[Bioperl-l] ontology paths in Bioperl-DB / Biosql

Hilmar Lapp hlapp at gnf.org
Fri Aug 26 17:21:46 EDT 2005

One thing I forgot to report to the list is that last Friday I fixed 
the Bioperl-db adaptor and driver module for ontology paths in Biosql 
to include the distance zero paths when computing the transitive 
closure over an ontology.

There are now also tests in t/12ontology.t that check for those 
distance zero paths. They pass on all three supported platforms (mysql, 
Pg, Oracle).

(load_ontology.pl in bioperl-db/scripts/biosql has an option 
--computetc that if supplied  will automatically recompute the 
transitive closure over the just loaded ontology)

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

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