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

[Mark Wilkinson]

Chris Mungall wrote:

> > It may or may not become a standard. $feature->go() would mean
> > putting it into the SeqFeatureI interface, which IMHO is too
> > vendor-heavy

> yup, agree here

I also agree (though note that it is "a" standard, not "the" standard...)


> foreach $ann ($feature->annotations) {
>   print $ann->description;
>   printf "%s said that %s is a %s because\n",
>     $ann->association->person,
>     $feature->name,
>     $ann->controlled_vocab_term->description,
>     $ann->association->evidence_as_text;

I guess in a sense this addresses exactly the problem that I am trying to deal
with - that there is not much structure to the annotations in BioPerl at the
moment.  Tag/Value is all well and good for simple things, but I am finding
that my hands are tied when I try to apply more complex annotations to a
Feature object.

My short-sighted solution was to stick GO directly onto the feature object, but
I see now that this is not a good way to go.  However, The above code is
exactly what I wanted to achieve!  If we come up with a consensus of what a
BioPerl hierarchical-structured "generic annotation" API should look like I
will get started.

I do believe, however, that (as in the code above) the annotation must be an
attribute of the feature, with a formal method for getting to it, rather than a
standalone thing (as Bio::Annotations are now).

M



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