[Open-bio-l] Status of OBDA and indexed flatfiles?

[Peter]

On Mon, Aug 31, 2009 at 7:22 PM, Chris Fields<cjfields at illinois.edu> wrote:
>> I didn't know if Bio::Index was using OBDA "under the hood" or not.
>> Does this mean BioPerl has multiple indexing systems available?
>
> Yes.  We have Bio::Index::*, Bio::DB::Flat (which I think is OBDA).  There
> is also the older Bio::DB::Fasta, which is actually still in wide use.  Note
> with Bio::Index::* we allow streaming of any report type (sequence,
> alignment, analysis like BLAST, etc).
>
> We have talked about switching many of the Bio::Index::* sequence-based
> one to OBDA but I haven't seen anyone take that up.
>
>> As I noted on Bug 2337 earlier today, Biopython used to have some
>> sort of OBDA compliant indexing, but for unrelated reasons we have
>> deprecated and removed that code. We're now revisiting this topic
>> due in part to having to deal with ever larger data files - and I wanted
>> to see if OBDA was still "alive" as a standard, and furthermore how
>> well it had scaled for the other OBF projects.
>>
>> Peter
>
> I think it's still alive and being used, just not sure what the compliance
> level is amongst the different Bio* projects.

That's Chris - so at least BioPerl and BioRuby are still using it. That's
good to know.  So right now (according to Bug 2337) there may be a
couple of compliance issues (or ambiguities in the spec)?

I don't think I have the time to look at it right now, but an SQLite
OBDA variant might be worth thinking about in future...

Peter