My results from the review of the release in Protege 4: Overall, this looks good, and I vote for releasing it as is.

In the next iteration (for the manuscript), I believe we should fix the following issues, among others, and these may already be noted elswhere:

Fix very high level classes:
1) Under GDC:
Sequence related stuff:
- propose to rename the imported SO terms 'region' to 'property of sequence region'???, 'polypeptide' to 'polypeptide sequence', ...
- 'secondary structure of sequence macromolecule' is under quality; should now be under GDC?

2) Under 'spatial region'
- 'interrogation point' should be a site, and 'jet_in_air_flow_chamber' seems to be a material entity (the chamber)

3) Everything needs parentage review (e.g. 'macromolecule' should be child of 'molecular entity'; all 'XXX document' should be child of document etc.)

4) Vote strongly to remove unused bfo classes ('spatial region', 'object boundary', 'object', 'object aggregate', 'fiat object part', and everything except 'processual entity'  from 'occurent'). They are extremely confusing in conjunction with the OBI hierarchy.

Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987