[BioSQL-l] Ontology.category

[Hilmar Lapp]

On bioperl we're currently thrashing out the best interface for 
Bio::Ontology::Term. ChrisM proposes a link from Term to the 
'ontology category', i.e. a virtual root term or something. I think 
having this is very useful; Dave Block has just hit this problem.

Of course it can be solved in the db by a materialized view that 
multiplies all relationships, and then you check for that parent 
that doesn't have parents. Somewhat tedious though. Also, foregoes 
the chance to have a UK on name within an ontology. Since I strongly 
believe that there should be a UK on name, within an ontology or 
globally (in fact, I've put one there), this means that with the 
present design terms can (often will) live in (have a path to) more 
than one ontology. The problem with this is that the definition of a 
term might not be exactly the same between different ontologies, 
i.e., the semantics of a particular term may differ depending on 
what the context-ontology is. You cannot capture this in the present 
design.

The alternative is to add a FK category_id on Ontology_Term to 
itself that shall point to the term specifying the name of the 
ontology. Subsequently, one can put a UK on (term_name,category_id).

Thoughts/comments/preferences/votes?

	-hilmar
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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