Chado Extensions: GAF / Sequencing Data / etc?

[Eric Rasche-3]

Just wanted to ping other Chado people and see if anyone is:

• storing full GAF2.0 annotations in Chado?
• storing sequencing data nearby the database in any way?
• e.g. filenames pointing to bam/bigwig/cram/etc in a cell that you could pull out for automated analyses
• storing any other interesting datasets?

We're building out our infrastructure for genome database. I saw these as possible future problems for us, and wanted to see if the community was doing anything cool that they would be willing to share?

Cheers,
Eric

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[Siddhartha Basu]

Hi Eric,

On Thu, 31 Mar 2016, Eric Rasche wrote:

>    Just wanted to ping other Chado people and see if anyone is:
>      * storing full GAF2.0 annotations in Chado?
My ex-colleague did but on a oracle instance of chado. Here is the
starting part of legacy code
https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/dictygaf2chado.pm
Kim Rutherford(pombase) has done work with GPAD(latest format for GO
annotations) and here is a helpful discussion
http://generic-model-organism-system-database.450254.n5.nabble.com/Storing-GO-annotation-extensions-in-Chado-td4564896.html#a4581460
I have an unfinished loader for GPAD, written in golang, the testing
sqlite backend works but the pg backed yet to be completed. Here is a my
visual interpretation of the data model that i developed after a email
conversation with kim.
https://github.com/dictyBase/gochado/issues/6
And some thought process that might help
https://github.com/dictyBase/gochado/issues/7

thanks,
-siddhartha

>      * storing sequencing data nearby the database in any way?
>           * e.g. filenames pointing to bam/bigwig/cram/etc in a cell that you
>             could pull out for automated analyses
>      * storing any other interesting datasets?
>
>    We're building out our infrastructure for genome database. I saw these as
>    possible future problems for us, and wanted to see if the community was
>    doing anything cool that they would be willing to share?
>
>    Cheers,
>    Eric
>
>    --
>    Eric Rasche
>    Programmer II
>
>    Center for Phage Technology
>    Rm 312A, BioBio
>    Texas A&M University
>    College Station, TX 77843
>    [hidden email]

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> Accelerate data analysis in your applications with
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[Eric Rasche-2]

Hi Siddhartha,

On 04. april 2016 20:55, Siddhartha Basu wrote:

Hi Eric,

On Thu, 31 Mar 2016, Eric Rasche wrote:

   Just wanted to ping other Chado people and see if anyone is:
     * storing full GAF2.0 annotations in Chado?

My ex-colleague did but on a oracle instance of chado. Here is the
starting part of legacy code 
https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/dictygaf2chado.pm

Huh, good to know.

Kim Rutherford(pombase) has done work with GPAD(latest format for GO
annotations) and here is a helpful discussion
http://generic-model-organism-system-database.450254.n5.nabble.com/Storing-GO-annotation-extensions-in-Chado-td4564896.html#a4581460

That is a helpful discussion. Good to know that GPAD (will?) superseded GAF at some point. I'd never heard of it before.

I have an unfinished loader for GPAD, written in golang, the testing
sqlite backend works but the pg backed yet to be completed. Here is a my
visual interpretation of the data model that i developed after a email
conversation with kim.
https://github.com/dictyBase/gochado/issues/6
And some thought process that might help
https://github.com/dictyBase/gochado/issues/7

Thanks for sharing this work! This will be very helpful, hopefully we can implement something like this.

thanks,
-siddhartha

     * storing sequencing data nearby the database in any way?
          * e.g. filenames pointing to bam/bigwig/cram/etc in a cell that you
            could pull out for automated analyses
     * storing any other interesting datasets?

   We're building out our infrastructure for genome database. I saw these as
   possible future problems for us, and wanted to see if the community was
   doing anything cool that they would be willing to share?

   Cheers,
   Eric

   --
   Eric Rasche
   Programmer II

   Center for Phage Technology
   Rm 312A, BioBio
   Texas A&M University
   College Station, TX 77843
   [hidden email]

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Thanks again,
Eric


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[Chris Mungall]

You can read about GPAD/GPI here:
http://geneontology.org/page/go-annotation-file-formats

Note that the GO will be moving towards a more expressive OWL-based
representation that will allow annotations to be connected into pathways
and pathway fragments, called LEGO. You can see the editor here:
http://noctua.berkeleybop.org/

We will continue to make annotations available in GAF/GPAD, but this
will not be expressive enough to capture the full details of a LEGO
model. This would require either a new Chado module, or storage outside
Chado. WormBase are taking the latter approach.

I'll post more details here, but if any of you will be at the ISB
Biocuration meeting in Geneva, lots of GO people will be present,
including Seth Carbon (cc'd), the Noctua developer - he would be happy
to chat with any GMOD folks about technical details.


On 5 Apr 2016, at 10:16, Eric Rasche wrote:

> Hi Siddhartha,
>
> On 04. april 2016 20:55, Siddhartha Basu wrote:
>> Hi Eric,
>>
>> On Thu, 31 Mar 2016, Eric Rasche wrote:
>>
>>>    Just wanted to ping other Chado people and see if anyone is:
>>>      * storing full GAF2.0 annotations in Chado?
>> My ex-colleague did but on a oracle instance of chado. Here is the
>> starting part of legacy code
>> https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/dictygaf2chado.pm
> Huh, good to know.
>> Kim Rutherford(pombase) has done work with GPAD(latest format for GO
>> annotations) and here is a helpful discussion
>> http://generic-model-organism-system-database.450254.n5.nabble.com/Storing-GO-annotation-extensions-in-Chado-td4564896.html#a4581460
> That is a helpful discussion. Good to know that GPAD (will?)
> superseded
> GAF at some point. I'd never heard of it before.
>> I have an unfinished loader for GPAD, written in golang, the testing
>> sqlite backend works but the pg backed yet to be completed. Here is a
>> my
>> visual interpretation of the data model that i developed after a
>> email
>> conversation with kim.
>> https://github.com/dictyBase/gochado/issues/6
>> And some thought process that might help
>> https://github.com/dictyBase/gochado/issues/7
> Thanks for sharing this work! This will be very helpful, hopefully we
> can implement something like this.
>>
>> thanks,
>> -siddhartha
>>
>>
>>>      * storing sequencing data nearby the database in any way?
>>>           * e.g. filenames pointing to bam/bigwig/cram/etc in a cell
>>> that you
>>>             could pull out for automated analyses
>>>      * storing any other interesting datasets?
>>>
>>>    We're building out our infrastructure for genome database. I saw
>>> these as
>>>    possible future problems for us, and wanted to see if the
>>> community was
>>>    doing anything cool that they would be willing to share?
>>>
>>>    Cheers,
>>>    Eric
>>>
>>>    --
>>>    Eric Rasche
>>>    Programmer II
>>>
>>>    Center for Phage Technology
>>>    Rm 312A, BioBio
>>>    Texas A&M University
>>>    College Station, TX 77843
>>>    [hidden email]
>>> ------------------------------------------------------------------------------
>>> Transform Data into Opportunity.
>>> Accelerate data analysis in your applications with
>>> Intel Data Analytics Acceleration Library.
>>> Click to learn more.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
> Thanks again,
> Eric
>
> --
> Eric Rasche
> Programmer II
>
> Center for Phage Technology
> Rm 312A, BioBio
> Texas A&M University
> College Station, TX 77843
> [hidden email] <mailto:[hidden email]>
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> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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