[Open-bio-l] Re: [GMOD-devel] Schema for genes & features & mappings to assemblies

[Lincoln Stein]

> 	- biosql is for sequences and features, not mappings to assemblies (is
> that intended to be added, too, or is it beyond its scope? ) 

> - GGB is
> running off the schema in Bio::DB:GFF, which is not biosql compatible
> (Lincoln? If so, do you have any plans to change that?) 

Bio::DB::GFF came about six months before biosql.  GGB runs on top of both 
Bio::DB::GFF and Gadfly, which magically enough have similar APIs even though 
we didn't plan it that way.  Someday soon I'm going to try to adapt BioSQL to 
support GGB, but to some extent its entry-based view of the world is at odds 
with the GGB view of the world.  GGB sees the genome as a series of landmarks 
that occupy (potentially split, potentially multiple) regions of the genome.

> - Wormbase is an AceDB

WormBase uses GGB now.  We dump into Bio::DB::GFF every two weeks when we do 
a release.

> While waiting for responses (hoping that there are going to be some :) I
> thought I reverse engineer ERDs from the DDL I find in biosql and
> Bio::DB::GFF, because I hate trying to understand a schema based on CREATE
> TABLE statements. Let me know if that's already been done and I just
> overlooked the respective URLs. Also, we'll eventually implement this
> database in Oracle, and my understanding is that none of the things I
> mentioned is in or has been ported to Oracle (the latter may be, better
> yet, hopefully is, wrong).

Bio::DB::GFF has a really simple ERD (there are only three tables for 
features, and one table for DNA).  If you haven't done it already, let me 
know and I'll draw one with powerpoint.

Lincoln