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Prior work on concept taxonomy – 2013 onwards

February, 2015. The first fleshed-out use case of reasoning over taxonomic concepts with the Euler/X toolkit is now published.

Franz, N.M., M. Chen, S. Yu, P. Kianmajd, S. Bowers & B. Ludäscher. 2015. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE 10(2): e0118247. doi:10.1371/journal.pone.0118247. Available on-line here.

An overview – initiated in early November, 2013 and regularly updated (throughout 2015) – of papers and presentations related to the taxonomic concept approach. Since the Fall/Winter of 2013 we have a working Python toolkit Euler/X (openly available on-line) that can read in two taxonomies (T1,T2), a set or articulations (A), and additional constraints (C). The toolkit then calls up Answer Set Programming reasoners to infer and visualize an alignment among the taxonomies that satisfies the constraints. A short video is posted here.

Hominoidea1993-2005

Euler/X merge of two Hominoidea classifications sec. Groves 1993/2005.


Relevant publications – reverse chronological order

10. Franz, N.M., M. Chen, S. Yu, S. Bowers & B. Ludäscher. 2014. Names are not good enough: reasoning over taxonomic change in the Andropogon complex. Semantic Web – Interoperability, Usability, Applicability – Special Issue on Semantics for Biodiversity. (In Review). pdf

  • Representation of the Alan Weakley-authored Andropogon use case (1889-2006) with Euler/X, with concomitant name/meaning analyses.

9. Franz, N.M., M. Chen, S. Yu, P. Kianmajd, S. Bowers & B. Ludäscher. 2014. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE. (In Press) Link to arXiv.

  • Complete Euler/X analysis of the Perelleschus use case as presented in Franz & Cardona-Duque (2013), variously aligning classifications and phylogenies (comprehensive / exemplar) to each other under hybrid, ostensive, and intensional interpretations. A “how to” paper that covers the interactive user/reasoner interaction of the alignment process.

8. Chen, M., S. Yu, N. Franz, S. Bowers & B. Ludäscher. 2014. A hybrid diagnosis approach combining Black-Box and White-Box reasoning. In: A. Bikakis et al. (Editors): RuleML 2014. Lecture Notes in Computer Science 8620: 127-141. pdf

  • Introduces a new diagnostic ASP reasoning approach for detecting inconsistencies in the input articulations of multi-taxonomy alignments.

7. Chen, M., S. Yu, N. Franz, S. Bowers & B. Ludäscher. 2014. Euler/X: a toolkit for logic-based taxonomy integration. WFLP 2013 – 22nd International Workshop on Functional and (Constraint) Logic Programming. Link to arXiv. pdf

  • A short, mostly technical update on the Euler/X project and its reasoning/input-output capabilities (as of mid 2013).

6. Franz, N.M. & J. Cardona-Duque. 2013. Description of two new species and phylogenetic reassessment of Perelleschus Wibmer & O’Brien, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013. Systematics and Biodiversity 11: 209–236. Link

  • An attempt to produce a semantically consistent set of new descriptions, revision, phylogeny, and new classification using taxonomic concepts. Introduces the concept (sec.) / name (traditional) / [non-focal] (no reasoning) distinction to highlight where intellectual authorship derives from and what reasoning expectations are associated with each. Sets the stage for analyses of this use case by reasoning tools created in the Euler and ETC projects.
  • Appendix – Table 5: Concept Circumscriptions.

5. Franz, N.M. & D. Thau. 2010. Biological taxonomy and ontology development: scope and limitations. Biodiversity Informatics 7: 45-66. pdf

  • A higher-level review of anticipated semantics challenges as systematics enters the SW realm; making the case that taxonomies – and taxonomic progress in particular – are not readily amenable to ontology representation; and that concept taxonomy is needed both to construct large single-view classifications and integrate semantic changes across multiple classifications.

4. Franz, N.M. & R.K. Peet. 2009. Towards a language for mapping relationships among taxonomic concepts. Systematics and Biodiversity 7: 5-20. pdf

  • A “how-to” paper that expands the concept articulation vocabulary of the TDWG-TCS 2005 Standard; introducing (Table 3) a set of additional terms (concept addition/subtraction, contatenation/disjointness/negation of articulations, intensional/ostensive articulation); and illustrating how jointly these additional terms allow for improved provenance tracking of concepts across classifications.

3. Franz, N.M. 2009. Letter to Linnaeus; pp. 63-74. In Knapp, S. & Q.D. Wheeler (Eds.): Letters to Linnaeus. Linnean Society of London, London, UK. pdf

  • Argues that using taxonomic concepts is the most appropriate way of enhancing semantics in biology beyond the Linnaean system, as opposed to the PhyloCode approach.

2. Franz, N.M., R.K. Peet & A.S. Weakley. 2008. On the use of taxonomic concepts in support of biodiversity research and taxonomy; pp. 63-86. In Wheeler, Q.D. (Ed.): The New Taxonomy, Systematics Association Special Volume Series 74. Taylor & Francis, Boca Raton, FL. pdf

  • Makes a general case for using taxonomic concepts in systematics and evolution/ecology research; offers quantitative assessments of concept stability; and introduces a more complete set of concept articulations.

1. Franz, N.M. 2005. On the lack of good scientific reasons for the growing phylogeny/classification gap. Cladistics 21: 495-500. pdf

  • Argues that a sustained separation of progress in taxonomy versus phylogenetics is undesirable, and that concept-level semantics are the most suitable way to overcome the trend towards separation.

Relevant presentations – reverse chronological order

 

Franz 2014 ESA Aligning Insect Phylogenies Perelleschus and Other Cases from taxonbytes

 

Franz 2014 BIGCB Tracking Change across Classifications and Phylogenies from taxonbytes

 

Franz. 2014. Explaining taxonomy’s legacy to computers – how and why? from taxonbytes

 

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

 

Franz Et Al – Concepts and Tools Needed to Increase Bottom-Up Taxonomic Expert Participation in a Global Names-Based Infrastructure from taxonbytes

 

Franz Et Al. Using ASP to Simulate the Interplay of Taxonomic and Nomenclatural Change from taxonbytes

 

Franz et. al. 2012. Reconciling Succeeding Classifications, ESA 2012 from taxonbytes

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