Franz et al 2015 escjam 2015 logic resolution taxonomic variable

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

Syntactic & semantic conventions

Name (author, year) sec. Source (year) "taxonomic concept label"

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.

All the time! Identification keys

All the time! Identification keys

Phylogenetic trees

All the time! Identification keys

Phylogenetic trees

Occurrence maps

Names taxonomic concept labels

Names taxonomic concept labels

Augment granularity(and thus number)

of identifiers

Names taxonomic concept labels

Doable. But why?

Augment granularity(and thus number)

of identifiers

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?

How? Euler/X toolkit

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

How does it work? 1

1 Toolkit demonstration available following this presentation and symposium.

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

No!

Workflow: diagnose and resolve logical inconsistencies

No!

Yes

Workflow: diagnose and resolve unintended ambiguities

MIR =Maximally Informative Relations

[==, >, <, ><, |]for each concept pair

Yes

Yes

Workflow: output of "MIR" and alignment visualizations

Remember this?

Oscillating meanings of the species epithet hyalites – 1911 to 2003

Phenotypic diversityTy

pe-a

ncho

red

nam

e id

entit

y re

latio

ns

Euler/X translation

Amauris input visualizations

1911

1940

1952

1980

1995

1997

1999

2003

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)

Amauris alignment visualizations (2–4)1952/1940

1980/1952

1995/1980

Amauris alignment visualizations (5–7)

1997/1995

1999/1997

2003/1999

Returning to Minyomerus..

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

Minyomerus alignment visualization – 2015/1982

6 congruent (paired) species-level entities

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/

Specimens identified to taxonomic names

• Taxonomy 1

Specimens identified to taxonomic names (Taxonomy 1)

• Taxonomy 2

• Taxonomy 1

Specimens identified to taxonomic names (Taxonomy 2)

• Taxonomy 2

• Taxonomy 1

Specimens identified to taxonomic names with conflicting meanings

What if…?

Specimens identified to taxonomic concept labels

Specimens identified to taxonomic concept labels

Specimens identified to taxonomic concept labels with consistent RCC-5 articulations

Or even…?

Specimens identified to taxonomic concept labels

Specimens identified to taxonomic concept labels and with aligned Euler subregions

Specimens identified to taxonomic concept labels and with aligned Euler subregions

In conclusion

Concept taxonomy – what can we achieve, and what do we need?

1. Taxonomic names

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