franz et al 2015 escjam 2015 logic resolution taxonomic variable
TRANSCRIPT
Logic resolutionof the taxonomic variable
for evolutionary and biodiversityinformation environments
Nico M. Franz1 , Andrew Jansen1 & Bertram Ludäscher2
1 School of Life Sciences, Arizona State University2 iSchool, University of Illinois at Urbana-Champaign
Symposium - Arthropod Biodiversity Informatics in the AnthropoceneJoint Annual Meeting, Entomological Societies of Canada and Québec
November 11, 2015 - Montréal, Canada
@ http://www.slideshare.net/taxonbytes/franz-et-al-escjam-2015-logic-resolution-taxonomic-variable
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New publication: http://zookeys.pensoft.net/articles.php?id=6001
DOI: 10.3897/zookeys.528.6001
Minyomerus aeriballux Jansen & Franzsec. Jansen & Franz (2015)
Minyomerus reburrus Jansen & Franzsec. Jansen & Franz (2015)
Minyomerus cracens Jansen & Franzsec. Jansen & Franz (2015)
Minyomerus trisetosus Jansen & Franzsec. Jansen & Franz (2015)
Minyomerus puticulatus Jansen & Franzsec. Jansen & Franz (2015)
Minyomerus politus Jansen & Franzsec. Jansen & Franz (2015)
Minyomerus rutellirostris Jansen & Franzsec. Jansen & Franz (2015)
Minyomerus microps (Say)sec. Jansen & Franz (2015)
Syntactic & semantic conventions
Name (author, year) sec. Source (year) "taxonomic concept label"
Concept-to-concept relationships "RCC-5 articulations"
Syntactic & semantic conventions
Name (author, year) sec. Source (year) "taxonomic concept label"
Concept-to-concept relationships "RCC-5 articulations"
Do this all the time.
The downsides are fairly obvious
• Cumbersome to write, read, and pronounce
• Too many identifiers are hard to remember
• Not really needed for human understanding
The downsides are fairly obvious
• Cumbersome to write, read, and pronounce
• Too many identifiers are hard to remember
• Not really needed for human understanding
• Which taxonomic concept labels to use?
• What are taxonomic concepts anyway?
• Why (when) are names not enough?
The upsides, in turn, are a bit subtle
• Human taxonomic knowledge continues to evolve
• Nomenclature tracks this evolution – imperfectly
Recognized primate species – 1912 to present
Source: Rylands & Mittermeier. 2014. Primate taxonomy: species and conservation. Evol. Anthropol. 23: 8–10.
4: Amauris (Amaura) (damocles) hyalites makuyuensis Carcasson (1964) sec. Vane-Wright (2003)genus superspecies subspecies subgenus semispecies
Oscillating meanings of the species epithet hyalites – 1911 to 2003
Phenotypic diversityTy
pe-a
ncho
red
nam
e id
entit
y re
latio
ns
The upsides, in turn, are a bit subtle
• Human taxonomic knowledge continues to evolve
• Nomenclature tracks this evolution – imperfectly
• Reliable interpretation of evolving name:meaning relations requires an (adequate) understanding of the (often implicit) context of name application
• Humans excel at this, yet computational logic struggles
The upsides, in turn, are a bit subtle
• Human taxonomic knowledge continues to evolve
• Nomenclature tracks this evolution – imperfectly
• Reliable interpretation of evolving name:meaning relations requires an (adequate) understanding of the (often implicit) context of name application
• Humans excel at this, yet computational logic struggles
• Thus, biodiversity data environments that use names to track evolving taxonomic meanings are (by design) logic-disabled
• There are some known, and likely unknown, costs to this
Questions:
How to make taxonomic evolutionlogically tractable?
Do the benefits of doing sooutweigh the costs?
Euler/X multi-taxonomy alignment toolkit – desktop version
URL: https://github.com/EulerProject/EulerX
Web version available via "Explorer of Taxon Concepts" platform
URLs: http://taxonconceptexplorer.org/pub/Main_Page and http://etc.cs.umb.edu/etcsite/start.html
Input constraints:
T1 = Taxonomy 1
T2 = Taxonomy 2...
TX = Taxonomy X
A = RCC-5 articulations [==, >, <, ><, |]
C = Taxonomic constraints
Workflow: designed to achieve well-specified alignments
Articulations are provided by users (taxonomists).
Input visualization: Minyomerus sec. 2015 versus 1982
2015 concepts
1982 concepts
RCC-5 inputarticulations
MIR =Maximally Informative Relations
[==, >, <, ><, |]for each concept pair
Yes
Yes
Workflow: output of "MIR" and alignment visualizations
Oscillating meanings of the species epithet hyalites – 1911 to 2003
Phenotypic diversityTy
pe-a
ncho
red
nam
e id
entit
y re
latio
ns
Amauris alignment visualizations (1)
1940/1911
Legend
"Reduced Containment Graph" Shows overlap among input concepts
Amauris alignment visualizations (1)
1940/1911
Legend
"Reduced Containment Graph" Shows overlap among input concepts
"Combined Concept Graph" Resolves overlap into Euler subregions
A >< B A*B , A\b , B\a (* = and ; \ = not)
Minyomerus input visualizations
• 14 classifications covered
• Time interval: 1831–2015
• sec. O'Brien & Wibmer 1982 is the most immediately pre-ceding classification
Minyomerus alignment visualization – 2015/1982
6 congruent (paired) species-level entities
2 names synonymized, = 2 concepts subsumed
Minyomerus alignment visualization – 2015/1982
10 newly described species-level entities
6 congruent (paired) species-level entities
2 names synonymized, = 2 concepts subsumed
Minyomerus alignment visualization – 2015/1982
10 newly described species-level entities
6 congruent (paired) species-level entities
2 names synonymized, = 2 concepts subsumed
Expanded genus-level
concept
Minyomerus alignment MIR – 2015/1982
• 21 input articulations 180 Maximally Informative Relations
• Interactive "ProvenanceMatrix" can sort and visualize the MIR
• Machine-interpretable MIR can guide information integration
Source: Dang et al. 2015. ProvenanceMatrix: a visualization tool for multi-taxonomy alignments. CEUR Workshop Proceedings 1456: 13–24. Software available @ https://github.com/CreativeCodingLab/ProvenanceMatrix
We can align/analyze much more…
Perelleschus salpinflexus sec. Franz & Cardona-Duque (2013)DOI:10.1080/14772000.2013.806371
Perelleschus input phylogenies – 2013/2001
• Two species-level concepts added in 2013 phylogenetic revision (single clade)
2001 2013
Source: Franz & Cardona-Duque. 2013. Description of two new species and phylogenetic reassessment of Perelleschus Wibmer & O'Brien, 1986 (Coleoptera: Curculionidae) […]. Systematics and Biodiversity 11: 209–236.
Perelleschus multi-phylogeny alignment – 2013/2001
"Ostensive encoding" (OST) Parents are circumscribed by their sampled children
Perelleschus multi-phylogeny alignment – 2013/2001
"Ostensive encoding" (OST) Parents are circumscribed by their sampled children
"Intensional encoding" (INT) Parents are circumscribed by their synapomorphies
Stepping back. Benefits, drawbacks.
What does it mean?
Loosely derived from: Franz et al. 2015. Names are not good enough: reasoning over taxonomic change in the Andropogon complex. Semantic Web Journal. (In Press) Specimen information: http://sernecportal.org/
Concept taxonomy – what can we achieve, and what do we need?
1. Taxonomic names
2. Aligned input concepts
Concept taxonomy – what can we achieve, and what do we need?
1. Taxonomic names
3. Aligned Euler subregions
2. Aligned input concepts
Logic resolution of the taxonomic variable
We are moving from "is it possible (even theoretically)?"
to "are the design/use trade-offs worth it?"
Not the worst place to be.
Acknowledgments
• Euler/X team: Shawn Bowers, Parisa Kianmajd, Timothy McPhillips & Shizhuo Yu.
• ETC team: Hong Cui, James Macklin & Thomas Rodenhausen.
• ProvenanceMatrix: Tuan Nhon Dang.
• SERNEC portal: Edward Gilbert.
• NSF DEB–1155984, DBI–1342595 (Franz); IIS–118088, DBI–1147273 (Ludäscher).
• Information @ http://taxonbytes.org/tag/concept-taxonomy/
• Euler/X code @ https://github.com/EulerProject/EulerX
• Symbiota.org @ http://symbiota.org/
http://taxonbytes.org/ http://biokic.asu.edu (in dev.)
Select references – concept taxonomy and the Euler/X toolkit
• Chen et al. 2014. Euler/X: a toolkit for logic-based taxonomy integration. WFLP 2013 – 22nd International Workshop on Functional and (Constraint) Logic Programming. Link
• Dang et al. 2015. ProvenanceMatrix: a visualization tool for multi-taxonomy alignments. CEUR Workshop Proceedings 1456: 13–24. Link
• Franz et al. 2015. Names are not good enough: reasoning over taxonomic change in the Andropogon complex. Semantic Web Journal – Interoperability, Usability, Applicability – Special Issue on Semantics for Biodiversity. (in press) Link
• Franz et al. 2015. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE 10(2): e0118247. Link
• Franz et al. 2015. Taxonomic evolution: two influential primate classifications logically aligned. Systematic Biology. (accepted pending revision) Link
• Jansen, M.A. & N.M. Franz. 2015. Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1–133. Link
• Franz, N.M. & B.W. Sterner. 2015. Taxonomy – for computers. biorXiv. Link