Re: chado modules

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Re: chado modules

Stephen Ficklin-3

Hi Sofia,

The Group Module is a candidate module for inclusion in a future release of Chado. I'm CC'ing my response to the Chado schema mailing list for input from others who have implemented it.   Currently, there is not Tripal module to support it.   Although I believe there are some Tripal sites that may be using it and have some support.  If they read this and respond they may be able to share some insights.

Stephen

On 4/8/2016 8:57 AM, Sofia Robb wrote:
Hello All,

I am still working on adding gene groups to one of my tripal installs.  I found this chado module:


Is there a recommended way to add these modules to the chado in tripal? 


Thanks,
Sofia




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Re: chado modules

Joe Carlson
Hi,

There is a need for a module like this. The existing solutions and work around are a bit messy. I’ve been trying out this module for representing our protein families. And trading some email with Mara Kim, the author.

I had a couple of suggestions about nomenclature and syntax (for example, in feature_grpmember, the column grpmember_id references grp and not grpmember.)

I also think that a couple more fields in grp are needed: dbxref_id to reference the primary dbxref and an is_obsolete boolean.

This also seems to me to be a case where table inheritance may be useful. I know there can be some performance problems with table inheritance but it might be useful if there are many different types of ‘things’ that people want to put into groups.

Joe

On Apr 15, 2016, at 9:50 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Sofia,

The Group Module is a candidate module for inclusion in a future release of Chado. I'm CC'ing my response to the Chado schema mailing list for input from others who have implemented it.   Currently, there is not Tripal module to support it.   Although I believe there are some Tripal sites that may be using it and have some support.  If they read this and respond they may be able to share some insights.

Stephen

On 4/8/2016 8:57 AM, Sofia Robb wrote:
Hello All,

I am still working on adding gene groups to one of my tripal installs.  I found this chado module:


Is there a recommended way to add these modules to the chado in tripal? 


Thanks,
Sofia




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Re: chado modules

David Emmert
Hi All,

FlyBase has implemented the Group Module in our chado instance and we're quite happy with it.   (And in case we didn't say it before: complements and many thanks, Mara!)

Here's some details on what we're using it for:

http://flybase.org/static_pages/feature/previous/articles/2015_05/gene_groups.html

And anyone who wants to have a look under the hood can grab the pg dump of the current FlyBase release here:

On Fri, Apr 15, 2016 at 2:27 PM, Joe Carlson <[hidden email]> wrote:
Hi,

There is a need for a module like this. The existing solutions and work around are a bit messy. I’ve been trying out this module for representing our protein families. And trading some email with Mara Kim, the author.

I had a couple of suggestions about nomenclature and syntax (for example, in feature_grpmember, the column grpmember_id references grp and not grpmember.)

I also think that a couple more fields in grp are needed: dbxref_id to reference the primary dbxref and an is_obsolete boolean.

This also seems to me to be a case where table inheritance may be useful. I know there can be some performance problems with table inheritance but it might be useful if there are many different types of ‘things’ that people want to put into groups.

Joe

On Apr 15, 2016, at 9:50 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Sofia,

The Group Module is a candidate module for inclusion in a future release of Chado. I'm CC'ing my response to the Chado schema mailing list for input from others who have implemented it.   Currently, there is not Tripal module to support it.   Although I believe there are some Tripal sites that may be using it and have some support.  If they read this and respond they may be able to share some insights.

Stephen

On 4/8/2016 8:57 AM, Sofia Robb wrote:
Hello All,

I am still working on adding gene groups to one of my tripal installs.  I found this chado module:


Is there a recommended way to add these modules to the chado in tripal? 


Thanks,
Sofia




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your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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