[Bioperl-l] Accessing GO through MYSQL?

Graham Melcher melcher at rescomp.berkeley.edu
Wed Oct 11 21:09:17 UTC 2006

Hey all,

Preface:: This is my first post to this list, please redirect if my
questions belong elsewhere.  

I need to lookup GO ontology information given GO:Accessors, and I have
a local mysql db that mirrors the GO db from that website.  I am not
sure if the Bio::Ontology::* libraries were designed to be used in a
dynamic, load-as-you-need sort of way, and am wondering how other people
have gone about solving this problem.  Details follow...

Right now I'm using Class::DBI to access the Mysql database, then made a
new set of subclassed Bio::Ontology::TermI and
Bio::Ontology::RelationshipI which use these class::DBI objects to
access the relevent information in the database on the fly.
Unfortunately, I was getting stuck with the implementation of some of
the other Bio::Ontology::*I, especially Ontology.   Making all of these
subclasses seems infeasible, or at least enough work that it might be
available somewhere.  Are mysql accessors out there, and I just haven't
found them, or is Bio::Ontology possibly not way to go?  

Alternatively, if I end up having to write this sort of Bio::Ontology -
Class::DBI interface, would anyone be interested in it being made
generally usable and available?

Finally, I just found go-perl, but although I haven't had a lot of time
to look into it, it doesn't seem to use mysql either.



Graham Melcher

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