[Gmod-help] Re: [mart-dev] Documentation request

[Nathaniel Street]

Hi Dave (et al.)

Yes, I would absolutely be interested in this. If we have to load our 
GFF file etc into Chado, no worries - it would be a small price to pay. 
In general though it would also be great to document the same procedure 
for a Bio::DB::SeqFeature::Store db as I have the impression there are 
more users there than there are for Chado.

If anyone can help me walk through the process and I am more than 
willing to put the time into writing it up for WIKI pages etc.

This would be a great resource for all GMOD user I'm sure.

Thanks for the reply :)

Nathaniel

On 19/02/10 19:28, Dave Clements, GMOD Help Desk wrote:
> Hi Nathaniel, Joelle, Michael, and the BioMart team,
>
> At the January 2010 GMOD Meeting
> (http://gmod.org/wiki/January_2010_GMOD_Meeting) Joelle Amselem and
> Michael Alaux of INRA-URGI gave a talk on the GNPAnnot project. They
> mentioned that they had successfully ported their Chado database
> (http://gmod.org/wiki/Chado) to BioMart. Documenting how this is done
> has been on my TODO list since.
>
> Nathaniel, going from Chado to BioMart is not exactly what you are
> looking for, but it is close (it adds the extra step of loading your
> GFF3 into Chado). If we could document this path, would you be
> interested in using it?
>
> Joelle and Michael: Would you be interesting in helping document how to
> load a Chado database into BioMart? If you could send me notes* I could
> wikify and prettify them and post them to the GMOD web site. This would
> be useful to a lot of Chado users.
>
> Thanks,
>
> Dave C.
>
> * In English, as I can't read French. :-(
>
> On Thu, Feb 18, 2010 at 11:27 PM, Nathaniel Street
> <nathaniel.street at plantphys.umu.se
> <mailto:nathaniel.street at plantphys.umu.se>> wrote:
>
>     Hi
>
>     We are setting up a web resource for a draft genome. We have GBrowse
>     up and running no problem but now want the same data (sequence and
>     basic annotation) to be available via BioMart. I am not a
>     computer/bioinformatics 'expert'. I'm a biologist learning to use
>     computers so I am at the hands of the quality of available
>     documentation for resources. Pointing me to an existing Mart doesn't
>     really help me know how to go from a starting point of nothing to a
>     working Mart.
>
>     I have searched the mailing list for anything relevant I can think
>     of. I have even found *identical* requests to this one but nothing
>     has come of those posts (other than 'look at one of our existing
>     ensembl marts').
>
>     What I want is to know how to go from a starting point of having
>     a)genomic, transcript and protein FASTA files b)a GFF3 file for
>     transcripts c)a table of gene annotation information to setting up
>     BioMart. I imagine this has to be a common task so I am surprised
>     there is no documentation on this. As part of the GMOD project it
>     would be great to see an integrated tutorial on setting up GBrowse
>     and getting the same data into a working Mart.
>
>     I have looked at and tried to use the gff2biomart script (various
>     versions of it) but after much effort got nowhere. I have also asked
>     someone far more familiar with mysql and perl to have a go. They got
>     a lot further than me but still not to a working Mart. We both
>     managed to get simple tables structures for location and annotation
>     information working but the sequence side of things is a complete
>     mystery.
>
>     So, is there any documentation available and if not can anyone help
>     me go from FASTA+GFF3+annotation table to a working Mart? If someone
>     can help I am more than willing to write up the end process into a
>     walk-through guide so that others benefit.
>
>     Thanks
>
>     Nathaniel
>     --
>     Nathaniel Street
>     Umeå Plant Science Centre
>     Department of Plant Physiology
>     University of Umeå
>     SE-901 87 Umeå
>     SWEDEN
>
>     email: nathaniel.street at plantphys.umu.se
>     <mailto:nathaniel.street at plantphys.umu.se>
>     tel: +46-90-786 5473
>     fax:  +46-90-786 6676
>
>     www.popgenie.org <http://www.popgenie.org>
>
>
>
>
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-- 
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
University of Umeå
SE-901 87 Umeå
SWEDEN

email: nathaniel.street at plantphys.umu.se
tel: +46-90-786 5473
fax:  +46-90-786 6676

www.popgenie.org