[Biojava-l] sp-ml modules

[Guoneng Zhong]

Thanks for the input, everyone.  Just to update you, the folks 
developing SP-ML say they don't have a url interface to getting XML 
results and they don't have a timeline for when they will have it 
ready.  In the meantime, I will assume (uh oh) that the xml format they 
will have when the url is available is what they have drafted now, with 
tiny tolerable differences.

Later,
G

On Wednesday, May 1, 2002, at 12:03 PM, Matthew Pocock wrote:

> 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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>
>
>