Biomedical ontologies, purpose, use cases, and research questions

I have argued in previous posts that the description and consequent inferences articulated through biomedical ontologies should be purpose-driven, in that different purposes can alter the way biology and health sciences are perceived. This seems to be in agreement with the perspectivalist principle of ontologies such as BFO, although perspectivalism clearly leaves room for reality being described in a number, possibly infinite number of ways. Whether a line between realist perspectivalism and relativism can be clearly drawn (Babich, 1994), and whether one perspective might be better than another, are both issues that I will come back to in a different post. For now, it suffices to say that purpose or perspective are inherent to anyone's perception and interpretation of the world.

So, why should we care? I will now argue that since purpose is central to a biomedical ontology, use cases do not suffice since they are too vague. Instead, specific research questions should be framed at the start of the ontology design and then throughout the ontology maintenance. If a new research question cannot be either accommodated or even fit, then either the existing ontology should be modified or it should be forked. Research questions imply the use of specific elements (or fields or variables depending on which scientific culture you come from) used in specific positions of the central hypothesis.