Sweeping statement ‘collaboration and community involvement should be maximised within the life-cycle of an ontology‘ – why? Costs vs. benefits. Mixed skill sets, who should be in the collaboration? What are their profiles and roles within a collaborative development?
Tooling is critical for development of collaborative ontologies, does the tooling work, is not being co-located a confounding factor? Some discussion of the social issues is needed. Experience with OBI suggests that a workshop where participants are co-located is the quickest way to work towards a shared understanding.
The description of biological research is quite general, does not make the point why biology needs ontologies more than any other evidence based discipline. I think there are valid points to be made about high volume, high complexity data in biological sciences.
‘However, with the diversity, there is equal homology‘ – homology is a potentially confusing word given the context.