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Posts tagged ‘concepts’

Weekly reading: Seltmann et al. on hymenopterists’ guide to the Hymenoptera Anatomy Ontology

If it were that kind of semester, maybe it would be neat to summarize our thoughts on all the ways in which last week’s paper – one of the theoretical foundations of the OBO Foundry approach – was puzzling to us. But, so far it isn’t (that kind of semester). Just three thoughts then.

1. Many of us seem to want to be realists.

2. Whatever the merits of the theory, implementation matters too. The two need not always be entirely and reciprocally consistent. (that is putting things mildly)

3. Consider this statement by Smith (2004), top of page 79 in the publisher paper.

“Good ontologies are reality representations, and the fact that such representations are possible is shown by the fact that, as is documented in our scientific textbooks, very many of them have already been achieved, though of course always only at some specific level of granularity and to some specific degree of precision, detail and completeness.”

I think it is fair to say that this statement leaves room for both the empiricist and the realist acknowledging the importance of theories and concepts in science while not elevating them a priori to a level where they are either unassailably reliable or misguided. It is a sensible enough statement to make. Strangely, to my thinking at least, Smith takes this statement to work as something of a wedge between reality- and concept-based ontology design maxims. But the statement itself speaks more to the notion of reality (which by the way remains under-defined) and concepts being intertwined in scientific advancement. Whatever else may be said here, we concluded that following his outlined path does require ‘a strong ontological commitment’. I doubt that this message has been received and ratified by most practitioners.

Anyway, onto to more practical issues; up this week:

Seltmann, K., M. Yoder, I. Miko, M. Forshage, M. Bertone, D. Agosti, A. Austin, J. Balhoff, M. Borowiec, S. Brady, G. Broad, D. Brothers, R. Burks, M. Buffington, H. Campbell, K. Dew, A. Ernst, J. Fernandez-Triana, M. Gates, G. Gibson, J. Jennings, N. Johnson, D. Karlsson, R. Kawada, L. Krogmann, R. Kula, M. Ohl, C. Rasmussen, F. Ronquist, S. Schulmeister, M. Sharkey, E. Talamas, E. Tucker, L. Vilhelmsen, P. Ward, R. Wharton & R. Deans. 2012. A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions. Journal of Hymenoptera Research 27: 67-88. Available on-line here.

Taxonomic names, identifications, and concepts – how to reconcile?

This post is motivated by my (late) discovery of the GBIF “Guidelines for the capture and management of digital zoological names information” (Version 1.1, released in March 2013), authored by Dr. Francisco Welter-Schultes who is (i.a.) the project leader of the resource http://www.animalbase.org/. Jump to the Addendum [response to Stephen Thorpe, May 06, 2014].

The GBIF Guidelines, a dense, informative, and authoritative 126-page document on representing and managing zoological names (which, as GBIF makes clear, ultimately reflects the author’s perspective), also include (pages 3-5) a Section 1.1.2 on Taxon concept models. I found this section to contain a mix of more or less accurate statements and assessments of the interaction among taxonomic names, identification events, and taxonomic concepts. This issue is of interest to me, and has on occasion been discussed on Taxacom, in the TDWG community, and elsewhere. I (henceforth NMF, regular font) will take the opportunity to examine Dr. Welter-Schultes’ (henceforth FWS, italics) perspectives and examples, point by point. Hopefully some readers will find this post helpful.

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