[Biojava-l] BioJava discussion board

[Patrick McConnell]

Looking at the schema, I believe that you can push around annotations
without the sequence.

The root element, sciobj, can have zero or more of any of the following:
      bio_sequence
      contig
      FeatureSet
      chromosome.

So, I think what you are looking for is the FeatureSet, which contains an
annotations element, distinct from the bio_sequence elements.

Please, an Agave expert correct me if I am wrong.

-Patrick





Matthew Pocock <matthew_pocock@yahoo.co.uk> on 08/28/2002 04:47:32 PM

To:    Thomas Down <td2@sanger.ac.uk>
cc:    Brian Gilman <gilmanb@genome.wi.mit.edu>, Patrick McConnell
       <MCCon012@mc.duke.edu>, biojava-l@biojava.org

Subject:    Re: [Biojava-l] BioJava discussion board


Does agave allow you to push annotations arround without the sequence?
In a web service environment we may not want to push the dna for chrom I
arround even though we may want to know all features within a region of
it. I am format agnostic. The important things are that:

a) any format can potentialy be easily made and consumed by lots of
services/clients (including our own)

b) the web services are sliced at the right level of granularity

Mmm.

Thomas Down wrote:
> On Wed, Aug 28, 2002 at 09:35:59AM -0400, Brian Gilman wrote:
>
>>I agree with Patrick on that one. Perhaps Agave could be used as the
>>serialzation layer here?? It would be a little bit of work to get
>>everything munged into Agave or BSML but think about the benefits for we
>>poor middleware guys!
>
>
> Yep, I'm with you on this, too.  I'm not actually that bothered
> about exactly /which/ schema gets used -- Agave seems about as
> sane as anything right now (and we have some support for it already in
> BioJava, which makes life easier for us :-).
>
>       Thomas.
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