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.
- See also the Euler Project website.
- Euler/X code is available here.
- David Thau et al.‘s work prior to Euler: listing and PDFs.
- Update February, 2014 (I): Analysis of the Andropogon use case.
- Update February, 2014 (II): Analysis of two weevil classifications.
- Update February, 2014 (III): Using the Euler/X toolkit to align taxonomies – introductory notes.
- Update March, 2014 (I): Alignment of two classifications of the Monotremata.
- Update April, 2014 (I): Perelleschus reasoning manuscript submitted to PLoS ONE. Abstract.
- Update April, 2014 (II): Progress in aligning the 1993/2005 Mammal Species of the World – Order Primates.
- Update May, 2014 (I): Names, identifications, and concepts (post related to GBIF Guidelines).
- Update June, 2014 (I): Perelleschus concept paper receives Outstanding Paper for 2013 Award.
- Update June, 2014 (II): We now have a completely aligned, consistent merge taxonomy for 317 x 483 concepts of Primates, sec. Groves (2003) and sec. Groves (2005), respectively. Manuscript in preparation.
- Update July, 2014 (I): TaPP 2014 – 6th USENIX Workshop on the Theory and Practice of Provenance – Poster by Chen et al.: Provenance for Explaining Taxonomy Alignments.
- Update July, 2014 (II): The new Euler/X server is set up at: http://euler.asu.edu/
- Update July, 2014 (III): Euler/X demonstration video.
- Update July, 2014 (IV): Zhang & Franz presentation on concept changes in the Heteroptera (5th Quadrennial Meeting of Heteropterists’ Society).
- Update August, 2014: Ludäscher et al. presentation at RuleML 2014.
- Update September,2014 (I): Revision – Franz et al. 2014. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE. PDF
- Update September, 2014 (II): 2014 Colorado “The Meaning of Names” Conference Presentation – Explaining taxonomy’s legacy to computers.
- Update September, 2014 (III): Euler server is now functional (internally) at http://euler.asu.edu/, we are working on increasing accessibility to external users.
- Update, November, 2014 (I): Perelleschus reasoning paper at arXiv
- Update, November, 2014 (II): BIGCB 2014 Workshop presentation.
- Update, November, 2014 (III): Entomological Society of America presentation.
- Update, December, 2014 (I): Primate alignment manuscript at arXiv.
- Update, January, 2015 (I): Radford, Ahles & Bell 1968 translated as Euler/X input tree.
- Update, January, 2015 (II): Euler source is migrating to GitHub at https://github.com/EulerProject.
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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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