[Biojava-l] sp-ml modules

[Matthew Pocock]

Hi Guoneng,

This sounds like a very worthwile project. Do you have any URLs 
describing the current state of the SPML format?

If SPML is an XML language for describing swissprot entries, then the 
obvious thing to do is to write some code to convert the xml sax events 
into org.biojava.bio.seq.io.SequenceIOListener callbacks. The whole 
swissprot database would probably best be encapsulated as an 
org.biojava.bio.seq.db.SequenceDBLite instance with some extra API for 
querying the database.

Good luck. Keep us posted.

Matthew

Guoneng Zhong wrote:
> Hi,
> I am working on classes that interact with the newly proposed SPML 
> format for Swissprot db.  I am still trying to figure out if a live 
> interface to an xml result exists yet.  Waiting for folks at ebi to 
> return my email.  In the meantime, I am new to developing stuff for 
> biojava.  I am not sure what most of you and your colleagues would 
> expect from my classes.  Do I simply let you set search criteria and 
> bam, you get a class that encapsulates all the information in the xml 
> data?  Or do I use some existing interface but create behind the scene 
> xml retrieval and parsing so that you don't need to write new code to 
> use my classes (with minor changes, of course).  if the latter case, 
> where are these interfaces that I must conform to?
> 
> Thanks,
> Guoneng
> 
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