[Bioperl-l] [BioSQL-l] Bio::Annotation issues with BioSQL

Mark Johnson johnsonm at gmail.com
Wed Aug 20 14:43:25 EDT 2008

On Tue, Aug 19, 2008 at 12:56 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
> On Aug 18, 2008, at 4:53 PM, Mark Johnson wrote:
> There's a single quote missing here, but I'm assuming that's a result of
> copy/paste editing?

Yes, I was a bit sloppy with the example.

> Your example code doesn't contain an example for where you are getting the
> B::A::StructuredValue object from. If you didn't create that yourself, it
> would be good to know what you did to end up with that. Chris Fields has
> written B::A::Tagtree which would be way forward, and if you created the
> object yourself, can you take a look at that and see whether that class
> wouldn't serve your purpose as well or even better?

I created the B::A::StructuredValue myself.  I'm using it to store the
output from PSORTb, which gives a cellular localization and a score
for a protein sequence (gene), which I'm trying to keep paired
together, if possible.  I'll take a look at B::A::Tagtree, that's
probably a better fit.

> In order to be stored in BioSQL structured (hierarchical, nested) annotation
> is flattened into a string representation, because BioSQL can't store nested
> annotation collections natively. Right now if I am not mistaken upon
> retrieval this is not converted back into a B::A::Tagtree object but rather
> left flat. This is being worked on though, we've just discussed some issues
> connected with that.

The data I have isn't really deeply nested.  I just like to keep
related annotation in one object, if possible.

> I could make B::A::StructuredValue work the same way, but I'm not sure what
> it provides that B::A::Tagtree doesn't. The latter uses Data::Stag under the
> hood, which is much cleaner, and more extensible in the future.

Perhaps B::A::StructuredValue should be deprecated?

> As for SimpleValue annotation versus tag/value annotation for seqfeatures,
> yes right now these are treated interchangeably for the purposes of BioSQL
> and Bioperl-db. You can do this easily too on your end by using
> Bio::SeqFeature::AnnotationAdaptor.

I'll check out the AnnotationAdaptor, but I'll probably just end using
seqfeature tags/values.  They're functionally equivalent to

>> Is there even a place in the BioSQL schema for a comment to be attached
>> to a DBLink?
> No there isn't. I thought it is but it turns out that this isn't yet one of
> the desirable extensions to BioSQL from 1.1.x onwards, as documented on the
> wiki:
> http://www.biosql.org/wiki/Enhancement_Requests
> I'll add it (but feel free to do so yourself, especially if you have other
> enhancmenets).

I'll take a look at the wiki....I'll file that as a feature request if
I get there before you do it.

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