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Franz 2014 BIGCB Tracking Change across Classifications and Phylogenies

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Slides presented on the Euler/X toolkit at the "Understanding Taxon Ranges in Space and Time" Workshop – Berkeley Initiative in Global Change Biology (BIGCB); held on November 07-09, 2014, University of California at Berkeley, CA. See also http://taxonbytes.org/bigcb-workshop-at-uc-berkeley-tackling-the-taxon-concept-problem/

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Franz 2014 BIGCB Tracking Change across Classifications and Phylogenies

  1. 1. Tracking taxonomic change across classifications and phylogenies Nico M. Franz 1,2 Arizona State University http://taxonbytes.org/ 1 Concepts and tools developed jointly with members of the Ludäscher Lab (UC Davis & UIUC): Mingmin Chen, Parisa Kianmajd, Shizhuo Yu, Shawn Bowers & Bertram Ludäscher 2 Understanding Taxon Ranges in Space and Time Workshop – Berkeley Initiative in Global Change Biology (BIGCB) November 07-09, 2014, University of California at Berkeley, CA On-line @ http://www.slideshare.net/taxonbytes/franz-2014-bigcb-tracking-change-across-classifications-and-phylogenies
  2. 2. "A toolkit for consistently aligning sets of hierarchically arranged entities under (relaxable) logic constraints, and using RCC-5 articulations."
  3. 3. Euler/X uses Answer Set Programming. The reasoner asks, and solves, the question: "Which possible worlds can be generated that satisfy (i.e., are consistent with) a given set of input constraints?"
  4. 4. Toolkit workflow. Objective: achieving well-specified alignments. Set of Input Constraints T1 = Taxonomy 1 T2 = Taxonomy 2 A = Input articulations [==, >, <, ><, |] C = Taxonomic constraints
  5. 5. Toolkit workflow. Objective: achieving well-specified alignments. Set of Input Constraints T1 = Taxonomy 1 T2 = Taxonomy 2 A = Input articulations [==, >, <, ><, |] C = Taxonomic constraints  Articulations are asserted by human toolkit users.
  6. 6. Toolkit workflow. Objective: achieving well-specified alignments. No! Set of Input Constraints T1 = Taxonomy 1 T2 = Taxonomy 2 A = Input articulations [==, >, <, ><, |] C = Taxonomic constraints
  7. 7. Toolkit workflow. Objective: achieving well-specified alignments. No! Set of Input Constraints T1 = Taxonomy 1 T2 = Taxonomy 2 A = Input articulations [==, >, <, ><, |] C = Taxonomic constraints
  8. 8. Toolkit workflow. Objective: achieving well-specified alignments. No! Yes Set of Input Constraints T1 = Taxonomy 1 T2 = Taxonomy 2 A = Input articulations [==, >, <, ><, |] C = Taxonomic constraints
  9. 9. Toolkit workflow. Objective: achieving well-specified alignments. No! Yes
  10. 10. Toolkit workflow. Objective: achieving well-specified alignments. MIR = Maximally Informative Relations [==, >, <, ><, |] for each concept pair Yes Yes
  11. 11. So, given an input set of [T1, T2, A, C], one gains: (1) Logical consistency in the alignment; (2) Intended degree of alignment resolution; (3) Additional, logically implied articulations; (4) Visualizations of taxonomic provenance; (5) Quantifications of name/meaning relations.
  12. 12. Use case: dwarf lemurs sec. MSW 1993 & 2005 1 Chirogaleus furcifer sec. Mühel (1890) – Brehms Tierleben. Public Domain: http://books.google.com/books?id=sDgQAQAAMAAJ 1 Franz et al. 2014. Taxonomic provenance: Two influential primate classifications logically aligned. (unpublished)
  13. 13. Toolkit demonstration. Overview of input and commands covered. (1) Input file: cheirogaleoidea.txt  well-specified (2) euler --help [available commands] (3) euler -i [filename] --iv [input visualization] (4) euler -i [filename] -e mnpw --rcgo [complete RCG run]
  14. 14. Toolkit demonstration. Overview of input and commands covered. (1) Input file: cheirogaleoidea.txt  well-specified (2) euler --help [available commands] (3) euler -i [filename] --iv [input visualization] (4) euler -i [filename] -e mnpw --rcgo [complete RCG run]  one articulation 'inverted'  over-specification (5) euler -i [filename] --cc [consistency check] (6) euler -i [filename] --ie [inconsistency explanation] (7) euler -i [filename] --repair=topdown [diagnosis, removal, run]
  15. 15. Toolkit demonstration. Overview of input and commands covered. (1) Input file: cheirogaleoidea.txt  well-specified (2) euler --help [available commands] (3) euler -i [filename] --iv [input visualization] (4) euler -i [filename] -e mnpw --rcgo [complete RCG run]  one articulation 'inverted'  over-specification (5) euler -i [filename] --cc [consistency check] (6) euler -i [filename] --ie [inconsistency explanation] (7) euler -i [filename] --repair=topdown [diagnosis, removal, run]  one articulation removed  under-specification (8) euler -i [filename] --ur [uncertainty reduction]
  16. 16. Suggested Workshop ideas for collective exploration.
  17. 17. 'Traditional' view – taxon concept hierarchies.
  18. 18. Expanded view 1 – vouchers drive taxon concept identity.
  19. 19. Expanded view 2 – vouchers instantiate character concept identity.
  20. 20. Expanded view 3 – taxon concepts, character concepts, vouchers.
  21. 21. Expanded view 3* – resolving concept overlap into merge regions.
  22. 22. Acknowledgments • Brent Mishler, Staci Markos & all BIGCB 2014Workshop organizers! • Euler/X team: Mingmin Chen, Parisa Kianmajd, Shizhuo Yu, Shawn Bowers & Bertram Ludäscher. • Edward Gilbert (oaks) & Naomi Pier (primates). • NSF DEB–1155984, DBI–1342595 (Franz); IIS–118088, DBI–1147273 (Ludäscher). • Information @ http://taxonbytes.org/tag/concept-taxonomy/ • Euler/X code @ https://bitbucket.org/eulerx • Euler server @ http://euler.asu.edu Franz Lab: http://taxonbytes.org/ https://sols.asu.edu/

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