[Gmod-help] questions

[Dave Clements, GMOD Help Desk]

Hi Brian,

In about 10 minutes I'm going to be away from my e-mail for the next 5
days, but I'll try to get as much typed as I can.

Chado does have expression and phenotype modules for this type of
data.  I know the phenotype module is used in several places, but I
don't know about the expression module at all.  Neither of them are in
widespread use, and therefore may not be as robust as the modules in
the core.  I can't answer your specific questions just now, because I
haven't looked at them for a while.

I mean to take a closer look at them when I get off holiday.  I have a
fair amount of experience with expression from my time at both
zfin.org and at EMAGE (I'm telecommuting from EMAGE as I type this in
fact), and I would love to work with someone to make Chado be as
useful for expression data as it is for genomic data.

However, as much as I would like to have you consider GMOD, have you
considered collaborating with EMAGE on the expression data?  I know
they welcome any data they can get.

Gotta run,

Dave C.
GMOD Help Desk

On Thu, Sep 11, 2008 at 4:48 PM, Brian Cox <lungboy at sickkids.ca> wrote:
> Hello,
> This looks like an interesting project. I have several datasets that I might
> like to try to fit into this schema. I have a data set of expression
> patterns in mouse embryos (colour images, different time points and points
> of view, both whole mount and sectioned) also some have phenotypes that
> would need to be scored. I noticed that your database program had a
> phenotype module but I didn't see any reference to modules for image
> information or for anatomical descriptions for expression patterns, not mRNA
> or protein levels. Have you looked at emage
> (http://genex.hgu.mrc.ac.uk/Emage/database/emageIntro.html)? Are there
> modules being created for this? I have a fair amount of experience with
> Java/biojava and mysql and would be willing to undertake some programming
> and development myself. My data set is currently in a filemakerpro database,
> but we have an interest in getting the data in an online format for
> publication.
>
> I am also generating protein interaction datasets in the mouse and will have
> a need for bring this data in to a web accessible resource, is that a module
> that would be created?
>
> Thanks
> Brian
>
> Brian Cox, Ph.D.
> Laboratory of Janet Rossant
> Hospital for Sick Children
>
> TMDT, room 13-305
> 101 College Street,
> Toronto Ontario
> Canada M5G 1L7
>
> cell: 416-358-5763
>
>
>



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