[BioSQL-l] ontology for transitive closure table

[Aaron J Mackey]

I think we need to let people come up with their own use cases on this
one.  I think we need the ontology_id namespace FK in the term_path table
for the same reason we needed it in the term_relationship table, that is,
to satisfy a specific situation which most people wont need to think
about (i.e. the ontology_id FK will be "redundant" to the predicate_id
term's ontology_id).

-Aaron

On Tue, 18 Mar 2003, Hilmar Lapp wrote:

>
> 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
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu