[Bioperl-l] GO annotatinos in BioPerl. A tentative proposal...

[Mark Wilkinson]

Hi All,

You have probably noticed that my fingers have been merrily playing with
various GO annotation modules as I wrap my mind around how best to deal
with this wonderful tool!  One of the walls that I am hitting is that
the things we would want to annotate - Features & Genes - are not really
"set up" to be annotated using GO.  I have racked my brain trying to
find a way to use tag/value to sensibly represent GO annotations, but
there was no obvious solution there (neither at the database level, nor
the Feature/Gene object level).  The Bio::Annotation object looked
promising for a moment, but it appears that Bio::Annotation objects are
not directly associatable with the Gene or Feature objects they are
describing.  i.e. there is a place in the Annotation object to include
one or several gene names, but the annotation is not a property of the
gene/feature object it is describing.  It seems to me that it should be.

This morning I committed a new version of GO_Browser, and a new object
type called GO_Annotation.  GO_Browser creates partially filled
GO_Annotation objects containing only the GO Accession number, term, and
definition.  This annotation can then be beefed up with evidence and
references as you see fit for the gene you are annotating.

What I propose to do is to create a new method of Feature objects,
$Feature->GO, which would set/return the GO annotation object associated
with that feature.  I would also modify the ->to_gff_string call such
that it checked for the presence of a GO annotation and dumped that
information into the GFF attributes field along with the other tag/value
information.

Is there anyone out there who would discourage this, or who might have a
better idea of how to approach this problem?  It seems to me that GO is
eventually going to be the standard to which we are all annotating, so I
think it is a good time to start making BioPerl features more
GO-friendly...  or?

All opinions welcome!

Cheers all!

Mark


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Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada