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Posts tagged ‘knowledge representation and reasoning’

New publication: Reasoning over taxonomic change – Perelleschus

The first, fleshed out use case of the Euler/X project was published yesterday in PLoS ONE. This paper is a companion to the phylogenetic revision of the acalyptine weevil genus Perelleschus sec. Franz & Cardona-Duque (2013), and translates the 54 taxonomic concepts and 75 RCC-5 articulations provided in that paper into 13 logically consistent alignments and visualizations, with additional inferred articulations.

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.

Very glad to see this one published; at the same time there are other use case papers in the pipeline (Andropogon, Primates). The particular motivation for this paper was to resolve sets of several small-scale yet taxonomically and phylogenetically complex input trees with the RCC-5 concept alignment approach and Euler/X toolkit. The paper is written in a “how to?” style, successively exploring and explaining the connections between the user-provided input constraints and the over-, under-, or well-specified reasoning outcomes. It deals with issues of logical consistency, input sufficiency, ambiguity, and alternative ways to align (parent) concepts in reference to either (1) their intensionally circumscribed properties (which may include synapomorphies) or (2) the ostensively indicated members. This corresponds to the program outlined in Franz & Thau (2010).

One reviewer wrote: “With an exceptionally suited use case, the complexity of taxonomic reasoning and its translation to machine processing are depicted in unprecedented form.” Our ultimate goal is to develop a widely applicable reference and linkage system for taxonomic products that human users create but which is actually optimized for computational processing – without compromising the Linnaean system whose services to humans are profoundly valuable.

ESA 2014 presentation – Aligning insect phylogenies: Perelleschus and other cases

Slides are up for the Euler/X Perelleschus (+) presentation at Entomology 2014.

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

Knowledge Representation in Systematic Biology – Edited book proposal seeking comments, contributions

I have an opportunity to edit a new book in the series “Species and Systematics” (originally UC Press; now CRC Press). The draft outline is below, but is subject to change and expansion as deemed appropriate.

I am looking for suggestions, and for potential contributors (naturally, while reserving standard/common sense rights to kindly accept or decline). The book will to collect a number of strong, diverse chapters on various projects and directions in this still very young field. Lead authors of chapters will coordinate with co-authors as preferred. I also intend to give authors much freedom to do and say things they maybe could not express using different publication outlets (while keeping things fair and high-minded).

Another key issue is (of course) – who may have time and motivation to contribute an original and impactful chapter in the coming six months? Either way, I am open to suggestions, contact me on- or off-line.

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BIGCB Workshop at UC Berkeley: Tackling the Taxon Concept Problem

November 7-9, 2014. Coolest workshop theme, like, ever. Organized by Brent Mishler and Staci Markos of the UC Berkeley Jepson Herbarium.

Understanding Taxon Ranges in Space and Time: Tackling the Taxon Concept Problem

A Workshop Sponsored by the Berkeley Initiative in Global Change Biology

Friday, November 7, 2014, 1002 VLSB, open to all who are interested.

1:00 pm: Brent Mishler  –  Introduction to the themes and goals of this workshop.

1:10 pm: Edward Gilbert  –  Ideas for incorporating taxonomic concepts into Symbiota.

1:40 pm: Robert Guralnick  –  Map of Life and the challenge of heterogeneous names data for determining species ranges.

2:10 pm: Gaurav Vaidya  –  Tracking taxonomic changes: how, where and why, with examples from the Avibase database of taxon concepts. Link & PDF

2:40 pm: Coffee Break.

3:00 pm: Robert Peet  –  Taxon concepts as essential infrastructure for large-scale data integration: lessons from VegBank, SEEK and BIEN. PDF

3:30 pm: Nico Franz  –  Tracking taxonomic change across classifications and phylogenies. PDF

4:00 pm: Alan Weakley  –  Applying concept maps to 7100 vascular plants of the Southeastern United States, and some thoughts on ‘atomic concepts’ and their utility at the specimen level.  PDF

4:30 pm: Nico Cellinese  –  Thoughts on the right approach to query trees based on phyloreferences (ontologized phylogenetic definitions).

Additional Workshop Notes

  • Communicated by Robert Peet  –  Taxonomic concept infrastructure-related entities requiring identifiers. PDF