[Biojava-l] Re: Proposed addition to the SequenceDB interface

[Matthew Pocock]

Controled vocabularies again. Round and round the mulbry bush.

Marc Colosimo wrote:
> Thomas Down <td2@sanger.ac.uk> wrote:
> 
> 
>>Hi...
>>
>>I'm considering adding a filter(FeatureFilter); method to
>>SequenceDB, which allows features to be extracted from a
>>whole database, rather than just a single sequence.  Typical
>>usage would be:
>>
>>  SequenceDB seqDB = ...
>>  FeatureHolder mygene = seqDB.filter(
>>      new FeatureFilter.ByAnnotation("gene.id", "BRCA2")
>>  );
> 
> 
> Would this return the feature as some sort of generic gene.id feature? My
> growing concern is that for each file/db/SQL format we are adding features with
> their original names rather than some defined BioJava enforced named feature. I
> noticed a dtd for features. Unfortunately, I don't know much about XML besides
> the simple things. Could we make something like gene_id, accession_no, etc...
> ? By using these set names, you don't have to know what a gene_id tag is for
> EMBL, genbank, SQL,.......
> 
> Or have I missed this ability in BioJava somehow?
> 
> Marc
> 
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