[Open-bio-l] Common SQLite3 schema for flat file indexing (a new OBDA standard)?

[Chris Fields]

On Jun 7, 2010, at 3:11 PM, Peter wrote:

> On Mon, Jun 7, 2010 at 8:08 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>> We typically implement multifile indexing in bioperl (either via a
>> directory or a list of files).  Not much point in limiting it to one file.
>> 
> 
> Well, I guess as always it depends on what you're doing - I've
> found single file indexes very handy on several occasions.

I think it depends on how complex the indexing is.

>> Have you looked at the OBDA standard? It is a good start along
>> these lines, but I think it dwindled a bit.  Might be worth reworking
>> and modernizing it to suit our needs.
> 
> I have looked at the OBDA documentation (I might even try and
> rewrite support for it in Biopython if anyone was interested), and
> an update using SQLite3 seems a sensible approach to try.
> 
> Peter

It would be nice to have a standard for this that works cross-Bio* (and possibly beyond).  That was the original intent.  Maybe OBDA v2 if needed?

chris