[MOBY-dev] A consequence of the new Object inheritence rules...

[Mark Wilkinson]

Hi all, 

I keep forgetting to mention, but it needs to be said so that people
know about it until we have time to code it into the API:

The way I see it, one of the consequences of not inheriting from
Primitives is that MOBY now has its first "reserved word".  The primary
content of a given object (i.e. the content that would have been the
CDATA, string, or integer content of the node in old-style objects) has
now been stuck into a primitive data-type, however there is nothing
preventing an object from having two HASA's, one containing the actual
content, and the other containing a primitive.

For example:

AnnotatedFASTA
	hasa String (content)  <--- this is the FASTA
	hasa String (Description)


Back when we were allowing inheritance from primitives, it was obvious
where the content was, but it isn't anymore, so we need a reserved word
as the articleName of the contained primitive :-/   An alternative route
would be to disallow use of primitives for anything *other* than
containing 'content'.  That would require another extensive re-working
of the Object ontology, but we would end up with something like this:

AnnotatedFASTA
	hasa String (content)
	hasa Description (anotation)
		hasa String (content)

The latter seems more "correct", but it would require us to re-write the
ontology again...

Comments?

M


-- 
"Ontologists do it with the edges!"

Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274