I’m slowly coming around to the idea that this is a very important issue. To me, it seems the problem is not how we describe objects (which are finite), but how we describe the relationships between them (which is very dependent on how individuals use words). I also feel that current ontologies attempt to do too
much and be all things to all people, whereas the aim should be to keep things as simple and tight as possible. In other words, there are too many verbs of the “interacts with, binds to etc.”
nature. I don’t need to know that p53 IS_RARELY SWALLOWED_BY parrots, for instance.
Surely all we need to do is sit down and make a big list of nouns (objects in biological systems) and verbs (things that they do), then stick to it.