This 8-minute screenshot video, produced in late April, 2015, demonstrates the interaction of the Exploring Taxonomic Concepts (ETC) and Euler/X software tools.
The ETC team has built a highly useful and effective front-end web service to the Euler/X reasoning services, allowing users to import two concept taxonomies through an on-line file management system, provide articulations, run input visualizations, obtain logically consistent alignments, and extract these products from the web interface to the desktop. The underlying ideas and methods are explained in Franz et al. (2015).
The capabilities of the user interface are illustrated with the Minyomerus use case, aligning two classifications authored in 2015 and 1982, respectively.
ETC Euler Taxonomic Concept Alignment Demonstration – Minyomerus 2015 versus 1982 from taxonbytes on Vimeo.
Another post on nomenclature, related to this previous post on the possibly thankfully strong influence of nomenclatural principles on taxonomic practice.
Many taxonomists, including myself certainly, continue to wonder and explore why exactly nomenclature is the way it is. The aim is first and foremost to obtain a sound explanatory account. Whether one likes the explanations, or the practice as illuminated in part by the explanations, is initially another subject.
This year, and for the first time, all Natural History Collections participated in the ASU Night of the Open Door event jointly and at the Alameda location. A shuttle service from the Tempe Campus to our collections allowed visitors to make the trip, participate in outreach games, and get access to the collections and people associated with them. Although we had hoped for slightly higher visitor numbers, the feedback was strong and very positive. The Insects also had a table on campus. Photos from the event are posted on Flickr here.
On March 27, 2015, the Hasbrouck Insect Collection group fronted a highly popular booth at the annual DiscoverE Days organized by ASU’s Ira A. Fulton Schools of Engineering. Andrew Jansen and Guanyang Zhang tirelessly introduced many hundreds of young visitors to the wonders of arthropods and insects on the pastures in front of the Old Main Building. Photos from the event are posted on Flickr here.
Biological nomenclature and taxonomy are both different yet also somehow interconnected. It is sometimes stated that the two kinds of practices are largely independent of each other. Yet we also know that – to some degree – Code-compliant nomenclature must respond to taxonomic change. Pyle & Michel (2008) review the relationship of nomenclature and taxonomy in (what seem to me) often reiterated terms. They write (pages 41-42):
This post on cynicism in academia is off-topic compared to what I usually write about on taxonbytes. And I wish to declare that it is not intended to project a high degree of scholarship on the subject because I lack such scholarship. An internet search of “cynicism academia” (or similar) produces abundant links to both casual and formal treatments. I will not deal with these, but only relate my own current thoughts.
This week we will try out Protégé and pizza ontologies. We will work through an updated version of this tutorial.
A short paper related to the Euler/X toolkit and concept taxonomy alignment project has been published. It deals with the issue of diagnosing inconsistent input constraints in an attempted pairwise taxonomy alignment, analyzing and visualizing their logical provenance so that the user can localize the inconsistencies and proceed towards repairing them. These logic services are already implemented in the toolkit.
Abstract. Derivations and proofs are a form of provenance in automated deduction that can assist users in understanding how reasoners derive logical consequences from premises. However, system-generated proofs are often overly complex or detailed, and making sense of them is non-trivial. Conversely, without any form of provenance, it is just as hard to know why a certain fact was derived. We study provenance in the application of Euler/X, a logic-based toolkit for aligning multiple biological taxonomies. We propose a combination of approaches to explain both, logical inconsistencies in the input alignment, and the derivation of new facts in the output taxonomies.
Chen, M., S. Yu, P. Kianmajd, N. Franz, S. Bowers & B. Ludäscher. 2015. Provenance for explaining taxonomy alignments. In: Ludäscher, B. & B. Plale (Editors), Provenance and Annotation of Data and Processes. Revised Selected Papers of the 5th International Provenance and Annotation Workshop, IPAW 2014, Cologne, Germany, June 9-13, 2014. Lecture Notes in Computer Science 8628: 258-260. Available on-line here.