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Posts tagged ‘concept taxonomy’

Thoughts: How many concepts are we talking about

Fourth post in this sequence (here are posts 1, 2, 3, respectively). Changing gears a little. The motivation for this post is to explore the interactions of explicitly and implicitly communicated taxonomic concepts in conversations among (living, meeting) humans with comparable levels of taxonomic expertise. How many identifiers are we talking about?

The exploration has two parts. The first part simulates a brief conversation of the kind that two human speakers may engage in while meeting in the hallways at a taxonomically oriented conference. The speakers know of each other, either through prior personal interactions or (minimally) by having read several of each other’s taxonomic publications. The conversation is hypothetical, and even though certain real persons are mentioned, the sole purpose of this is to add some realism, not to pass my judgment on any taxonomic particulars. The post is about exploring how the issue of taxonomic name/concept identifier resolution relates to this kind of communication, generally.

The second part examines the conservation from the perspective of representing taxonomic reference – “logically”. By that I mean framing the taxonomic content identifiers communicated explicitly or implicitly by the human speakers in such a way that a computational, logic-based application can adequately represent them. Ok, so here goes (in part, as it will turn out).

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SPNHC 2015 presentation – Taxonomic concept resolution for voucher-based biodiversity information platforms

Slides are up for our SPNHC 2015 concept taxonomy presentation.

Franz 2015 SPNHC Taxonomic concept resolution for voucher-based biodiversity information platforms from taxonbytes

PathwayMatrix visualization software shows Euler/X taxonomy alignment products and ambiguities

This post serves as an update on a new Euler/X compatible visualization software called PathwayMatrix, and also as a mini-review of the Exploring Taxonomic Concepts (ETC) Information Visualization Workshop, held on May 11-13, 2015, at the National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign. The workshop was organized by Bertram Ludäscher of the Euler/X Project and ETC lead information scientist Hong Cui.

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Thoughts: Humans, computers, and identifier granularity

Third post in this sequence. In the first post, I reviewed that biological nomenclature promotes (even requires) fairly deep taxonomic semantics, due to semantically forceful principles such as Typification, Priority, Coordination, and Binomial Names. In the second post, I suggested (again, nothing very new here) that the Linnaean system has many features which, given the task on hand (reliably identifying nature’s hierarchy), are nearly optimally aligned with evolutionarily constrained human cognitive universals.

Both posts are ultimately about advancing biodiversity informatics infrastructure design. That motivation points to finding sound models of knowledge communication in the taxonomic domain. Lessons from the two preceding posts may be as follows. (1) If the goal is to build data environments that largely continue to reflect the strengths and weaknesses of human cognitive universals, then the particular balance struck by Linnaean names and name relationships acting as identifiers of evolving human taxonomy making is adequate. (2) There may be better solutions out there, particularly solutions that more effectively utilize the reasoning and scalability strengths of computational logic.

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ETC-Euler Taxonomic Concept Alignment Demonstration Video – Minyomerus 2015 versus Minyomerus 1982

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.

Thoughts: Why stability in nomenclature, and at what cost?

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.

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New publication: Provenance for explaining taxonomy alignments

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.

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.