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

Wed Apr 21 12:38:50 EDT 2010

Hi Aminah,

Thanks so much for writing this.  I will attempt to get it transfered to the
wiki in the next week or so.  I will let you know if I have any questions.

Thanks again,

Dave C

On Tue, Apr 20, 2010 at 2:13 AM, Aminah Keliet <
aminah-olivia.keliet at versailles.inra.fr> wrote:

> Hi,
>
> The document "how to load chado database into BioMart" is attached. If
> informations is missing, please let me know. If the English translation is
> not correct, you can edit this document (.doc format).
>
> In the hope that it serves Chado users,
>
> Best regards,
>
> Aminah,
>
>
> Aminah Keliet 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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