A Toolkit for Reconciling Multiple Taxonomic Perspectives: Euler/X and the Perelleschus Use Case...
-
Upload
chester-houston -
Category
Documents
-
view
214 -
download
0
Transcript of A Toolkit for Reconciling Multiple Taxonomic Perspectives: Euler/X and the Perelleschus Use Case...
![Page 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/1.jpg)
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
![Page 2: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/2.jpg)
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/homeOpen source:https://bitbucket.org/eulerx/euler-project Overview paper:http://taxonbytes.org/pdf/ChenEtAl2013-EulerToolkit.pdf
![Page 3: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/3.jpg)
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/homeOpen source:https://bitbucket.org/eulerx/euler-project Overview paper:http://taxonbytes.org/pdf/ChenEtAl2013-EulerToolkit.pdf
![Page 4: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/4.jpg)
congruence proper inclusion
overlapinverse 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
![Page 5: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/5.jpg)
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.
![Page 6: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/6.jpg)
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:
![Page 7: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/7.jpg)
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.
![Page 8: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/8.jpg)
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.
![Page 9: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/9.jpg)
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).
![Page 10: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/10.jpg)
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.
![Page 11: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/11.jpg)
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.
![Page 12: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/12.jpg)
Euler/X is ready1 for real-lifeuse cases – Perelleschus
1 After many iterations of testing/optimization with abstract cases, PW visualizations, and reasoner benchmarking.
![Page 13: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/13.jpg)
1986 2001
Perelleschus use case – overview of 6 classifications/phylogenies
1936 1954
2006 2013
= "carludovicae" (name), cumulative history
![Page 14: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/14.jpg)
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)
![Page 15: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/15.jpg)
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)
![Page 16: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/16.jpg)
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).
![Page 17: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/17.jpg)
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.
![Page 18: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/18.jpg)
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 speciesconcepts '36/'54
Color legend
Overlap (><)
![Page 19: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/19.jpg)
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
><
![Page 20: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/20.jpg)
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
><
![Page 21: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/21.jpg)
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].
![Page 22: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/22.jpg)
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.
![Page 23: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/23.jpg)
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 tr
unk2001: 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.
![Page 24: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/24.jpg)
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 onoverlap
![Page 25: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/25.jpg)
A201. Merge view – overlap
2. Zoom view – 2 levels
Level 1:
Level 2:
B47
A20' B47'
><
[3 new labels]
A20' B47'"AB2047"
B52A23A21B45 A22B46
In progress – zooming in on overlap, "combined concept" resolution
"AB2047"
![Page 26: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/26.jpg)
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.
![Page 27: 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.](https://reader035.fdocuments.us/reader035/viewer/2022062803/56649ce65503460f949b3c87/html5/thumbnails/27.jpg)
• 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