Chado Comparative Module

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Chado Comparative Module

Mara Kim-2
Hello gmod-ers!

Here is a proposal for the implementation of featuregroups in Chado as discussed earlier today at GMOD San Diego.

http://gmod.org/wiki/Chado_Comparative_Module

Sincerely,
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Re: [Gmod-schema] Chado Comparative Module

Sook Jung
Hello,
Could you tell us what was the use case for featuregroup? I would think feature_relationship table can take care of the need for grouping features together..
Thanks
Sook


On Thu, Jan 16, 2014 at 8:53 PM, Mara Kim <[hidden email]> wrote:
Hello gmod-ers!

Here is a proposal for the implementation of featuregroups in Chado as discussed earlier today at GMOD San Diego.

http://gmod.org/wiki/Chado_Comparative_Module

Sincerely,
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Re: [Gmod-schema] Chado Comparative Module

Mara Kim-2
The classic use case would be for the representation of a protein family.  These are generally determined using an HMM, and thus do not really represent relationships back to a specific feature.  Additionally, annotations to that protein family could be represented in a normalized fashion using featuregroupprop.


On Thu, Jan 16, 2014 at 5:59 PM, Sook Jung <[hidden email]> wrote:
Hello,
Could you tell us what was the use case for featuregroup? I would think feature_relationship table can take care of the need for grouping features together..
Thanks
Sook


On Thu, Jan 16, 2014 at 8:53 PM, Mara Kim <[hidden email]> wrote:
Hello gmod-ers!

Here is a proposal for the implementation of featuregroups in Chado as discussed earlier today at GMOD San Diego.

http://gmod.org/wiki/Chado_Comparative_Module

Sincerely,
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Vanderbilt University
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Re: [Gmod-schema] Chado Comparative Module

Robert Buels-2

The way I did Gene families when I was at SGN was to have a feature for the group itself,  and then have feature_relationships between it and it's members.  Worked pretty well.

On Jan 17, 2014 9:55 AM, "Mara Kim" <[hidden email]> wrote:
The classic use case would be for the representation of a protein family.  These are generally determined using an HMM, and thus do not really represent relationships back to a specific feature.  Additionally, annotations to that protein family could be represented in a normalized fashion using featuregroupprop.


On Thu, Jan 16, 2014 at 5:59 PM, Sook Jung <[hidden email]> wrote:
Hello,
Could you tell us what was the use case for featuregroup? I would think feature_relationship table can take care of the need for grouping features together..
Thanks
Sook


On Thu, Jan 16, 2014 at 8:53 PM, Mara Kim <[hidden email]> wrote:
Hello gmod-ers!

Here is a proposal for the implementation of featuregroups in Chado as discussed earlier today at GMOD San Diego.

http://gmod.org/wiki/Chado_Comparative_Module

Sincerely,
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Re: [Gmod-schema] Chado Comparative Module

Scott Cain
Ah, yes, the fake feature solution!


On Fri, Jan 17, 2014 at 11:45 AM, Robert Buels <[hidden email]> wrote:

The way I did Gene families when I was at SGN was to have a feature for the group itself,  and then have feature_relationships between it and it's members.  Worked pretty well.

On Jan 17, 2014 9:55 AM, "Mara Kim" <[hidden email]> wrote:
The classic use case would be for the representation of a protein family.  These are generally determined using an HMM, and thus do not really represent relationships back to a specific feature.  Additionally, annotations to that protein family could be represented in a normalized fashion using featuregroupprop.


On Thu, Jan 16, 2014 at 5:59 PM, Sook Jung <[hidden email]> wrote:
Hello,
Could you tell us what was the use case for featuregroup? I would think feature_relationship table can take care of the need for grouping features together..
Thanks
Sook


On Thu, Jan 16, 2014 at 8:53 PM, Mara Kim <[hidden email]> wrote:
Hello gmod-ers!

Here is a proposal for the implementation of featuregroups in Chado as discussed earlier today at GMOD San Diego.

http://gmod.org/wiki/Chado_Comparative_Module

Sincerely,
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Re: [Gmod-schema] Chado Comparative Module

Mara Kim-2
We have investigated this solution.  Not only does this blow up the already overloaded feature table, but there is the additional problem of selecting an organism_id for these features.  I suppose you could add a "null" organism, but that sounds incredibly hacky and loses the connection to a biological reality.


On Fri, Jan 17, 2014 at 2:02 PM, Scott Cain <[hidden email]> wrote:
Ah, yes, the fake feature solution!


On Fri, Jan 17, 2014 at 11:45 AM, Robert Buels <[hidden email]> wrote:

The way I did Gene families when I was at SGN was to have a feature for the group itself,  and then have feature_relationships between it and it's members.  Worked pretty well.

On Jan 17, 2014 9:55 AM, "Mara Kim" <[hidden email]> wrote:
The classic use case would be for the representation of a protein family.  These are generally determined using an HMM, and thus do not really represent relationships back to a specific feature.  Additionally, annotations to that protein family could be represented in a normalized fashion using featuregroupprop.


On Thu, Jan 16, 2014 at 5:59 PM, Sook Jung <[hidden email]> wrote:
Hello,
Could you tell us what was the use case for featuregroup? I would think feature_relationship table can take care of the need for grouping features together..
Thanks
Sook


On Thu, Jan 16, 2014 at 8:53 PM, Mara Kim <[hidden email]> wrote:
Hello gmod-ers!

Here is a proposal for the implementation of featuregroups in Chado as discussed earlier today at GMOD San Diego.

http://gmod.org/wiki/Chado_Comparative_Module

Sincerely,
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Vanderbilt University
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Mara Kim

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Computational Biology
Vanderbilt University
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Re: [Gmod-schema] Chado Comparative Module

Sook Jung
I think we need to think this over carefully since I think the hierarchical nature of feature or other tables is the key concept in Chado. What Rob said was exactly the way I was thinking.

We applied the same principle to store anything related to stock in 'stock' table when we developed ND module. Population, group of individual, individual, sample (half of an apple), etc - fake stocks...

Sook


On Fri, Jan 17, 2014 at 5:06 PM, Mara Kim <[hidden email]> wrote:
We have investigated this solution.  Not only does this blow up the already overloaded feature table, but there is the additional problem of selecting an organism_id for these features.  I suppose you could add a "null" organism, but that sounds incredibly hacky and loses the connection to a biological reality.


On Fri, Jan 17, 2014 at 2:02 PM, Scott Cain <[hidden email]> wrote:
Ah, yes, the fake feature solution!


On Fri, Jan 17, 2014 at 11:45 AM, Robert Buels <[hidden email]> wrote:

The way I did Gene families when I was at SGN was to have a feature for the group itself,  and then have feature_relationships between it and it's members.  Worked pretty well.

On Jan 17, 2014 9:55 AM, "Mara Kim" <[hidden email]> wrote:
The classic use case would be for the representation of a protein family.  These are generally determined using an HMM, and thus do not really represent relationships back to a specific feature.  Additionally, annotations to that protein family could be represented in a normalized fashion using featuregroupprop.


On Thu, Jan 16, 2014 at 5:59 PM, Sook Jung <[hidden email]> wrote:
Hello,
Could you tell us what was the use case for featuregroup? I would think feature_relationship table can take care of the need for grouping features together..
Thanks
Sook


On Thu, Jan 16, 2014 at 8:53 PM, Mara Kim <[hidden email]> wrote:
Hello gmod-ers!

Here is a proposal for the implementation of featuregroups in Chado as discussed earlier today at GMOD San Diego.

http://gmod.org/wiki/Chado_Comparative_Module

Sincerely,
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Computational Biology
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Re: [Gmod-schema] Chado Comparative Module

Siddhartha Basu
In reply to this post by Scott Cain
Hi,
I definitely think chado needs a generic grouping module. It's been
asked and discussed for last 6 years, however there is still no clear
path. Here are two interesting blasts from the past...
http://generic-model-organism-system-database.450254.n5.nabble.com/Feature-Lists-tp460032.html
http://generic-model-organism-system-database.450254.n5.nabble.com/Guidance-on-loading-multiple-assemblies-feature-naming-etc-tp4299131p4331117.html

We might have bypassed the issue(with varying solutions) for quite a
while but with changing time and demand maybe its time to put a
implementation. I think we should get the ball rolling and start Mara's proposed schema
as a starting point. It might not have to show up directly in the
default schema right away, but could start in a contrib section. At
least it would not be get lost and anybody can use it when it is needed.
And like any other open source contribution if it gathers solid user
cases, tool support could easily slide it back to the main tree.

What about interested parties join in one of the GMOD conference call,
kind of similar we did it for health module. Mara and her lab members could
pitch in the module and use cases. We are still hot off the GMOD 2014,
may be its a good time.

thanks,
-siddhartha


On Fri, 17 Jan 2014, Scott Cain wrote:

>    Ah, yes, the fake feature solution!
>
>    On Fri, Jan 17, 2014 at 11:45 AM, Robert Buels <[hidden email]> wrote:
>
>      The way I did Gene families when I was at SGN was to have a feature for
>      the group itself,  and then have feature_relationships between it and
>      it's members.  Worked pretty well.
>
>      On Jan 17, 2014 9:55 AM, "Mara Kim" <[hidden email]> wrote:
>
>        The classic use case would be for the representation of a protein
>        family.  These are generally determined using an HMM, and thus do not
>        really represent relationships back to a specific feature.
>        Additionally, annotations to that protein family could be represented
>        in a normalized fashion using featuregroupprop.
>
>        On Thu, Jan 16, 2014 at 5:59 PM, Sook Jung <[hidden email]> wrote:
>
>          Hello,
>          Could you tell us what was the use case for featuregroup? I would
>          think feature_relationship table can take care of the need for
>          grouping features together..
>          Thanks
>          Sook
>
>          On Thu, Jan 16, 2014 at 8:53 PM, Mara Kim <[hidden email]>
>          wrote:
>
>            Hello gmod-ers!
>
>            Here is a proposal for the implementation of featuregroups in
>            Chado as discussed earlier today at GMOD San Diego.
>
>            http://gmod.org/wiki/Chado_Comparative_Module
>            Sincerely,
>            Mara Kim
>
>            Ph.D. Candidate
>            Computational Biology
>            Vanderbilt University
>            Nashville, TN
>            ------------------------------------------------------------------------------
>            CenturyLink Cloud: The Leader in Enterprise Cloud Services.
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>            Critical Workloads, Development Environments & Everything In
>            Between.
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>            https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>        --
>        Mara Kim
>
>        Ph.D. Candidate
>        Computational Biology
>        Vanderbilt University
>        Nashville, TN
>        ------------------------------------------------------------------------------
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>
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D.                                   scott at scottcain
>    dot net
>    GMOD Coordinator (http://gmod.org/)                     216-392-3087
>    Ontario Institute for Cancer Research

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Re: [Gmod-schema] Chado Comparative Module

Mara Kim-3
Hello everyone,

Kris and I would be able to do a conference call either Thursday 1-5 CST, or all day Friday.

In my opinion, the final implementation in the schema is less important than establishing a standard way of representing sets of features.  That way there is at least a common interface that could be supported by the community.  It would be nice to know that so long as our idea of what a set of features conforms to some standard, it could potentially be displayed in Tripal, JBrowse, etc.


On Mon, Jan 20, 2014 at 9:57 AM, Siddhartha Basu <[hidden email]> wrote:
Hi,
I definitely think chado needs a generic grouping module. It's been
asked and discussed for last 6 years, however there is still no clear
path. Here are two interesting blasts from the past...
http://generic-model-organism-system-database.450254.n5.nabble.com/Feature-Lists-tp460032.html
http://generic-model-organism-system-database.450254.n5.nabble.com/Guidance-on-loading-multiple-assemblies-feature-naming-etc-tp4299131p4331117.html

We might have bypassed the issue(with varying solutions) for quite a
while but with changing time and demand maybe its time to put a
implementation. I think we should get the ball rolling and start Mara's proposed schema
as a starting point. It might not have to show up directly in the
default schema right away, but could start in a contrib section. At
least it would not be get lost and anybody can use it when it is needed.
And like any other open source contribution if it gathers solid user
cases, tool support could easily slide it back to the main tree.

What about interested parties join in one of the GMOD conference call,
kind of similar we did it for health module. Mara and her lab members could
pitch in the module and use cases. We are still hot off the GMOD 2014,
may be its a good time.

thanks,
-siddhartha


On Fri, 17 Jan 2014, Scott Cain wrote:

>    Ah, yes, the fake feature solution!
>
>    On Fri, Jan 17, 2014 at 11:45 AM, Robert Buels <[hidden email]> wrote:
>
>      The way I did Gene families when I was at SGN was to have a feature for
>      the group itself,  and then have feature_relationships between it and
>      it's members.  Worked pretty well.
>
>      On Jan 17, 2014 9:55 AM, "Mara Kim" <[hidden email]> wrote:
>
>        The classic use case would be for the representation of a protein
>        family.  These are generally determined using an HMM, and thus do not
>        really represent relationships back to a specific feature.
>        Additionally, annotations to that protein family could be represented
>        in a normalized fashion using featuregroupprop.
>
>        On Thu, Jan 16, 2014 at 5:59 PM, Sook Jung <[hidden email]> wrote:
>
>          Hello,
>          Could you tell us what was the use case for featuregroup? I would
>          think feature_relationship table can take care of the need for
>          grouping features together..
>          Thanks
>          Sook
>
>          On Thu, Jan 16, 2014 at 8:53 PM, Mara Kim <[hidden email]>
>          wrote:
>
>            Hello gmod-ers!
>
>            Here is a proposal for the implementation of featuregroups in
>            Chado as discussed earlier today at GMOD San Diego.
>
>            http://gmod.org/wiki/Chado_Comparative_Module
>            Sincerely,
>            Mara Kim
>
>            Ph.D. Candidate
>            Computational Biology
>            Vanderbilt University
>            Nashville, TN
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>        --
>        Mara Kim
>
>        Ph.D. Candidate
>        Computational Biology
>        Vanderbilt University
>        Nashville, TN
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>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D.                                   scott at scottcain
>    dot net
>    GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>    Ontario Institute for Cancer Research

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--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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