[BioSQL-l] ontology for transitive closure table

[Hilmar Lapp]

On Tuesday, March 18, 2003, at 05:27  AM, Matthew Pocock wrote:

> If you did the transitive closure calculation considering a set of 
> namespaces, then I guess you could give a unique ID to that set and 
> label the path with that set. Thinking about it, that set is much more 
> sane a label for the path. It says 'I can get from this term to this 
> term using information only from these domains'.

Wouldn't you do this (at least, wouldn't you be able to do this) just 
as well or even better by depicting the relationship type, as that one 
inherently is from a domain?

In other words, if I define (GO::isa,CORE::isa,CORE::isa) and then 
asked whether there is a path between two GO terms a and b that 
satisfies CORE::isa, how is this query going to be resolved? By a SQL 
query after physically duplicating all GO::isa relationship paths as 
CORE::isa relationship paths, or by first expanding (in SQL or memory) 
CORE::isa to all possible (i.e., connected) relationship types and then 
running the relationship path query for as many rel.types as GO::isa 
expanded to?

The first option IMHO would quickly become unwieldy, a maintenance 
nightmare, and bug-prone. In the latter option you do not stick (I 
think) that set label onto anything physically, the set is rather 
determined by what a chosen relationship type expands to, given your 
definitions of how relationship types relate to other relationship 
types.

	-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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