The notation ws* is introduced but not defined. As section 2.1 table 1 says 
zero or more will be noted with curly braces, it would probably make more sense 
to use {ws} instead of ws*. SImilarly for nl* in the section 2.2 above.
I am not sure how to define a Qualifier. Maybe something along the lines of "A 
Qualifier expresses a relationship between the object of the annotation and a 
well-defined semantic entity." from 
http://code.google.com/p/annotation-ontology/wiki/Qualifiers

Maybe having an example of OBO file with different elements examplified and 
named would help? Maybe as an annex to the spec?