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Posts tagged ‘theory’

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: Smith 2004 on ontology as reality representation

Last week’s paper on the merits of “realism as practiced by the BFO” left us with a sense of dissatisfaction (which cannot fairly be credited to the paper itself). First, since this was predominantly a “con” paper, it seems important to also examine the “pro” stance. And second, yes, we are getting further away from applications. We will address both issues, though necessarily in sequence. Therefore, up this week is a foundations paper on how to conceive of and construct realist (OBO-compliant) ontologies.

Smith, B. 2004. Beyond concepts: ontology as reality representation; pp. 73-84. In: Proceedings of the 3rd International Conference on Formal Ontology in Information Systems (FOIS 2004); November 4-6, 2014; Torino, Italy. IOS Press, Amsterdam. Available on-line here.