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
<[email protected]
<mailto:[email protected]>> 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: [email protected]
    <mailto:[email protected]>
    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: [email protected]
tel: +46-90-786 5473
fax:  +46-90-786 6676

www.popgenie.org

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