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).
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.
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.
“Part 1” – allowing for subsequent parts (e.g., for the blue/non-blue use case; now added at end of post). The relevant OpenTree background discussion is here:
There as several interesting and generally closely overlapping issues and views here. I will pick just (or mainly) the one introduced by Jonathan Rees (November 02, 2014).
“Here’s another example I’m struggling with: there are currently a couple of species in OTT that are misclassified as crustaceans instead of molluscs. When we fix this problem, there will be an incompatible ‘change’ in the membership of Arthropoda. Does this mean that the new group should get a new identifier? – after all its identity in some sense has changed. If so, annotations and OTU mappings linked to the old id have no home in the tree. It doesn’t get a new id with the current taxonomy generator, which assumes that names are tied uniquely to taxon concepts (with some exceptions), but with a more principled system where groups are defined by membership or phylogenetic hypotheses, it might. This would have an impact on OTU mappings and annotation carryover. I don’t have a good answer to this one, but am working on ways to anchor the semantics of ids.”
I am attempting to reproduce this under varying scenarios in the Euler/X toolkit. Starting simple, then expanding. I have created an initial scenario with two phylogenetic perspectives of the Ecdysozoa (molting animals) sec. ott1 (= OpenTree Topology at time =1; the later version) versus Ecdysozoa sec. ott0 (OTT at time = 0; the earlier version. Initially, an alignment with complete taxonomic congruence.
I will give an updated presentation on the Euler/X project and concept taxonomy at the conference “The Meaning of Names: Naming Diversity in the 21st Century”, held at the Museum of Natural History, University of Colorado – Boulder, on September 29 to October 01, 2014. Slides are posted on Slideshare, and linked here. Thanks to Rob Guralnick for the invitation!
No, this not concept taxonomy. Instead this post is intended to set up a nomenclaturally and taxonomically correct use case for an Answer Set Programming (ASP) reasoning project. The post will limit itself to: (1) getting the required nomenclatural emendations “right” (Section 4), given (2) a specific set of starting conditions (Sections 1 & 2), and (3) a new taxonomic insight that necessitates change (Section 3).
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
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.
Euler/X merge of two Hominoidea classifications sec. Groves 1993/2005.
- 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.