[Gmod-help] Evaluating chado as a model organism data resource

[Dave Clements, GMOD Help Desk]

Hi Kevin,

Good to hear from you.  My notes said that you were at the January
meeting, but I don't think I ever got to speak with you.

Chado was originally designed to support multiple organisms, and there
are a number of organizations that use it that way.  You won't be
breaking new ground if you store data for multiple organisms in the
same Chado instance.

To serve DAS data from Chado using Perl see
http://search.cpan.org/~lds/GBrowse-1.988/lib/Bio/DB/Das/Chado.pm.  I
believe this will only serve data associated with sequence regions,
but I think that is what DAS is all about anyway.

Your questions are right in Scott's area of expertise, but he is
travelling this week.  He may expand on my answers in a day or two.

Thanks,

Dave C

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On Thu, Feb 26, 2009 at 3:08 PM, Clancy, Kevin
<Kevin.Clancy at invitrogen.com> wrote:
>
> Hello
> I am interested in using CHADO to host data for a number of model organisms.
> I've been looking through your documentation, attended the meeting after PAG
> and I still have a couple of questions:
>
> 1. I will be hosting several organisms, eg human, rat, mouse, arabidopsis
> and so on. How do I maintain these as separate instances? Do I need to have
> several instances of CHADO running for each organism or does the database
> manage the data for each organism based upon the originating organism?
>
> 2. I see that you have a number of annotation and browsing softwares. I am
> interested in serving data via a DAS server - do you have a recommended DAS
> server (preferably Perl) that has already been configured to run with CHADO?
>
> Tank you for your time and reply
> Sincerely
> Kevin
>
> Kevin Clancy, PhD
> Senior Scientist, Informatic Sciences
> Invitrogen Corp
> Carlsbad, CA 92008
> Phone: (768) 268 8356
> Email: kevin.clancy at invitrogen.com