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

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

Dave Clements, GMOD Help Desk-3
Hello all,

Aminah Keliet, Joëlle Amselem, Sandra Derozie, and Delphine Steinbach have written a guide to loading data from Chado into BioMart.  This guide is based on their experience of doing this at INRA URGI ( It includes step by step instructions and some specific examples for common situations in Chado. If you are interested in loading your Chado data into a BioMart instance then I recommend starting with this guide.  See for links.

Many, many thanks to the URGI team for making this available 


Dave C.

On Fri, Feb 19, 2010 at 11:41 AM, Nathaniel Street <[hidden email]> wrote:
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 :)


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
( 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
( 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.


Dave C.

* In English, as I can't read French. :-(

On Thu, Feb 18, 2010 at 11:27 PM, Nathaniel Street
<[hidden email]
<mailto:[hidden email]>> wrote:


   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

   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.


   Nathaniel Street
   Umeå Plant Science Centre
   Department of Plant Physiology
   University of Umeå
   SE-901 87 Umeå

   email: [hidden email]
   <mailto:[hidden email]>

   tel: +46-90-786 5473
   fax:  +46-90-786 6676 <>

Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
University of Umeå
SE-901 87 Umeå

email: [hidden email]
tel: +46-90-786 5473
fax:  +46-90-786 6676



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