[Bioperl-l] ontology loader

[Hilmar Lapp]

I committed an ontology loader to bioperl-db in 
scripts/biosql/load_ontology.pl. Many command line arguments will be 
familiar from load_seqdatabase.pl, but some are specific to ontologies, 
for instance those specifying the action to be taken on obsoleted 
terms. The loader loads terms, relationships, and at the end can on 
demand also generate the transitive closure table for the ontology.

I tested it on SOFA and GO and it works meanwhile. Getting it to work 
on GO revealed a whole series of subtle and not-so-subtle issues, 
mostly caused by the dagflat parser and some of the ontology-related 
modules in bioperl. I migrated all the fixes that were necessary to the 
stable branch (1.2). Those fixes also considerably silenced the 
ontology.t test in bioperl-db.

	-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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