[Bioperl-l] [BioSQL-l] Bio::Annotation::StructuredValue

Hilmar Lapp 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
> SwissProt)?

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.

>   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  
SeqProcessor.

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  
rel.ships).


>
> 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.

	-hilmar

>
> chris
> _______________________________________________
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> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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