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

[Peter]

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?

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