1. A Toolkit for Reconciling Multiple Taxonomic Perspectives: Euler/X and the Perelleschus Use Case Nico Franz 1, Mingmin Chen 2, Shizhuo Yu 2, Shawn Bowers 3 & Bertram Ludäscher 2 1 School of Life Sciences, Arizona State University 2 Department of Computer Science, UC Davis 3 Department of Computer Science, Gonzaga University TDWD 2013 Annual Conference, Florence, Italy Semantics for Biodiversity – Formal Models and Ontologies November 01, 2013 Slides @ http://taxonbytes.org/tdwg-2013-a-toolkit-for-reconciling-multiple-taxonomic-perspectiveshttp://taxonbytes.org/tdwg-2013-a-toolkit-for-reconciling-multiple-taxonomic-perspectives

2. Introduction – the Euler project & Euler/X toolkit The project builds on a ~ 25 year history of using taxonomic concepts in the TDWG community; primarily in Australia, Germany, United Kingdom, Japan. Prior extensive uses of concept articulations include Koperski et al. (2000); and concatenation of articulations by Berendsohn, Geoffroy & Güntsch (2003). Homepage: https://sites.google.com/site/eulerdi/home Open source: https://bitbucket.org/eulerx/euler-project Overview paper: http://taxonbytes.org/pdf/ChenEtAl2013-EulerToolkit.pdf

3. Introduction – the Euler project & Euler/X toolkit The project builds on a ~ 25 year history of using taxonomic concepts in the TDWG community; primarily in Australia, Germany, United Kingdom, Japan. Prior extensive uses of concept articulations include Koperski et al. (2000); and concatenation of articulations by Berendsohn, Geoffroy & Güntsch (2003). David Thau's (2006-2010) work on CleanTax prototyped the use of RCC-5 relations in combination for First-Order Logic reasoning over taxonomies. The Euler project (2011-) succeeds CleanTax, with performance optimizations, many added functions, and an increasing focus on Answer Set Programming. Homepage: https://sites.google.com/site/eulerdi/home Open source: https://bitbucket.org/eulerx/euler-project Overview paper: http://taxonbytes.org/pdf/ChenEtAl2013-EulerToolkit.pdf

4. congruence proper inclusion overlap inverse proper inclusion exclusion Source: Franz & Peet. 2009. Towards a language for mapping relationships among taxonomic concepts. Systematics and Biodiversity 7: 5–20.  Use of "OR" to express uncertainty. Example: C1 == OR > C2 Review: RCC-5 articulations between two concepts C1, C2

5. Interactive taxonomy alignment: Euler/X toolkit workflow Challenge: asserting articulations across 2 taxonomies may lead to ambiguities, inconsistencies, and omissions, resulting in an imperfect alignment.

6. Interactive taxonomy alignment: Euler/X toolkit workflow Challenge: asserting articulations across 2 taxonomies may lead to ambiguities, inconsistencies, and omissions, resulting in an imperfect alignment. Solution: Euler/X reads in 2 concept taxonomies (TCs + T 1 + T 2 ) plus a set of initial, expert-made articulations (A). The toolkit then allows for:

7. Interactive taxonomy alignment: Euler/X toolkit workflow Challenge: asserting articulations across 2 taxonomies may lead to ambiguities, inconsistencies, and omissions, resulting in an imperfect alignment. Solution: Euler/X reads in 2 concept taxonomies (TCs + T 1 + T 2 ) plus a set of initial, expert-made articulations (A). The toolkit then allows for: Checking for, and identification of, alignment inconsistencies.

8. Interactive taxonomy alignment: Euler/X toolkit workflow Challenge: asserting articulations across 2 taxonomies may lead to ambiguities, inconsistencies, and omissions, resulting in an imperfect alignment. Solution: Euler/X reads in 2 concept taxonomies (TCs + T 1 + T 2 ) plus a set of initial, expert-made articulations (A). The toolkit then allows for: Checking for, and identification of, alignment inconsistencies. Interactive inconsistency repair.

9. Interactive taxonomy alignment: Euler/X toolkit workflow Challenge: asserting articulations across 2 taxonomies may lead to ambiguities, inconsistencies, and omissions, resulting in an imperfect alignment. Solution: Euler/X reads in 2 concept taxonomies (TCs + T 1 + T 2 ) plus a set of initial, expert-made articulations (A). The toolkit then allows for: Checking for, and identification of, alignment inconsistencies. Interactive inconsistency repair. Generation of the set of mir – maximally informative relations (necessary and sufficient to yield a complete alignment).

10. Interactive taxonomy alignment: Euler/X toolkit workflow Challenge: asserting articulations across 2 taxonomies may lead to ambiguities, inconsistencies, and omissions, resulting in an imperfect alignment. Solution: Euler/X reads in 2 concept taxonomies (TCs + T 1 + T 2 ) plus a set of initial, expert-made articulations (A). The toolkit then allows for: Checking for, and identification of, alignment inconsistencies. Interactive inconsistency repair. Generation of the set of mir – maximally informative relations (necessary and sufficient to yield a complete alignment). Interactive uncertainty reduction.

11. Interactive taxonomy alignment: Euler/X toolkit workflow Challenge: asserting articulations across 2 taxonomies may lead to ambiguities, inconsistencies, and omissions, resulting in an imperfect alignment. Solution: Euler/X reads in 2 concept taxonomies (TCs + T 1 + T 2 ) plus a set of initial, expert-made articulations (A). The toolkit then allows for: Checking for, and identification of, alignment inconsistencies. Interactive inconsistency repair. Generation of the set of mir – maximally informative relations (necessary and sufficient to yield a complete alignment). Interactive uncertainty reduction. Visualization of one or more "Possible World" merge taxonomies.

12. Euler/X is ready 1 for real-life use cases – Perelleschus 1 After many iterations of testing/optimization with abstract cases, PW visualizations, and reasoner benchmarking.

13. 19862001   Perelleschus use case – overview of 6 classifications/phylogenies 19361954  20062013    = "carludovicae" (name), cumulative history

14. Key properties of the Perelleschus concept history use case 6 classifications (3 taxonomic, 3 phylogenetic), 54 concepts, from 1936 to 2013 Complete concept history from 1 st concept E. carludovicae sec. Günther (1936) to current phylogenetic arrangement (2013) with 10 species-level concepts. All instances of taxonomic incongruence occur above the species level. DOI:10.1080/14772000.2013.806371 (link)link

15. Key properties of the Perelleschus concept history use case 6 classifications (3 taxonomic, 3 phylogenetic), 54 concepts, from 1936 to 2013 Complete concept history from 1 st concept E. carludovicae sec. Günther (1936) to current phylogenetic arrangement (2013) with 10 species-level concepts. All instances of taxonomic incongruence occur above the species level. Franz & Cardona-D. (2013) provide 54 concepts + Trees 1-6 + 76 articulations. Only 5 of 54 higher-level concept articulations are unambiguously congruent. Articulations take into account membership & diagnostic features. DOI:10.1080/14772000.2013.806371 (link)link

16. Concept evolution – Günther (1936) to Voss (1954)  Reconciliation appears easy enough; except E. carludovicae sec. Günther (1936; [2]) – a Costa Rican taxon/concept – was placed in Elleschus sec. Günther (1936; [1]) – a European taxon/concept with several other children which the author omitted in his 1936 treatment (issue: incomplete listing of children).

17. Concept evolution – Günther (1936) to Voss (1954)  Reconciliation appears easy enough; except E. carludovicae sec. Günther (1936; [2]) – a Costa Rican taxon/concept – was placed in Elleschus sec. Günther (1936; [1]) – a European taxon/concept with several other children which the author omitted in his 1936 treatment (issue: incomplete listing of children).  Thus "overlap" (><) is an intuitive articulation among [1] and [3]; however Euler/X would not infer this unless we either: 1.Relax the "coverage assumption" for [1] (coverage means that a parent's extension is fully defined by its children); or 2.Add a child "1 Imp" (implied) to obtain the proper mir and merge.

18. Concept evolution – Günther (1936) to Voss (1954) 1.1 Imp Euler/X mergeEuler/X mir  Once "1 Imp" is added, Euler/X yields a consistent merge that is intuitive at all levels. 1954 concepts 1936 concepts Congruent species concepts '36/'54 Color legend Overlap (><)

19. Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001)  Euler/X infers a consistent and plausible merge of the 1986 three- species taxonomy and the eight- species 2001 phylogeny. 2001 1986 Congr. '86/'01 Color legend Euler/X merge ><

20. Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001)  The overlap (><) articulations among 2001 higher-level concepts [14,16,20,…] and Perelleschus sec. W. & O. 1986 [7] are rooted in the inclusion/exclusion of "subcinctus" [10/13] in "Perelleschus" [7/14]. 2001 1986 Congr. '86/'01 Color legend Euler/X merge ><

21. Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001) 2001 1986 Congr. '86/'01 Color legend Euler/X merge ><  The 2001 authors transferred "subcinctus" into Phyllotrox [12].

22. Concept evolution – Franz & O'Brien (2001) to Franz & Cardona-D. (2013)  At the surface and beyond, the two phylogenies share many congruent terminals and seemingly also higher-level entities.  However, the 2013 treatment includes two new species/concepts [53,54] and one new clade [52] nested well within the genus-level topology.

23. Concept evolution – Franz & O'Brien (2001) to Franz & Cardona-D. (2013)  Initial merge results: "noisy" due in part because of divergent outgroup assumptions. Main 2013 higher-level trunk Main 2001 higher-level trunk 2001: Derelomini  out of position 14 = 2001: Perelleschus 38 = 2013: Perelleschus 2013: Phyllotrogina Outgroups  too much "noise" Unwanted overlap???  Once the outroups were "stipulated" as congruent and "sealed off" (through application of coverage) from the ingroups, the merge got solidified and simplified.

24. 2013 higher-level concepts 2001 higher-level concepts 2013/2001 congruence Concept evolution – Franz & O'Brien (2001) to Franz & Cardona-D. (2013) New 2013 clade  "Clean" merge with overlapping, parallel 2001/2013 mid-level trunks that reflect the addition of a new, nested 2013 clade. Zoom in on overlap

25. A20 1. Merge view – overlap 2. Zoom view – 2 levels Level 1: Level 2: B47 A20'B47' >< [3 new labels] A20'B47' "AB2047" B52 A23 A21B45A22B46 In progress – zooming in on overlap, "combined concept" resolution "AB2047"

26. Conclusions & outlook 1.The Euler/X toolkit is moving towards logically sound, interactive, scalable, and visually effective solutions to the challenge of reasoning over concept and classification / phylogeny provenance in real-life use cases. 2.Many agencies and projects aim towards integration of taxonomic names and concepts, including the Global Names Architecture initiative. 3.The Euler concept approach represents a robust and powerful way to achieve this through interactive, semi-automated reasoning and visualization of merge taxonomies.

27. TDWG 2013 Symposium organizers – John Deck, Mark Schildhauer, Ramona Walls Juliana Cardona-Duque – Universidad de Antioquia, Medellín, Colombia NSF Award IIS-1118088. "III: Small: A Logic-Based, Provenance-Aware System for Merging Scientific Data under Context and Classification Constraints." Acknowledgments http://taxonbytes.org https://sols.asu.edu https://sites.google.com/site/eulerdi/home