[Gmod-help] questions

Thu Sep 18 10:00:47 EDT 2008

Dave,
Slow motion is the pace that most science goes....
Okay sounds like this might do what we are looking for. I will wait for some
kind of documentation from you as to the feasibility of setting up images.
Like I said we do have much of this in a database and could export tables in
a variety of formats so we have some organized datasets to play with. Maybe
I could start with setting up the X chromosome database first and then see
if we can layer on the images later when you have sorted that issue out. Are
there some tutorials for setting up the database and loading files into it
(could I be more lazy, there are probably links on your wiki)?

Re Emage,
When we originally tried to enter the data they told us there was no file or
table reader app that we could use to read data in to the database. Perhaps
by now they have these, but three years ago when we started the project they
didn't.

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

-----Original Message-----
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com] 
Sent: Wednesday, September 17, 2008 11:20 PM
To: b.cox at utoronto.ca
Cc: GMOD Help Desk
Subject: Re: [Gmod-help] questions

Hi Brian,

I'm back in Oregon and reasonably caffeinated, but I am headed off again
tomorrow for two days.  This may be a slow motion exchange.

> 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.

I'm sorry to hear that you had to manually re-enter data to get it into
EMAGE.  If you haven't already done so, I would let the EMAGE editorial
office (Jeff, Lorna, Venkat or Peter) know that you could not find an easier
way to do this.  That's discouraging and frustrating.

> 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.

GBrowse, GMOD's genome browser, can certainly be configured to display an
almost infinite amount of extra information as long as it is related to some
genomic region.  GBrowse could include links to EMAGE pages or to a custom
database at Sick Kids.

A harder question is "Could that custom database be a Chado database?"
Storing the sequence / alleles / mutations is not a problem.  A closer look
at the tables in the expression module hint at an intent to support both
images and anatomy annotation, but there is not enough documentation (that's
my job) for this to be clear.  Again, I'll take a closer look at this.

Thanks,

Dave C.

> 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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