Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

Marya Schechtman takes issue with analytic philosophy's emphasis on the first sort of question to the exclusion of the second.

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

This is a well-behaved concept in Newtonian physics. But a center of gravity is not an atom or a subatomic particle or any other physical item in the world. It has no mass; it has no color; it has no physical properties at all, except for spatio-temporal location. It is a fine example of what Hans Reichenbach would call an abstractum. It is a purely abstract object. It is, if you like , a theorist's fiction. It is not one of (...) the real things in the universe in addition to the atoms. But it is a fiction that has nicely defined, well delineated and well behaved role within physics. (shrink)

What is a self? I will try to answer this question by developing an analogy with something much simpler, something which is nowhere near as puzzling as a self, but has some properties in common with selves. What I have in mind is the center of gravity of an object. This is a well-behaved concept in Newtonian physics. But a center of gravity is not an atom or a subatomic particle or any other physical item in the world. It has (...) no mass; it has no color; it has no physical properties at all, except for spatio-temporal location. It is a fine example of what Hans Reichenbach would call an abstractum. It is a purely abstract object. It is, if you like , a theorist's fiction. It is not one of the real things in the universe in addition to the atoms. But it is a fiction that has nicely defined, well delineated and well behaved role within physics. (shrink)