References to ontologies which use the upper level ontologies cited BFO, DOLCE etc would be useful, as would some examples of ontologies that use these, and the differences between them. A reference to a review article would suffice.
This is not a comprehensive list of upper level ontologies, SUMO and BioTOP could be added, or some statement that there are others.
Some critique of available upper level ontologies would help the user – there are several, why are they different, what is their philosophical perspective?
Upper level ontologies are not necessarily stable, specifically BFO has changed a lot during the development of OBI. Some discussion of the consequences and process of this would be useful.
There are unsolved problems with upper level ontologies, representation of numbers, temporal representation, etc . A list of these problems would help readers understand that this a discursive field, with no single truth, rather current prevailing opinion
What are the overheads of using an upper level ontology vs. the benefits. GO was built initially without this, does it matter, should GO be refactored to fit BFO?
This may not be the most relevant place, but relations also provide some of the structure needed to integrate ontologies, so some reference to the relations ontology and RO2 would be useful.
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The paper and its publication environment form part of the work of the Ontogenesis Network, supported by EPSRC grant EP/E021352/1.