[Bioperl-l] [BioSQL-l] Bio::Annotation::StructuredValue
hlapp at gmx.net
Sat Mar 17 10:26:04 EDT 2007
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
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.
> 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 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.
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: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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