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

[Chris Fields]

On Aug 31, 2009, at 10:45 AM, Peter wrote:

> On Mon, Aug 31, 2009 at 4:33 PM, Chris Fields<cjfields at illinois.edu>  
> wrote:
>>
>> I don't use OBDA, personally, but I can check on the status with  
>> Brian
>> Osborne (he was heading it up last I checked).  However, I don't  
>> think
>> BioPerl has an OBDA FASTQ parser.
>>
>> You may be thinking about Bio::Index::FASTQ?  That one is not OBDA,
>> but just a simple flat file indexer.  We could probably set an OBDA  
>> parser
>> up fairly easily if needed.
>
> 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 ones 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.

chris