreement in grammatical gender between a generic name and Latin or latinized adjectival or participial species-group names combined with it originally or subsequently.
  22. 22. ASP code sample – modeling priority, new combination, synonymy
  23. 23. Next up – improved output visualization, more complex cases • "20-name/taxon use case" can include 36 *one-species-moves* permutations • Compute, tabulate, visualize complete set of nomenclatural changes for each • At the genus level, moving entire non-type genera requires no name change
  24. 24. Conclusions & outlook 1. This work is a novel representation of the Principles of Nomenclature in a formal logic system with default conditions and transitional properties. 2. The model can be elaborated to include an increasing wide range of taxonomic / nomenclatural change scenarios, and specific rule exceptions. 3. ASP could be utilized to validate proposed nomenclatural emendations or infer additional required changes, and implemented in a nomenclatoral repository such as ZooBank. 4. In complex change scenarios, ASP could be used to perform optimizations and minimize nomenclatural instability given the need to move one or more taxa.
  25. 25. Acknowledgments • TDWG 2013 Symposium organizers – John Deck, Mark Schildhauer, Ramona Walls • Stanley Blum, David Patterson, Richard Pyle – nomenclatural use case input • Euler team, UC Davis – Bertram Ludäscher, Mingmin Chen – ASP support https://sols.asu.edu http://taxonbytes.org
  26. 26. What is ASP? – introductory reading list & links Brewka, G., T. Either & M. Truszczyoski. 2011. Answer set programming at a glance. Communications of the ACM 54: 92-103. Available at http://people.scs.carleton.ca/~bertossi/KR11/material/communications201112ASP.pdf Eiter, T. 2008. Answer Set Programming in a nutshell. Available at http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf Gelfond, M. 2008. Answer sets; pp. 285-316. In: van Harmelen, F., V. Lifschitz & B. Porter. Handbook of Knowledge Representation. Elsevier. Available at http://www.depts.ttu.edu/cs/research/krlab/pdfs/papers/gel07b.pdf Gebser, M., B. Kaufmann, R. Kaminski, M. Ostrowski, T. Schaub & M. Schneider. 2011. Potassco: the Potsdam Answer Set Solving Collection. Available at http://www.cs.unipotsdam.de/wv/pdfformat/gekakaosscsc11a.pdf Lifschitz, V. 2008. What is Answer Set Programming? Available at http://www.cs.utexas.edu/~ai-lab/pubs/wiasp.pdf Potassco Group website: http://potassco.sourceforge.net/ (programs, tutorials)

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