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

[Joelle Amselem]

Dear Dave,

First of a	ll, sorry for the delay of my answer (I was out of office without network for 8 days)

I guess that we have some technical documentation written in french, but it will be probably possible to translate and to send something useful for the GMOD community
Concerning the biomart on chado,  it has to be configured to be compliant with the chado schema and Gbrowse for the output result link, but also with the data you insert in chado via GFF3 and particularly the field 9 with data inserted in featureproperty table.
For exemple if biomart find a result associated with a feature which is Target, you cannot serach it via GBrowse, we have to add in biomart, SQL request to find all the reference features on which these target are located. 

You can try on our website: http://urgi.versailles.inra.fr/gnpis/ -> Advanced Search -> Biomart
Request exemples: 
CHOOSE DATABASE: Query local single mart: GnpGenome (annotations) for Botrytis
	Description (% for wildcard) : %kinase%
	Program : blastx
	Library : uniprot_sprot

CHOOSE DATABASE: Query local single mart: GnpGenome (annotations) for Poplar
	Feature Type : gene
	Program : eugene


Aminah Keliet (in charge of Biomart at the lab) and Delphine Steinbach(responsible of the GnpIS and interoperability) are copy of this mail and will give you more information.

Best regards
Joelle
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Joelle Amselem
INRA-URGI
Fungal genomic annotation platform
Bat 18, Route de Saint-Cyr, 78026 Versailles cedex
Tel: +33 1 30 83 33 95, Fax: +33 1 30 83 38 99
http://urgi.versailles.inra.fr
email: joelle.amselem at versailles.inra.fr
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Le 19 févr. 2010 à 19:28, Dave Clements, GMOD Help Desk a écrit :

> 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> 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
> tel: +46-90-786 5473
> fax:  +46-90-786 6676
> 
> www.popgenie.org
> 
> 
> 
> -- 
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