[BioSQL-l] Importing GFF3 files into a BioSQL database?

[Peter]

> Hello all.
>
> I'd like to stick my oar in here and say that regularising the
> GFF3<>BioSQL mapping accross Bio* is an essential step towards
> round-tripping between the different language bindings, ...

Absolutely - that's why I started this thread.  On a related note,
there is probably still room for improvement in the GenBank<>BioSQL
mapping across the Bio* projects, where the "gold standard" also needs
documenting.

> ... and also towards portable export of bioentry annotation via DAS
> (which has its roots in GFF, and is isomorphic for most practical
> purposes).
>
> Some of you might remember that back in Dec'08 I made the promise that
> I'd try and document the DAS<>BioSQL mapping. I've finally started to
> make good on this and have added a preliminary GFF section to the BioSQL
> wiki page describing Annotation Mapping conventions :
> http://www.biosql.org/wiki/Annotation_Mapping#GFF3
>
> Its very rough and ready, probably biased and not quite correct at the
> moment. It does, however, provide a central home for the information
> that Brad has put up on his blog, and the various other notes that have
> been made in this thread. Please add and amend as appropriate.

Is this based on the current behaviour of BioPerl code - or just what
you think would be sensible?

Peter