From p.j.a.cock at googlemail.com  Thu Apr 24 04:31:35 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 24 Apr 2014 09:31:35 +0100
Subject: [BioSQL-l] [Bioperl-l] Writing and retrieving Genbank files
	from BioSQL
In-Reply-To: <035D9884-D673-4B54-97FB-E9404C40E2A0@illinois.edu>
References: <948ace19-ea00-493b-821f-92836ac3b02a@googlegroups.com>
	<5357E7DD.8060609@gmail.com> <5357F141.4010505@gmail.com>
	<035D9884-D673-4B54-97FB-E9404C40E2A0@illinois.edu>
Message-ID: <CAKVJ-_7jpH8xRqEP25_Uxm1-WDqUoWeofnxxhqCWfaCV5iV+4w@mail.gmail.com>

CC'ing Hilmar and the BioSQL list.

Yes, it might be nice to extend the BioSQL schema for these
fields (circular, molecule type, etc).

Right now, whatever bioperl-db does is the effective standard,
so any assistance specifying what exactly it does would be
enough to make Biopython do the same.

Given we didn't get a GSoC project student to work on
BioSQL and SQLite, perhaps a plan B is needed?

Thanks,

Peter.

On Wednesday, April 23, 2014, Fields, Christopher J <cjfields at illinois.edu>
wrote:

> I do think Roy is correct in saying this could be set as annotation.  In
> my opinion I would like Seq-pertinent information (alphabet, circular, mol
> type) at the level of the sequence.  At least, to me that makes more sense,
> as it describes information directly relevant about the sequence itself,
> whereas to me annotation are more about the sequence record (pubs,
> taxonomy, etc).  But I?m probably splitting hairs.
>
> BTW I agree re: SQLite support in bioperl-db.  However, bioperl-db uses a
> home-grown ORM, so this would entail creating a SQLite-specific DB loader.
>  The intent has been to move bioperl-db over to a consistent ORM
> (DBIx::Class) that would easily allow this, but that GSoC project didn?t
> have takers :P
>
> chris
>
> On Apr 23, 2014, at 11:58 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com<javascript:;>>
> wrote:
>
> > Hi Peter,
> >
> > Just found your message on the Google group.
> >
> > I think the correct way to deal with this would be to modify the BioSQL
> schema to include columns for is_circular and molecule type in the bioentry
> table.
> >
> > However, if the BioSQL schema is considered immutable, a workaround
> would be for BioPerl, BioPython etc. to agree on a standard way of storing
> the information in the existing BioSQL schema.
> >
> > I'd suggest we do this with two annotation tags:
> > "is_circular", with a value of BioPerl $seq->is_circular (1 or NULL)
> > "molecule", with a value of BioPerl $seq->molecule (DNA, RNA etc.)
> >
> > Once a sequence is removed from the database, these annotation tags
> could be removed and put in the correct place in the BioPerl/BioPython
> object model.
> >
> > Cheers,
> > Roy.
> >
> > > Thank you for chasing this issue Rik :)
> > >
> > > From the Biopython point of view, all I really need to know
> > > is where the linear/circular and molecule type information
> > > from the GenBank LOCUS line end up in the BioSQL tables
> > > (to make Biopython put it in the same place).
> > >
> > > https://redmine.open-bio.org/issues/2578
> > >
> > > Sadly I don't currently have a working BioSQL + BioPerl test
> > > setup (it would be great if BioPerl could add SQLite support -
> > > which would make it easy to do cross project testing).
> > >
> > > Thanks,
> > >
> > > Peter
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org <javascript:;>
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From p.j.a.cock at googlemail.com  Thu Apr 24 08:31:35 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 24 Apr 2014 09:31:35 +0100
Subject: [BioSQL-l] [Bioperl-l] Writing and retrieving Genbank files
	from BioSQL
In-Reply-To: <035D9884-D673-4B54-97FB-E9404C40E2A0@illinois.edu>
References: <948ace19-ea00-493b-821f-92836ac3b02a@googlegroups.com>
	<5357E7DD.8060609@gmail.com> <5357F141.4010505@gmail.com>
	<035D9884-D673-4B54-97FB-E9404C40E2A0@illinois.edu>
Message-ID: <CAKVJ-_7jpH8xRqEP25_Uxm1-WDqUoWeofnxxhqCWfaCV5iV+4w@mail.gmail.com>

CC'ing Hilmar and the BioSQL list.

Yes, it might be nice to extend the BioSQL schema for these
fields (circular, molecule type, etc).

Right now, whatever bioperl-db does is the effective standard,
so any assistance specifying what exactly it does would be
enough to make Biopython do the same.

Given we didn't get a GSoC project student to work on
BioSQL and SQLite, perhaps a plan B is needed?

Thanks,

Peter.

On Wednesday, April 23, 2014, Fields, Christopher J <cjfields at illinois.edu>
wrote:

> I do think Roy is correct in saying this could be set as annotation.  In
> my opinion I would like Seq-pertinent information (alphabet, circular, mol
> type) at the level of the sequence.  At least, to me that makes more sense,
> as it describes information directly relevant about the sequence itself,
> whereas to me annotation are more about the sequence record (pubs,
> taxonomy, etc).  But I?m probably splitting hairs.
>
> BTW I agree re: SQLite support in bioperl-db.  However, bioperl-db uses a
> home-grown ORM, so this would entail creating a SQLite-specific DB loader.
>  The intent has been to move bioperl-db over to a consistent ORM
> (DBIx::Class) that would easily allow this, but that GSoC project didn?t
> have takers :P
>
> chris
>
> On Apr 23, 2014, at 11:58 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com<javascript:;>>
> wrote:
>
> > Hi Peter,
> >
> > Just found your message on the Google group.
> >
> > I think the correct way to deal with this would be to modify the BioSQL
> schema to include columns for is_circular and molecule type in the bioentry
> table.
> >
> > However, if the BioSQL schema is considered immutable, a workaround
> would be for BioPerl, BioPython etc. to agree on a standard way of storing
> the information in the existing BioSQL schema.
> >
> > I'd suggest we do this with two annotation tags:
> > "is_circular", with a value of BioPerl $seq->is_circular (1 or NULL)
> > "molecule", with a value of BioPerl $seq->molecule (DNA, RNA etc.)
> >
> > Once a sequence is removed from the database, these annotation tags
> could be removed and put in the correct place in the BioPerl/BioPython
> object model.
> >
> > Cheers,
> > Roy.
> >
> > > Thank you for chasing this issue Rik :)
> > >
> > > From the Biopython point of view, all I really need to know
> > > is where the linear/circular and molecule type information
> > > from the GenBank LOCUS line end up in the BioSQL tables
> > > (to make Biopython put it in the same place).
> > >
> > > https://redmine.open-bio.org/issues/2578
> > >
> > > Sadly I don't currently have a working BioSQL + BioPerl test
> > > setup (it would be great if BioPerl could add SQLite support -
> > > which would make it easy to do cross project testing).
> > >
> > > Thanks,
> > >
> > > Peter
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org <javascript:;>
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>