Hello, Consider: (a) Protein in BioPAX Level 2 (b) Protein in the Protein Ontology (c) A class protein how it is usually understood by biologists.
Is it a sub class of BFO's object aggregate? Or of BFO's object? Or what else? Take care Oliver -- Oliver Ruebenacker, Computational Cell Biologist BioPAX Integration at Virtual Cell (http://vcell.org/biopax) Center for Cell Analysis and Modeling http://www.oliver.curiousworld.org