I screen-recorded a 7:35 minute video demonstrating the current (July 2014), basic functionality of the Euler/X toolkit for aligning multiple taxonomies (see: Concept Taxonomy). The video is up on Vimeo.
Euler/X toolkit demonstration – July 2014 from taxonbytes on Vimeo.
Abstract. The Euler/X toolkit (bitbucket.org/eulerx/euler-project) takes in two input taxonomies, a set of concept-to-concept articulations, and additional logic constraints to assess their logical consistency, infer the set of maximally informative relationships among the input concepts, and visualize a merge taxonomy. The basic functionality of the toolkit is shown based on a use case of aligning two alternative concept phylogenies of the weevil genus Perelleschus sec. 2001/2013. More information is available at taxonbytes.org/prior-work-on-concept-taxonomy-2013/
We have a new collaborative paper out in Lecture Notes in Computer Science, with Mingmin Chen of UC Davis as lead author, on inconsistency checking and repair of conflicting concept articulations for the Euler/X toolkit. Complete citation:
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. Link to publication.
Echidnas, platypus – monotremes are amazing. They are also subject of an exploratory project to align two highly influential classifications of mammals using the Euler/X toolkit. Of course we are talking about:
- Mammal Species of the World, 3rd Edition. 2005.
- Mammal Species of the World, 2nd Edition. 1993. [not or no longer available on-line; which relates to our project’s aims.]
The respective 1993 & 2005 monotreme classifications were authored by Colin Groves. Thanks to MSW Editor DeeAnn Reeder for enthusiasm and support. Below is an abbreviated representation of how we aligned the two classifications. Most critically, in 1998 Zaglossus sec. Flannery & Groves (1998) was revised, and a new species (concept) Z. attenboroughi was added. Let us see what else changed..
Most recent update: July 15, 2014 (minor editing updates; link to video).
Our group is involved in promoting concept taxonomy. Here are some preliminary, and evolving, step-by-step instructions on how to employ the Euler/X toolkit to align two taxonomies or phylogenies. A short video is also available here.
Lead members of the Exploring Taxon Concepts (ETC) and Euler projects held a joint workshop at the School of Information Resources and Library Sciences (SIRLS) at the University of Arizona on February 19-20, 2014. On the meeting agenda were mutual updates, project coordination, and the formulation of detailed user scenarios for ETC tools; including: taxon-character matrix generation, matrix review, multi-entry interactive identification key generation, taxon concept similarity comparison, taxonomic revision support, and ETC/Euler interfaces and workflow integration.
Shown on the group photo, from left to right: (sitting) Lorena Endara, Hong Cui (ETC PI), Heather Cole, and Elvis Yu; (standing) Nico Franz, Bertram Ludäscher (Euler PI), James Macklin, Joel Sachs, Robert Morris, Thomas Rodenhausen, and Shizhuo Yu.
Linked here is an interim result of my attempt to align two influential weevil classifications by Thompson (1992) and Alonso-Zarazaga & Lyal (1999) with the Euler/X toolkit. For additional information see this link.
Update, February 18, 2014: Here is another alignment of two phylogenetic classifications of weevil families and subfamilies, according to Kuschel (1995) and Marvaldi & Morrone (2002).
We have a new manuscript ready for submission that uses the Euler/ASP toolkit to reason over taxonomic change in the Andropogon (glomeratus-virginicus) ‘complex’ – an illuminating use case assembled by the visionary Alan Weakley. More on this toolkit soon; it is ready for application to larger and more complex use cases.
Nico M. Franz, Mingmin Chen, Shizhuo Yu, Shawn Bowers & Bertram Ludäscher
Names Are Not Good Enough: Reasoning over Taxonomic Change in the Andropogon Complex