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Representing Sequence version in GFF3

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Representing Sequence version in GFF3

Jeff Bowes
Hi,

Is there a standard way to represent the sequence version in a GFF3 file
for loading into chado?

Thanks,

Jeff

--
Jeff Bowes M.Sc.
DBA/Technical Architect, Xenbase
Department of Biological Sciences
University of Calgary
Calgary, Alberta T2N 1N4
CANADA
Tel: (403) 220-2824
Fax: (403) 284-4707





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Re: Representing Sequence version in GFF3

Allen Day
Well, gff3 allows you to put fasta at the end of the file.  I don't think
we currently support loading those records though.  Scott?

-Allen


On Tue, 6 Sep 2005, Jeff Bowes wrote:

> Hi,
>
> Is there a standard way to represent the sequence version in a GFF3 file
> for loading into chado?
>
> Thanks,
>
> Jeff
>
>


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Re: Representing Sequence version in GFF3

Scott Cain-2
No, the sequence gets loaded.  The question Jeff asked though is about
seequence versions.  I don't think this is any real support for sequence
versions in chado (and there certainly isn't in the gff loader).

Scott

On Tue, 2005-09-06 at 10:48 -0700, Allen Day wrote:

> Well, gff3 allows you to put fasta at the end of the file.  I don't think
> we currently support loading those records though.  Scott?
>
> -Allen
>
>
> On Tue, 6 Sep 2005, Jeff Bowes wrote:
>
> > Hi,
> >
> > Is there a standard way to represent the sequence version in a GFF3 file
> > for loading into chado?
> >
> > Thanks,
> >
> > Jeff
> >
> >
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
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Cold Spring Harbor Laboratory



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Re: Representing Sequence version in GFF3

Chris Mungall

Any feature can have a primary dbxref, which is versioned

On Tue, 6 Sep 2005, Scott Cain wrote:

> No, the sequence gets loaded.  The question Jeff asked though is about
> seequence versions.  I don't think this is any real support for sequence
> versions in chado (and there certainly isn't in the gff loader).
>
> Scott
>
> On Tue, 2005-09-06 at 10:48 -0700, Allen Day wrote:
> > Well, gff3 allows you to put fasta at the end of the file.  I don't think
> > we currently support loading those records though.  Scott?
> >
> > -Allen
> >
> >
> > On Tue, 6 Sep 2005, Jeff Bowes wrote:
> >
> > > Hi,
> > >
> > > Is there a standard way to represent the sequence version in a GFF3 file
> > > for loading into chado?
> > >
> > > Thanks,
> > >
> > > Jeff
> > >
> > >
> >
> >
> > -------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software Conference & EXPO
> > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                         [hidden email]
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
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> _______________________________________________
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>




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Re: Representing Sequence version in GFF3

Scott Cain-2
Right.  And the GFF3 loader properly handles dbxrefs; you could have:

chrI . chromosome 1 1000000 . . . ID=chrI;Dbxref=genbank:AA111111.2
##FASTA
>chrI
atgcatgc.......

The only tricky thing is that now your database will likely have (at
least) two features named 'chrI'.  From gbrowse's perspective, that
could be annoying, as you will be given a 'multiple hit' page every time
you want to view something on your current chrI.  To avoid that, I
suppose you would want to build the version into the name of the feature
(or only old features, so that you could refer to the current feature
with just its name).

>From the features on the chromosomes perspective, though, it shouldn't
matter, as the feature will have only one version of the chromosome as a
srcfeature.  That of course leaves out the considerable fun associated
with migrating features from one version of a genome to the next.

I'm sure there are issues I haven't thought of yet--one just occurred to
me that I am aware of but haven't fixed yet: the GFF3 bulk loader will
just assume that a uniquename that it has constructed is valid without
checking--that needs to change in the very near future.

Scott




On Tue, 2005-09-06 at 11:51 -0700, Chris Mungall wrote:

> Any feature can have a primary dbxref, which is versioned
>
> On Tue, 6 Sep 2005, Scott Cain wrote:
>
> > No, the sequence gets loaded.  The question Jeff asked though is about
> > seequence versions.  I don't think this is any real support for sequence
> > versions in chado (and there certainly isn't in the gff loader).
> >
> > Scott
> >
> > On Tue, 2005-09-06 at 10:48 -0700, Allen Day wrote:
> > > Well, gff3 allows you to put fasta at the end of the file.  I don't think
> > > we currently support loading those records though.  Scott?
> > >
> > > -Allen
> > >
> > >
> > > On Tue, 6 Sep 2005, Jeff Bowes wrote:
> > >
> > > > Hi,
> > > >
> > > > Is there a standard way to represent the sequence version in a GFF3 file
> > > > for loading into chado?
> > > >
> > > > Thanks,
> > > >
> > > > Jeff
> > > >
> > > >
> > >
> > >
> > > -------------------------------------------------------
> > > SF.Net email is Sponsored by the Better Software Conference & EXPO
> > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> > > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> > > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> > > _______________________________________________
> > > Gmod-schema mailing list
> > > [hidden email]
> > > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                         [hidden email]
> > GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> > Cold Spring Harbor Laboratory
> >
> >
> >
> > -------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software Conference & EXPO
> > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
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> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
>
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         [hidden email]
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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