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A Toolkit for Reconciling
Multiple Taxonomic Perspectives:
Euler/X and the Perelleschus Use Case
Nico Franz1, Mingmin Chen2, Shizhuo Yu2, Shawn Bowers3 & Bertram Ludäscher2
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-perspectives
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
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
Review: RCC-5 articulations between two concepts C1, C2

congruence

inverse proper
inclusion

exclusion

proper inclusion

overlap

Use of "OR" to express uncertainty.
Example: C1 == OR > C2

Source: Franz & Peet. 2009. Towards a language for mapping relationships among taxonomic concepts. Systematics and Biodiversity 7: 5–20.
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.
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 + T1 + T2) plus a set of
initial, expert-made articulations (A). The toolkit then allows for:
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 + T1 + T2) plus a set of
initial, expert-made articulations (A). The toolkit then allows for:
• Checking for, and identification of, alignment inconsistencies.
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 + T1 + T2) plus a set of
initial, expert-made articulations (A). The toolkit then allows for:
• Checking for, and identification of, alignment inconsistencies.
• Interactive inconsistency repair.
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 + T1 + T2) 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 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 + T1 + T2) 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.
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 + T1 + T2) 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.
Euler/X is ready1 for real-life
use cases – Perelleschus

1

After many iterations of testing/optimization with abstract cases, PW visualizations, and reasoner benchmarking.
Perelleschus use case – overview of 6 classifications/phylogenies
1936

1954




1986

 = "carludovicae" (name),
cumulative history

2001


2006

2013






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 1st 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)
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 1st 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)
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).
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.
Concept evolution – Günther (1936) to Voss (1954)

Once "1 Imp" is added, Euler/X yields a consistent merge that is intuitive at all levels.
Euler/X mir

Euler/X merge
1.1 Imp

Color legend
1936 concepts
1954 concepts
Congruent species
concepts '36/'54
Overlap (><)
Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001)

Euler/X merge
Color legend
1986
2001
Congr.
'86/'01
><

Euler/X infers a consistent and
plausible merge of the 1986 threespecies taxonomy and the eightspecies 2001 phylogeny.
Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001)

Euler/X merge
Color legend
1986
2001
Congr.
'86/'01
><

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].
Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001)

Euler/X merge
Color legend
1986
2001
Congr.
'86/'01
><

The 2001 authors transferred
"subcinctus" into Phyllotrox [12].
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.
Concept evolution – Franz & O'Brien (2001) to Franz & Cardona-D. (2013)
Once the results: were due in part as congruent and "sealed off" (through
Initial mergeoutroups "noisy" "stipulated"because of divergent outgroup assumptions.
application of coverage) Outgroups ingroups, "noise"
from the too much the merge got solidified and simplified.

2013: Phyllotrogina

Unwanted overlap???

2001: Derelomini
out of position

38 = 2013: Perelleschus

Main 2013 higher-level trunk

14 = 2001: Perelleschus
Concept evolution – Franz & O'Brien (2001) to Franz & Cardona-D. (2013)
2013 higher-level concepts
2001 higher-level concepts
2013/2001 congruence

Zoom in on
overlap
"Clean" merge with overlapping,
parallel 2001/2013 mid-level trunks
that reflect the addition of a new,
nested 2013 clade.

New 2013 clade
In progress – zooming in on overlap, "combined concept" resolution
1. Merge view – overlap

A20

A20'

[3 new labels]

><

"AB2047"

B47

B47'

2. Zoom view – 2 levels
Level 1:

Level 2:

A20'
A21B45

A22B46

"AB2047"

B47'

A23

B52
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.
Acknowledgments
• 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."

https://sites.google.com/site/eulerdi/home

https://sols.asu.edu

http://taxonbytes.org

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Franz Et Al. A Toolkit for Reconciling Multiple Taxonomic Perspectives: Euler/X and the Perelleschus Use Case

  • 1. A Toolkit for Reconciling Multiple Taxonomic Perspectives: Euler/X and the Perelleschus Use Case Nico Franz1, Mingmin Chen2, Shizhuo Yu2, Shawn Bowers3 & Bertram Ludäscher2 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-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. Review: RCC-5 articulations between two concepts C1, C2 congruence inverse proper inclusion exclusion proper inclusion overlap Use of "OR" to express uncertainty. Example: C1 == OR > C2 Source: Franz & Peet. 2009. Towards a language for mapping relationships among taxonomic concepts. Systematics and Biodiversity 7: 5–20.
  • 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 + T1 + T2) 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 + T1 + T2) 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 + T1 + T2) 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 + T1 + T2) 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 + T1 + T2) 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 + T1 + T2) 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 ready1 for real-life use cases – Perelleschus 1 After many iterations of testing/optimization with abstract cases, PW visualizations, and reasoner benchmarking.
  • 13. Perelleschus use case – overview of 6 classifications/phylogenies 1936 1954   1986  = "carludovicae" (name), cumulative history 2001  2006 2013   
  • 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 1st 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)
  • 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 1st 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)
  • 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) Once "1 Imp" is added, Euler/X yields a consistent merge that is intuitive at all levels. Euler/X mir Euler/X merge 1.1 Imp Color legend 1936 concepts 1954 concepts Congruent species concepts '36/'54 Overlap (><)
  • 19. Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001) Euler/X merge Color legend 1986 2001 Congr. '86/'01 >< Euler/X infers a consistent and plausible merge of the 1986 threespecies taxonomy and the eightspecies 2001 phylogeny.
  • 20. Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001) Euler/X merge Color legend 1986 2001 Congr. '86/'01 >< 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].
  • 21. Concept evolution – Wibmer & O'Brien (1986) to Franz & O'Brien (2001) Euler/X merge Color legend 1986 2001 Congr. '86/'01 >< 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) Once the results: were due in part as congruent and "sealed off" (through Initial mergeoutroups "noisy" "stipulated"because of divergent outgroup assumptions. application of coverage) Outgroups ingroups, "noise" from the too much the merge got solidified and simplified. 2013: Phyllotrogina Unwanted overlap??? 2001: Derelomini out of position 38 = 2013: Perelleschus Main 2013 higher-level trunk 14 = 2001: Perelleschus
  • 24. Concept evolution – Franz & O'Brien (2001) to Franz & Cardona-D. (2013) 2013 higher-level concepts 2001 higher-level concepts 2013/2001 congruence Zoom in on overlap "Clean" merge with overlapping, parallel 2001/2013 mid-level trunks that reflect the addition of a new, nested 2013 clade. New 2013 clade
  • 25. In progress – zooming in on overlap, "combined concept" resolution 1. Merge view – overlap A20 A20' [3 new labels] >< "AB2047" B47 B47' 2. Zoom view – 2 levels Level 1: Level 2: A20' A21B45 A22B46 "AB2047" B47' A23 B52
  • 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. Acknowledgments • 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." https://sites.google.com/site/eulerdi/home https://sols.asu.edu http://taxonbytes.org