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: 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: 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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Re: 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-devel] 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-devel] 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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Mara Kim

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Computational Biology
Vanderbilt University
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Re: [GMOD-devel] 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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Mara Kim

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


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Re: [GMOD-devel] Chado Comparative Module

adf_ncgr
FWIW, we've been using this solution for gene family data as well. In our implementation, the feature that represents
the gene family itself is the consensus sequence emitted by the HMM representing the gene family. This seems
more like a true feature in that it actually has "residues" and also allows us to represent the multiple sequence
alignment via feature_locations of the members to the consensus. On the other hand, the organism we have associated
with these is definitely a hack  ("Consensus consensus"). I could imagine introducing putative ancestral species instead,
though I guess an HMM consensus doesn't really represent an ancestral reconstruction.

That said, I agree with Mara that it seems problematic to introduce fake features to represent groupings of features
that really have nothing to do with some form of inter-sequence alignment (co-expressed genes might be an example).
In some sense, it seems like what is being proposed is conceptually more similar to cvterm in the sense that the latter
can represent classes of objects. However, I don't think it would be appropriate to use cvterm for "extensionally" defined
sets of features; the proposed featuregroup seems preferable. But the analogy with cvterm suggests that featuregroup
could be made less specific to features and just represent a generalized "grouping" construct. Maybe that's too
abstract (but who would ever say such a thing of Chado?)...

I certainly haven't been in the trenches with Chado as long as others on this thread, though, so these are just my
speculative 2c....

regards

Andrew Farmer
Legume Information System

On 1/17/14 3:18 PM, Sook Jung wrote:
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
Vanderbilt University
Nashville, TN



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Re: [GMOD-devel] Chado Comparative Module

Stéphanie Sidibé--Bocs
Hello,


The iPlant Tree of Life (iPToL) database schema could meet our needs. It seems compatible with Chado and Ensembl Compara.
https://pods.iplantcollaborative.org/wiki/display/iptol/Database+Schema#DatabaseSchema-SchemaOverview


Best,

Le 18/01/2014 00:00, Andrew Farmer a écrit :
FWIW, we've been using this solution for gene family data as well. In our implementation, the feature that represents
the gene family itself is the consensus sequence emitted by the HMM representing the gene family. This seems
more like a true feature in that it actually has "residues" and also allows us to represent the multiple sequence
alignment via feature_locations of the members to the consensus. On the other hand, the organism we have associated
with these is definitely a hack  ("Consensus consensus"). I could imagine introducing putative ancestral species instead,
though I guess an HMM consensus doesn't really represent an ancestral reconstruction.

That said, I agree with Mara that it seems problematic to introduce fake features to represent groupings of features
that really have nothing to do with some form of inter-sequence alignment (co-expressed genes might be an example).
In some sense, it seems like what is being proposed is conceptually more similar to cvterm in the sense that the latter
can represent classes of objects. However, I don't think it would be appropriate to use cvterm for "extensionally" defined
sets of features; the proposed featuregroup seems preferable. But the analogy with cvterm suggests that featuregroup
could be made less specific to features and just represent a generalized "grouping" construct. Maybe that's too
abstract (but who would ever say such a thing of Chado?)...

I certainly haven't been in the trenches with Chado as long as others on this thread, though, so these are just my
speculative 2c....

regards

Andrew Farmer
Legume Information System

On 1/17/14 3:18 PM, Sook Jung wrote:
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
Vanderbilt University
Nashville, TN



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Re: [GMOD-devel] 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.
>            Learn Why More Businesses Are Choosing CenturyLink Cloud For
>            Critical Workloads, Development Environments & Everything In
>            Between.
>            Get a Quote or Start a Free Trial Today.
>            http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>            _______________________________________________
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>            [hidden email]
>            https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>        --
>        Mara Kim
>
>        Ph.D. Candidate
>        Computational Biology
>        Vanderbilt University
>        Nashville, TN
>        ------------------------------------------------------------------------------
>        CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>        Learn Why More Businesses Are Choosing CenturyLink Cloud For
>        Critical Workloads, Development Environments & Everything In Between.
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>      https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D.                                   scott at scottcain
>    dot net
>    GMOD Coordinator (http://gmod.org/)                     216-392-3087
>    Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
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Re: [GMOD-devel] 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
>            ------------------------------------------------------------------------------
>            CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>            Learn Why More Businesses Are Choosing CenturyLink Cloud For
>            Critical Workloads, Development Environments & Everything In
>            Between.
>            Get a Quote or Start a Free Trial Today.
>            http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>            _______________________________________________
>            Gmod-schema mailing list
>            [hidden email]
>            https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>        --
>        Mara Kim
>
>        Ph.D. Candidate
>        Computational Biology
>        Vanderbilt University
>        Nashville, TN
>        ------------------------------------------------------------------------------
>        CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>        Learn Why More Businesses Are Choosing CenturyLink Cloud For
>        Critical Workloads, Development Environments & Everything In Between.
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>        https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
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>
>    --
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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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Nashville, TN

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Re: [GMOD-devel] Chado Comparative Module

adf_ncgr
Hi all-
not sure how such discussions are normally organized- is there a regular schedule for "official" GMOD conference
calls, or would it make more sense to self-organize this topic among interested parties via a Doodle poll? I'd be
interested in participating either way. It might also be worth clarifying a bit up front whether the focus of the
discussion will be specifically on gene family representation or more generally about use cases for generic grouping
of features and/or other entities in the schema.

thanks

Andrew Farmer
Legume Information System

On 1/21/14 3:21 PM, Mara Kim wrote:
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
>            ------------------------------------------------------------------------------
>            CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>            Learn Why More Businesses Are Choosing CenturyLink Cloud For
>            Critical Workloads, Development Environments & Everything In
>            Between.
>            Get a Quote or Start a Free Trial Today.
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>            _______________________________________________
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>            [hidden email]
>            https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>        --
>        Mara Kim
>
>        Ph.D. Candidate
>        Computational Biology
>        Vanderbilt University
>        Nashville, TN
>        ------------------------------------------------------------------------------
>        CenturyLink Cloud: The Leader in Enterprise Cloud Services.
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>    dot net
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>    Ontario Institute for Cancer Research

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Re: [GMOD-devel] Chado Comparative Module

Siddhartha Basu
Hi Andrew,
I am up for the Doodle poll. Even it might not have to a official GMOD
conference call, we interested parties could set it up through skype.
So, what we poll for, any suggestions ?

thanks,
-siddhartha

On Wed, 22 Jan 2014, Andrew Farmer wrote:

>    Hi all-
>    not sure how such discussions are normally organized- is there a regular
>    schedule for "official" GMOD conference
>    calls, or would it make more sense to self-organize this topic among
>    interested parties via a Doodle poll? I'd be
>    interested in participating either way. It might also be worth clarifying
>    a bit up front whether the focus of the
>    discussion will be specifically on gene family representation or more
>    generally about use cases for generic grouping
>    of features and/or other entities in the schema.
>
>    thanks
>
>    Andrew Farmer
>    Legume Information System
>
>    On 1/21/14 3:21 PM, Mara Kim wrote:
>
>      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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>        Services.
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>        >            Critical Workloads, Development Environments & Everything
>        In
>        >            Between.
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>        >
>        >        --
>        >        Mara Kim
>        >
>        >        Ph.D. Candidate
>        >        Computational Biology
>        >        Vanderbilt University
>        >        Nashville, TN
>        >      
>         ------------------------------------------------------------------------------
>        >        CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>        >        Learn Why More Businesses Are Choosing CenturyLink Cloud For
>        >        Critical Workloads, Development Environments & Everything In
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>        >        _______________________________________________
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>        >
>        >    
>         ------------------------------------------------------------------------------
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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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>        > _______________________________________________
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>
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>      --
>      Mara Kim
>
>      Ph.D. Candidate
>      Computational Biology
>      Vanderbilt University
>      Nashville, TN
>
>  ------------------------------------------------------------------------------
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Re: [GMOD-devel] Chado Comparative Module

McGary, Kris L
In reply to this post by adf_ncgr
Andrew,

I work with Mara at Vanderbilt.  From our perspective, gene families are not the primary reason that we want groups of features, but one that we think is common.  For our first use case, we are interested in groups of orthologs, which are closely related to gene families (but attempt to treat them in a phylogenetically accurate manner).  Our second use case is sets of genes that are related in some fashion (e.g., molecular function, enrichment in a set of experiments, membership in a pathway, etc).  Obviously, we can use CV terms and feature properties for some of this, but my understanding is that we end up doing a lot more table scans (i.e., not very performant). Alternatively, others have used fake features to accomplish the same thing.

Scott Cain has also proposed finding a more general approach than ours, which allows the formation of groups in multiple tables (e.g., groups of organisms, groups of publications, groups of groups!).  We would actually prefer the more general solution, but we have some concerns about performance due to challenges of defining Foreign Keys in such a generic implementation (i.e., simplest version would have FKs that point to multiple tables).

Kris McGary
Vanderbilt University

________________________________________
From: Andrew Farmer [[hidden email]]
Sent: Wednesday, January 22, 2014 4:17 PM
To: [hidden email]
Subject: Re: [Gmod-schema] [GMOD-devel] Chado Comparative Module

Hi all-
not sure how such discussions are normally organized- is there a regular schedule for "official" GMOD conference
calls, or would it make more sense to self-organize this topic among interested parties via a Doodle poll? I'd be
interested in participating either way. It might also be worth clarifying a bit up front whether the focus of the
discussion will be specifically on gene family representation or more generally about use cases for generic grouping
of features and/or other entities in the schema.

thanks

Andrew Farmer
Legume Information System

On 1/21/14 3:21 PM, Mara Kim wrote:
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.

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Re: [GMOD-devel] Chado Comparative Module

adf_ncgr
In reply to this post by Siddhartha Basu
Hi Siddhartha-
Mara had suggested some times this Thurs (1-5CST)/Fri (all day); these
have started to fill up for me,
though there may be a few slots I could still manage. I'd suggest (if it
works OK for you and Mara's group)
that we poll for next week, to give other interested people a little
more lead time. Also, might be good to
see if there are international participants interested so we can find a
decent slot for all relevant time zones
(thinking specifically about the CIRAD folks who posted regarding the
iPlant Compara/Chado hybrid solution).

Does that seem reasonable?

thanks!

Andrew

On 1/22/14 3:50 PM, Siddhartha Basu wrote:

> Hi Andrew,
> I am up for the Doodle poll. Even it might not have to a official GMOD
> conference call, we interested parties could set it up through skype.
> So, what we poll for, any suggestions ?
>
> thanks,
> -siddhartha
>
> On Wed, 22 Jan 2014, Andrew Farmer wrote:
>
>>     Hi all-
>>     not sure how such discussions are normally organized- is there a regular
>>     schedule for "official" GMOD conference
>>     calls, or would it make more sense to self-organize this topic among
>>     interested parties via a Doodle poll? I'd be
>>     interested in participating either way. It might also be worth clarifying
>>     a bit up front whether the focus of the
>>     discussion will be specifically on gene family representation or more
>>     generally about use cases for generic grouping
>>     of features and/or other entities in the schema.
>>
>>     thanks
>>
>>     Andrew Farmer
>>     Legume Information System
>>
>>     On 1/21/14 3:21 PM, Mara Kim wrote:
>>
>>       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
>>         >
>>          ------------------------------------------------------------------------------
>>         >            CenturyLink Cloud: The Leader in Enterprise Cloud
>>         Services.
>>         >            Learn Why More Businesses Are Choosing CenturyLink Cloud
>>         For
>>         >            Critical Workloads, Development Environments & Everything
>>         In
>>         >            Between.
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>>         >            _______________________________________________
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>>         >
>>         >        --
>>         >        Mara Kim
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>>         >    dot net
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Re: [GMOD-devel] Chado Comparative Module

Mara Kim-3
Hi everyone,

I have set up a WhenIsGood for people to fill out. http://whenisgood.net/ixr8gne

Skype should be fine.  My username is resultsreturned


On Wed, Jan 22, 2014 at 5:08 PM, Andrew Farmer <[hidden email]> wrote:
Hi Siddhartha-
Mara had suggested some times this Thurs (1-5CST)/Fri (all day); these
have started to fill up for me,
though there may be a few slots I could still manage. I'd suggest (if it
works OK for you and Mara's group)
that we poll for next week, to give other interested people a little
more lead time. Also, might be good to
see if there are international participants interested so we can find a
decent slot for all relevant time zones
(thinking specifically about the CIRAD folks who posted regarding the
iPlant Compara/Chado hybrid solution).

Does that seem reasonable?

thanks!

Andrew

On 1/22/14 3:50 PM, Siddhartha Basu wrote:
> Hi Andrew,
> I am up for the Doodle poll. Even it might not have to a official GMOD
> conference call, we interested parties could set it up through skype.
> So, what we poll for, any suggestions ?
>
> thanks,
> -siddhartha
>
> On Wed, 22 Jan 2014, Andrew Farmer wrote:
>
>>     Hi all-
>>     not sure how such discussions are normally organized- is there a regular
>>     schedule for "official" GMOD conference
>>     calls, or would it make more sense to self-organize this topic among
>>     interested parties via a Doodle poll? I'd be
>>     interested in participating either way. It might also be worth clarifying
>>     a bit up front whether the focus of the
>>     discussion will be specifically on gene family representation or more
>>     generally about use cases for generic grouping
>>     of features and/or other entities in the schema.
>>
>>     thanks
>>
>>     Andrew Farmer
>>     Legume Information System
>>
>>     On 1/21/14 3:21 PM, Mara Kim wrote:
>>
>>       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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>>         Services.
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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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>>         > _______________________________________________
>>         > Gmod-schema mailing list
>>         > [hidden email]
>>         > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>         ------------------------------------------------------------------------------
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>>
>>       --
>>       Mara Kim
>>
>>       Ph.D. Candidate
>>       Computational Biology
>>       Vanderbilt University
>>       Nashville, TN
>>
>>   ------------------------------------------------------------------------------
>>   CenturyLink Cloud: The Leader in Enterprise Cloud Services.
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--
Mara Kim

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

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Re: [GMOD-devel] Chado Comparative Module

adf_ncgr
In reply to this post by McGary, Kris L
Thanks, this is helpful context; sounds like we have similar
perspectives on the general problem.
I see that Mara just set up a poll, so I'll sign up and we can continue
the discussion then.

regards

Andrew

On 1/22/14 4:03 PM, McGary, Kris L wrote:

> Andrew,
>
> I work with Mara at Vanderbilt.  From our perspective, gene families are not the primary reason that we want groups of features, but one that we think is common.  For our first use case, we are interested in groups of orthologs, which are closely related to gene families (but attempt to treat them in a phylogenetically accurate manner).  Our second use case is sets of genes that are related in some fashion (e.g., molecular function, enrichment in a set of experiments, membership in a pathway, etc).  Obviously, we can use CV terms and feature properties for some of this, but my understanding is that we end up doing a lot more table scans (i.e., not very performant). Alternatively, others have used fake features to accomplish the same thing.
>
> Scott Cain has also proposed finding a more general approach than ours, which allows the formation of groups in multiple tables (e.g., groups of organisms, groups of publications, groups of groups!).  We would actually prefer the more general solution, but we have some concerns about performance due to challenges of defining Foreign Keys in such a generic implementation (i.e., simplest version would have FKs that point to multiple tables).
>
> Kris McGary
> Vanderbilt University
>
> ________________________________________
> From: Andrew Farmer [[hidden email]]
> Sent: Wednesday, January 22, 2014 4:17 PM
> To: [hidden email]
> Subject: Re: [Gmod-schema] [GMOD-devel] Chado Comparative Module
>
> Hi all-
> not sure how such discussions are normally organized- is there a regular schedule for "official" GMOD conference
> calls, or would it make more sense to self-organize this topic among interested parties via a Doodle poll? I'd be
> interested in participating either way. It might also be worth clarifying a bit up front whether the focus of the
> discussion will be specifically on gene family representation or more generally about use cases for generic grouping
> of features and/or other entities in the schema.
>
> thanks
>
> Andrew Farmer
> Legume Information System
>
> On 1/21/14 3:21 PM, Mara Kim wrote:
> 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.


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Re: [GMOD-devel] Chado Comparative Module

Siddhartha Basu
In reply to this post by adf_ncgr
Hi Andrew,
Makes sense, no problem, lets wait and see what the poll comes up with,
hopefully we will have a productive discussion.

thanks,
-siddhartha

On Wed, 22 Jan 2014, Andrew Farmer wrote:

> Hi Siddhartha-
> Mara had suggested some times this Thurs (1-5CST)/Fri (all day); these
> have started to fill up for me,
> though there may be a few slots I could still manage. I'd suggest (if it
> works OK for you and Mara's group)
> that we poll for next week, to give other interested people a little
> more lead time. Also, might be good to
> see if there are international participants interested so we can find a
> decent slot for all relevant time zones
> (thinking specifically about the CIRAD folks who posted regarding the
> iPlant Compara/Chado hybrid solution).
>
> Does that seem reasonable?
>
> thanks!
>
> Andrew
>
> On 1/22/14 3:50 PM, Siddhartha Basu wrote:
> > Hi Andrew,
> > I am up for the Doodle poll. Even it might not have to a official GMOD
> > conference call, we interested parties could set it up through skype.
> > So, what we poll for, any suggestions ?
> >
> > thanks,
> > -siddhartha
> >
> > On Wed, 22 Jan 2014, Andrew Farmer wrote:
> >
> >>     Hi all-
> >>     not sure how such discussions are normally organized- is there a regular
> >>     schedule for "official" GMOD conference
> >>     calls, or would it make more sense to self-organize this topic among
> >>     interested parties via a Doodle poll? I'd be
> >>     interested in participating either way. It might also be worth clarifying
> >>     a bit up front whether the focus of the
> >>     discussion will be specifically on gene family representation or more
> >>     generally about use cases for generic grouping
> >>     of features and/or other entities in the schema.
> >>
> >>     thanks
> >>
> >>     Andrew Farmer
> >>     Legume Information System
> >>
> >>     On 1/21/14 3:21 PM, Mara Kim wrote:
> >>
> >>       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
> >>         >
> >>          ------------------------------------------------------------------------------
> >>         >            CenturyLink Cloud: The Leader in Enterprise Cloud
> >>         Services.
> >>         >            Learn Why More Businesses Are Choosing CenturyLink Cloud
> >>         For
> >>         >            Critical Workloads, Development Environments & Everything
> >>         In
> >>         >            Between.
> >>         >            Get a Quote or Start a Free Trial Today.
> >>         >
> >>          http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
> >>         >            _______________________________________________
> >>         >            Gmod-schema mailing list
> >>         >            [hidden email]
> >>         >            https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>         >
> >>         >        --
> >>         >        Mara Kim
> >>         >
> >>         >        Ph.D. Candidate
> >>         >        Computational Biology
> >>         >        Vanderbilt University
> >>         >        Nashville, TN
> >>         >
> >>          ------------------------------------------------------------------------------
> >>         >        CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> >>         >        Learn Why More Businesses Are Choosing CenturyLink Cloud For
> >>         >        Critical Workloads, Development Environments & Everything In
> >>         Between.
> >>         >        Get a Quote or Start a Free Trial Today.
> >>         >
> >>          http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
> >>         >        _______________________________________________
> >>         >        Gmod-schema mailing list
> >>         >        [hidden email]
> >>         >        https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>         >
> >>         >
> >>          ------------------------------------------------------------------------------
> >>         >      CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> >>         >      Learn Why More Businesses Are Choosing CenturyLink Cloud For
> >>         >      Critical Workloads, Development Environments & Everything In
> >>         Between.
> >>         >      Get a Quote or Start a Free Trial Today.
> >>         >
> >>          http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
> >>         >      _______________________________________________
> >>         >      Gmod-devel mailing list
> >>         >      [hidden email]
> >>         >      https://lists.sourceforge.net/lists/listinfo/gmod-devel
> >>         >
> >>         >    --
> >>         >
> >>          ------------------------------------------------------------------------
> >>         >    Scott Cain, Ph. D.                                   scott at
> >>         scottcain
> >>         >    dot net
> >>         >    GMOD Coordinator (http://gmod.org/)
> >>         216-392-3087
> >>         >    Ontario Institute for Cancer Research
> >>
> >>         >
> >>         ------------------------------------------------------------------------------
> >>         > CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> >>         > Learn Why More Businesses Are Choosing CenturyLink Cloud For
> >>         > Critical Workloads, Development Environments & Everything In
> >>         Between.
> >>         > Get a Quote or Start a Free Trial Today.
> >>         >
> >>         http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
> >>
> >>         > _______________________________________________
> >>         > Gmod-schema mailing list
> >>         > [hidden email]
> >>         > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>
> >>         ------------------------------------------------------------------------------
> >>         CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> >>         Learn Why More Businesses Are Choosing CenturyLink Cloud For
> >>         Critical Workloads, Development Environments & Everything In Between.
> >>         Get a Quote or Start a Free Trial Today.
> >>         http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
> >>         _______________________________________________
> >>         Gmod-schema mailing list
> >>         [hidden email]
> >>         https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>
> >>       --
> >>       Mara Kim
> >>
> >>       Ph.D. Candidate
> >>       Computational Biology
> >>       Vanderbilt University
> >>       Nashville, TN
> >>
> >>   ------------------------------------------------------------------------------
> >>   CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> >>   Learn Why More Businesses Are Choosing CenturyLink Cloud For
> >>   Critical Workloads, Development Environments & Everything In Between.
> >>   Get a Quote or Start a Free Trial Today.
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> >>
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> >>   [hidden email]
> >>   https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >> ------------------------------------------------------------------------------
> >> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> >> Learn Why More Businesses Are Choosing CenturyLink Cloud For
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> >> Get a Quote or Start a Free Trial Today.
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> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
> > ------------------------------------------------------------------------------
> > CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> > Learn Why More Businesses Are Choosing CenturyLink Cloud For
> > Critical Workloads, Development Environments & Everything In Between.
> > Get a Quote or Start a Free Trial Today.
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>
>
> ------------------------------------------------------------------------------
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Re: [GMOD-devel] Chado Comparative Module

Siddhartha Basu
In reply to this post by Mara Kim-3
Thanks Mara, i already filled it out.

-siddhartha

On Wed, 22 Jan 2014, Mara Kim wrote:

>    Hi everyone,
>
>    I have set up a WhenIsGood for people to fill out.
>    http://whenisgood.net/ixr8gne
>
>    Skype should be fine.  My username is resultsreturned
>
>    On Wed, Jan 22, 2014 at 5:08 PM, Andrew Farmer <[hidden email]> wrote:
>
>      Hi Siddhartha-
>      Mara had suggested some times this Thurs (1-5CST)/Fri (all day); these
>      have started to fill up for me,
>      though there may be a few slots I could still manage. I'd suggest (if it
>      works OK for you and Mara's group)
>      that we poll for next week, to give other interested people a little
>      more lead time. Also, might be good to
>      see if there are international participants interested so we can find a
>      decent slot for all relevant time zones
>      (thinking specifically about the CIRAD folks who posted regarding the
>      iPlant Compara/Chado hybrid solution).
>
>      Does that seem reasonable?
>
>      thanks!
>      Andrew
>      On 1/22/14 3:50 PM, Siddhartha Basu wrote:
>      > Hi Andrew,
>      > I am up for the Doodle poll. Even it might not have to a official GMOD
>      > conference call, we interested parties could set it up through skype.
>      > So, what we poll for, any suggestions ?
>      >
>      > thanks,
>      > -siddhartha
>      >
>      > On Wed, 22 Jan 2014, Andrew Farmer wrote:
>      >
>      >>     Hi all-
>      >>     not sure how such discussions are normally organized- is there a
>      regular
>      >>     schedule for "official" GMOD conference
>      >>     calls, or would it make more sense to self-organize this topic
>      among
>      >>     interested parties via a Doodle poll? I'd be
>      >>     interested in participating either way. It might also be worth
>      clarifying
>      >>     a bit up front whether the focus of the
>      >>     discussion will be specifically on gene family representation or
>      more
>      >>     generally about use cases for generic grouping
>      >>     of features and/or other entities in the schema.
>      >>
>      >>     thanks
>      >>
>      >>     Andrew Farmer
>      >>     Legume Information System
>      >>
>      >>     On 1/21/14 3:21 PM, Mara Kim wrote:
>      >>
>      >>       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
>      >>         >
>      >>        
>       ------------------------------------------------------------------------------
>      >>         >            CenturyLink Cloud: The Leader in Enterprise
>      Cloud
>      >>         Services.
>      >>         >            Learn Why More Businesses Are Choosing
>      CenturyLink Cloud
>      >>         For
>      >>         >            Critical Workloads, Development Environments &
>      Everything
>      >>         In
>      >>         >            Between.
>      >>         >            Get a Quote or Start a Free Trial Today.
>      >>         >
>      >>        
>       http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>      >>         >            _______________________________________________
>      >>         >            Gmod-schema mailing list
>      >>         >            [hidden email]
>      >>         >          
>       https://lists.sourceforge.net/lists/listinfo/gmod-schema
>      >>         >
>      >>         >        --
>      >>         >        Mara Kim
>      >>         >
>      >>         >        Ph.D. Candidate
>      >>         >        Computational Biology
>      >>         >        Vanderbilt University
>      >>         >        Nashville, TN
>      >>         >
>      >>        
>       ------------------------------------------------------------------------------
>      >>         >        CenturyLink Cloud: The Leader in Enterprise Cloud
>      Services.
>      >>         >        Learn Why More Businesses Are Choosing CenturyLink
>      Cloud For
>      >>         >        Critical Workloads, Development Environments &
>      Everything In
>      >>         Between.
>      >>         >        Get a Quote or Start a Free Trial Today.
>      >>         >
>      >>        
>       http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>      >>         >        _______________________________________________
>      >>         >        Gmod-schema mailing list
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Re: [GMOD-devel] Chado Comparative Module

Mara Kim-2
Hi everyone,

It looks like the best times for everyone who has responded so far are Monday 2-4p CST and Thursday 1-4p CST.

How about we arrange to have the call Monday at 2p CST via Skype, and if we find that we need to discuss more we could meet on Thursday as well?  My Skype username is resultsreturned.  I could set up the call so long as everyone either messages me their username or sends me a friend invite.


On Wed, Jan 22, 2014 at 8:11 PM, Siddhartha Basu <[hidden email]> wrote:
Thanks Mara, i already filled it out.

-siddhartha

On Wed, 22 Jan 2014, Mara Kim wrote:

>    Hi everyone,
>
>    I have set up a WhenIsGood for people to fill out.
>    http://whenisgood.net/ixr8gne
>
>    Skype should be fine.  My username is resultsreturned
>
>    On Wed, Jan 22, 2014 at 5:08 PM, Andrew Farmer <[hidden email]> wrote:
>
>      Hi Siddhartha-
>      Mara had suggested some times this Thurs (1-5CST)/Fri (all day); these
>      have started to fill up for me,
>      though there may be a few slots I could still manage. I'd suggest (if it
>      works OK for you and Mara's group)
>      that we poll for next week, to give other interested people a little
>      more lead time. Also, might be good to
>      see if there are international participants interested so we can find a
>      decent slot for all relevant time zones
>      (thinking specifically about the CIRAD folks who posted regarding the
>      iPlant Compara/Chado hybrid solution).
>
>      Does that seem reasonable?
>
>      thanks!
>      Andrew
>      On 1/22/14 3:50 PM, Siddhartha Basu wrote:
>      > Hi Andrew,
>      > I am up for the Doodle poll. Even it might not have to a official GMOD
>      > conference call, we interested parties could set it up through skype.
>      > So, what we poll for, any suggestions ?
>      >
>      > thanks,
>      > -siddhartha
>      >
>      > On Wed, 22 Jan 2014, Andrew Farmer wrote:
>      >
>      >>     Hi all-
>      >>     not sure how such discussions are normally organized- is there a
>      regular
>      >>     schedule for "official" GMOD conference
>      >>     calls, or would it make more sense to self-organize this topic
>      among
>      >>     interested parties via a Doodle poll? I'd be
>      >>     interested in participating either way. It might also be worth
>      clarifying
>      >>     a bit up front whether the focus of the
>      >>     discussion will be specifically on gene family representation or
>      more
>      >>     generally about use cases for generic grouping
>      >>     of features and/or other entities in the schema.
>      >>
>      >>     thanks
>      >>
>      >>     Andrew Farmer
>      >>     Legume Information System
>      >>
>      >>     On 1/21/14 3:21 PM, Mara Kim wrote:
>      >>
>      >>       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" target="_blank">216-392-3087
>      >>         >    Ontario Institute for Cancer Research
>      >>
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>      ------------------------------------------------------------------------------
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>      >>       --
>      >>       Mara Kim
>      >>
>      >>       Ph.D. Candidate
>      >>       Computational Biology
>      >>       Vanderbilt University
>      >>       Nashville, TN
>      >>
>      >>
>      ------------------------------------------------------------------------------
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>      > CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>      > Learn Why More Businesses Are Choosing CenturyLink Cloud For
>      > Critical Workloads, Development Environments & Everything In Between.
>      > Get a Quote or Start a Free Trial Today.
>      >
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>      CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>      Learn Why More Businesses Are Choosing CenturyLink Cloud For
>      Critical Workloads, Development Environments & Everything In Between.
>      Get a Quote or Start a Free Trial Today.
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>    --
>    Mara Kim
>
>    Ph.D. Candidate
>    Computational Biology
>    Vanderbilt University
>    Nashville, TN

> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk

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> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



--
Mara Kim

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

------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
12