[Gmod-help] questions

Wed Sep 17 23:19:48 EDT 2008

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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>

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