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/

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. "A toolkit for consistently aligning
sets of hierarchically arranged entities
under (relaxable) logic constraints,
and using RCC-5 articulations."

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. Toolkit workflow. Objective: achieving well-specified alignments.
Set of Input Constraints
T1 = Taxonomy 1
T2 = Taxonomy 2
A = Input articulations
[==, >, <, ><, |]
C = Taxonomic constraints

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. 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. 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. 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. Toolkit workflow. Objective: achieving well-specified alignments.
No!
Yes

10. Toolkit workflow. Objective: achieving well-specified alignments.
MIR =
Maximally Informative Relations
[==, >, <, ><, |]
for each concept pair
Yes
Yes

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. 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. 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. 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. 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]

17. Suggested Workshop ideas
for collective exploration.

18. 'Traditional' view – taxon concept hierarchies.

19. Expanded view 1 – vouchers drive taxon concept identity.

20. Expanded view 2 – vouchers instantiate character concept identity.

21. Expanded view 3 – taxon concepts, character concepts, vouchers.

22. Expanded view 3* – resolving concept overlap into merge regions.

23. 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/