[Gmod-help] questions

[Brian Cox]

Dave,
You are probably gone, but thanks for replying. You should set up an auto
reply; I would have waited. 
We do submit image data to emage and have used their database format but it
was not realy easy to port data into and we (i.e. two summerr students) had
to manually re enter the data into their database. That paper is nearly
accepted so the data will be released soon (quite large over 200 expression
pattern). So I do not mind depositing the data there. Why I was more
interested in your project was the tie in with the genome. We have been
systematically characterizing mutations and expression patterns on the X
chromosome (>60 different genes so far with funding for another 30-40). So
we would like to link or expand our database to include mappings to the
human and mouse X chromosome and human diseases of the X chromosome as well
as other mouse knock outs of X chromosome genes. A sort of X specific genome
database.

Talk to you again in 5 days. Hope you have/had a good vacation.
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


-----Original Message-----
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com] 
Sent: Thursday, September 11, 2008 12:10 PM
To: Brian Cox
Cc: GMOD Help Desk
Subject: Re: [Gmod-help] questions


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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