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

Mon Mar 15 12:40:26 EDT 2010

Hi Aminah,

Thank you for doing this.  I think it will help anyone who works with both
Chado and BioMart.  The translation can be in any format. Once I have it,
I'll put it up on the GMOD wiki.

Thanks,

Dave C

On Mon, Mar 15, 2010 at 8:13 AM, Aminah Keliet <
aminah-olivia.keliet at versailles.inra.fr> wrote:

> Hi,
>
> I am in charge of biomart in lab URGI, and i am ready to translate document
> describing how to load a Chado database into BioMart, in english, it is done
> in french.
> It is not difficult to load it, on following the steps to load dataset in
> BioMart.
> I will make quickly this document, to be useful to a lot of Chado users.
>
>
> Best regards,
>
> Aminah,
>
>
>
> Joelle Amselem wrote:
>
>> 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
>> -------------------------------------------------------------------------
>> 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
>> -------------------------------------------------------------------------
>>
>>
>> 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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>>>
>>>
>>>
>>
>>
>>
>
>
> --
> Aminah Olivia KELIET
> Ingenieur d'études en Bio-informatique
>
> Unité de recherche en Génomique-Info
> INRA Centre de Versailles
> Route de Saint Cyr
> 78026 Versailles Cedex
>
> email: Aminah-Olivia.keliet at versailles.inra.fr
> url:http://urgi.versailles.inra.fr
> tel: 01.30.83.37.74
>
>

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