[Gmod-help] a questions

[Scott Cain]

Hi Zhiliang,

The schema for GBrowse is included in the BioPerl module that talks to
the database, so if you are using Bio::DB::GFF::Adaptor::dbi::mysql,
the schema is in mysql.pm in a method called schema.

Scott


On Fri, Oct 10, 2008 at 4:48 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
> Hi Dave,
>
> Along the same line of questions, I wonder where can I find the (MySQL) database schema behind the GBrowse?  Also, is there a map between the database schema and the GFF fields -- it will help to understand better how things work.
>
> I apologize if the info is already in the public domain but I just have not read thorough enough (please point it out to me :-)
>
> Thanks,
> Zhiliang
>
>
>>Date: Tue, 07 Oct 2008 15:19:42 -0500
>>To: help at gmod.org
>>From: Zhiliang Hu <zhu at iastate.edu>
>>Subject: Re: [Gmod-help] a questions
>>Cc: "GMOD Help Desk" <help at gmod.org>
>>
>>Hi Dave,
>>
>>I have loaded my GBrowse (<http://www.animalgenome.org:2358/cgi-bin/gbrowse/>http://www.animalgenome.org/cgi-bin/gbrowse/) using Scott's script "load_genbank.pl" without involving GFF files. I have yet to figure out how the changes you suggested be done with the script... I am learning that the column 9 of GFF3 file can be very "information rich"! ;-)
>>
>>Thank you!
>>
>>Zhiliang
>>
>>
>>At 10:08 AM 10/7/2008 -0700, Dave Clements, GMOD Help Desk wrote:
>>>Hi Zhiliang,
>>>
>>>I don't know the answer to your question, but...
>>>
>>>How are you loading the Genbank data into GBrowse?  If you are first
>>>creating a GFF3 file then you can modify the GFF3 file before loading
>>>it.  In particular, I think you could leave column 1 of the GFF as
>>>"NC_007299" on all the lines for chromosome 1, and change column 9 of
>>>just the line that defines the chromosome from "Name=NC_007299" to
>>>"Name="Chr.1"  This leaves the internal ID as NC_007299, but displays
>>>it as Chr.1
>>>
>>>Or does this not address what you are trying to do?
>>>
>>>Alternatively, If you can't find any links that are broken with your
>>>current approach, then you can leave it as it is.
>>>
>>>Hope this helps,
>>>
>>>Dave C.
>>>
>>>On Fri, Oct 3, 2008 at 12:02 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>>> I have a technical question -- I set up my Gbrowse with Genbank files, and wish to call each chromosome by a name like "Chr.1", and tried so by changing "ACCESSION" name from "NC_007299" to "Chr.1".  It displayed alright, but just wonder if this is the right way to do?  (wonder if ACCESSION also used for other things like web links).
>>>>
>>>> Zhiliang
>>>
>>>--
>>>Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research