[BioSQL-l] ontology for transitive closure table

[Aaron J Mackey]

On Wed, 19 Mar 2003, Aaron J Mackey wrote:

> my $dbigraph = new DBIx::Graph @params;
> my $graph = $dbigraph->graph;
>
> my $tc = $graph->transitive_closure; # or whatever Graph.pm calls it, can't remember

So this bit now works for me (including being able to access all various
"paths" described by a given transitive closure edge, useful for
determining predicate type of the new edge).  But, computing the tc via
Graph::Directed on GO isa/partof is extraordinarily slow (I've waited more
than 4 hours now; by comparison, an SQL-only solution finishes in less
than 20 minutes).

> 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?

I'll ask again - I need to be able to calculate tc graphs in a reasonable
amount of time; are people willing to go through the extra hassle of
installing bioperl-ext to get faster Graph functionality?

-Aaron