[Bioperl-l] [BioSQL-l] Bio::Annotation::StructuredValue
cjfields at uiuc.edu
Thu Mar 22 18:29:15 EDT 2007
On Mar 17, 2007, at 9:26 AM, Hilmar Lapp wrote:
> On Mar 16, 2007, at 3:44 PM, Chris Fields wrote:
>> Does bioperl-db store Bio::Annotation::StructuredValue (i.e. in
> It does b/c B::A::StructuredValue ISA B::A::SimpleValue and it
> handles the latter.
> This isn't ideal because if you're like me you'd want all the
> individual values to each translate to its own row. I was using a
> SeqProcessor to convert the StructuredValue objects into arrays of
> SimpleValue objects.
> Obviously, this will lose the structure between them (i.e., in
> reality it's not just a flat array), but for enabling indexed
> searches it works well.
> With Uniprot no longer collapsing per sequence, the thing that gets
> lost is the semantic context of each token, but as you found out
> correctly it gets lost at the bioperl level already.
Yes, unfortunately, though the use of an ontology would help as you
>> I am thinking of using StructuredValue, Data::Stag, or
>> Class::Meta for some of my RNA structural data work but didn't know
>> if StructuredValues would persist via bioperl-db.
> At this point they are either flattened out (through the overridden
> value() method), or you convert them upfront into an array, using a
> BioSQL has no provision for storing the fact that a number of tag/
> value associations (which is what B::A::SimpleValues are) comprise of
> a "bag" of annotation that belongs together.
> You could, however, persist that through embedding the tags in an
> ontology (tags are ontology terms) that captures that (through
I will likely use this approach, though there are no applicable SO/GO
terms that I can use so I'll have to roll my own for now. I may use
something similar to the RNAML tags for sec. structure.
>> I also noticed there is an outstanding BioPerl bug (http://
>> bugzilla.open-bio.org/show_bug.cgi?id=1825) where Hilmar suggested
>> reimplementing StructuredValueto use Data::Stag, so I thought I might
>> give it a try.
> Sounds good :-)
> I hope the above makes some sense. Let me know if not.
Makes perfect sense! Just needed to run it by someone on the BioSQL
end since I'll want to make my data a bit more persistent. I think I
will go with Bio::StructuredValue implementing Data::Stag since it
has pretty much everything I need.
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