[BioSQL-l] ontology for transitive closure table

[Hilmar Lapp]

If this is meant for storing the whole thing along (which DBIx::Tree 
doesn't do, at least not according to what's documented on CPAN) with 
maintaining the transitive closure table too then I may join you as 
early as next week, as this is more or less exactly what I need here.

	-hilmar

On Wednesday, March 19, 2003, at 04:26  AM, Aaron J Mackey wrote:

>
> I'm writing this, with help from ChrisM (I hope), although it's still 
> in
> planning stages.  But for a very high-level preview, you can take a 
> look
> at DBIx::Tree to get a flavor for what DBIx::Graph will do (which is: 
> map
> database tables representing graphs into Graph.pm-like structures and
> vice versa).  Some not-guaranteed-to-work code:
>
> my $dbigraph = new DBIx::Graph @params;
> my $graph = $dbigraph->graph;
>
> my $tc = $graph->transitive_closure; # or whatever Graph.pm calls it, 
> can't remember
> my $dbitc = new DBIx::Graph @tc_params;
> $dbitc->graph($tc); # save the tc graph away.
>
> where @params and @tc_params define the various tables/keys/whatnot for
> the relationship and path tables.
>
> Of course, Graph.pm has no idea about ontology terms and whatnot; but I
> believe we'll be able to register callbacks at each "merge" state to
> qualify the attributes of the edge about to be added to the tc (or deny
> that the edge should be made at all).  I'm working with the author on 
> this
> at the moment, but he's a slightly busy guy (Jarkko Hietaneimi of perl 
> 5.8
> fame, and I'm sure I've butchered his last name).  This is why 
> DBIx::Graph
> hasn't moved much further beyond planning yet, because I need the 
> hooks in
> Graph.pm
>
> Slightly OT, but if I were to implement our own Graph.pm-like object 
> via
> an Inline::C-wrapped graph library, would people be keen on that?
>
> -Aaron
>
> On Tue, 18 Mar 2003, Hilmar Lapp wrote:
>
>>
>> On Tuesday, March 18, 2003, at 04:40  AM, Aaron J Mackey wrote:
>>
>>> Maintenance of these graphs is left as an exercise to the reader (but
>>> DBIx::Graph is coming to a CPAN to near you).
>>
>> Are you writing this? Is there a preview?
>>
>> I'm going to write the RelationshipI adaptor now. I'm wondering 
>> whether
>> I can take advantage of DBIx::Graph if you're writing this?
>>
>> 	-hilmar
>>
>
> -- 
>  Aaron J Mackey
>  Pearson Laboratory
>  University of Virginia
>  (434) 924-2821
>  amackey at virginia.edu
>
>
>
-- 
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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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