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Posts tagged ‘OBO Foundry’

Weekly reading: Leonelli on classificatory theory in biology

Sabina Leonelli has authored numerous papers on bio-ontologies that relate to our Spring 2015 theme. For this week we will read:

Leonelli, S. 2013. Classificatory theory in biology. Biological Theory 7: 338-345. Available here.

Also consider my post summarizing where we are right now and might considering going.

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.

Weekly reading: Daduhl et al. on the Teleost Anatomy Ontology

Last semester’s Weekly Discussion series dealt with Next Generation Sequencing technologies and related informatics challenges and advances. A review of what we read and discussed remains pending. Meanwhile we have selected a topic for the coming Spring 2014 semester:

Phenotype ontologies – origins, theory, applications, prospects, and challenges.

As usual we will place an emphasis on the utility of ontology-centered approaches for systematics – phylogenetics, taxonomy – in particular. The series starts off with a helpful paper that covers a lot of ground and is closely aligned with the OBO Foundry community.

Dahdul, W.M., J.G. Lundberg, P.E. Midford, J.P. Balhoff, H. Lapp, T.J. Vision, M.A. Haendel, M. Westerfield & P.M. Mabee. 2010. The teleost anatomy ontology: anatomical representation for the genomics age. Systematic Biology 59: 369-383. Available on-line here.