Chado Comparative Module

classic Classic list List threaded Threaded
33 messages Options
12
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Mara Kim-2
I am still missing the contact info from Stephen Finklin and Ethy.


On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]> wrote:
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
>      >>         >
>      >>
>       ------------------------------------------------------------------------------
>      >>         >            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/)
>      >>         <a href="tel:216-392-3087" value="+12163923087" target="_blank">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.
>      >>
>      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
>      >
>      >
>      ------------------------------------------------------------------------------
>      > 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.
> 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



--
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
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Mara Kim-2
Hello all,

The conference call today went very well!  The general consensus seems to be to implement a generic "group" table, with linker tables to each relevant member type (ex. organism_group, feature_group, stock_group).

I have updated the proposal schematic on the wiki (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL implementation, and added use cases that were discussed during the call.


A few discussion points:

Which modules should be responsible for their respective linker tables?  For example, should the "feature_group" table be part of the Comparative module or the Sequence module?  Currently I'm leaning towards the latter, and this is reflected in the schematic.

Perhaps we should consider an alternative name for the "group" table?  As it is a SQL keyword (ie. GROUP BY), it requires all references to the table to quote the name (ex. SELECT * FROM "group";).  Of course, Chado already has this problem in PostgreSQL with the "identity" column in analysisfeature (see http://www.postgresql.org/docs/8.4/static/sql-truncate.html).


On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]> wrote:
I am still missing the contact info from Stephen Finklin and Ethy.


On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]> wrote:
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
>      >>         >
>      >>
>       ------------------------------------------------------------------------------
>      >>         >            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/)
>      >>         <a href="tel:216-392-3087" value="+12163923087" target="_blank">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.
>      >>
>      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
>      >
>      >
>      ------------------------------------------------------------------------------
>      > 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.
> 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



--
Mara Kim

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



--
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
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Stephen Ficklin-2
Hi All,

I have created a GoToMeeting meeting for our next discussion this Thursday at 2pm Central US time to further discuss the tables that Mara has described below.  Anyone is invited to join the discussion.  Below is connection information.  If you log on via a computer with a headset the connection is free.  If you call in, it is not a toll-free number.

Stephen

1. Please join my meeting, Thursday, January 30, 2014 at 2:00 PM Central Standard Time.
https://global.gotomeeting.com/join/641119493

2. Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (213) 493-0605
Access Code: 641-119-493
Audio PIN: Shown after joining the meeting

Meeting ID: 641-119-493

GoToMeeting®
Online Meetings Made Easy®

Not at your computer? Click the link to join this meeting from your iPhone®, iPad® or Android® device via the GoToMeeting app.



On 1/27/2014 6:44 PM, Mara Kim wrote:
Hello all,

The conference call today went very well!  The general consensus seems to be to implement a generic "group" table, with linker tables to each relevant member type (ex. organism_group, feature_group, stock_group).

I have updated the proposal schematic on the wiki (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL implementation, and added use cases that were discussed during the call.


A few discussion points:

Which modules should be responsible for their respective linker tables?  For example, should the "feature_group" table be part of the Comparative module or the Sequence module?  Currently I'm leaning towards the latter, and this is reflected in the schematic.

Perhaps we should consider an alternative name for the "group" table?  As it is a SQL keyword (ie. GROUP BY), it requires all references to the table to quote the name (ex. SELECT * FROM "group";).  Of course, Chado already has this problem in PostgreSQL with the "identity" column in analysisfeature (see http://www.postgresql.org/docs/8.4/static/sql-truncate.html).


On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]> wrote:
I am still missing the contact info from Stephen Finklin and Ethy.


On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]> wrote:
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
>      >>         >
>      >>
>       ------------------------------------------------------------------------------
>      >>         >            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/)
>      >>         <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">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.
>      >>
>      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
>      >
>      >
>      ------------------------------------------------------------------------------
>      > 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.
> 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



--
Mara Kim

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



--
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


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Andy Schroeder
In reply to this post by Mara Kim-2
Hi Mara,

My 2cents on your first discussion point.  I personally would  go with adding the linking tables (and presumably their respective prop tables) to the group module itself.  One reason is group_feature suggests to me that you have a bunch of features with membership in a group, while feature_group sounds to me like you would be more likely to have many groups associated with one feature (which is certainly possible but not the spirit of the usage).  And the same would apply to other linking tables.  This is just an argument of convention and not one that has been strictly enforced in chado.  Reason 2 is that it may be less painful to extend the grouping concept by adding the linking tables to the group module as needed rather than having to extend the individual modules i.e. if you decide you want to group interactions being able to add the group_interaction and group_interactionprop table to the group module rather than having to add interaction_group and the interaction_groupprop tables to the interaction module.  But if you have a good argument for the latter implementation then I could be convinced..

Also in your diagram can you explain the group_group table?  Why not relate groups through the group_relationship table?  It seems that group_group could potentially introduce redundancy?

cheers,
Andy


On Mon, Jan 27, 2014 at 6:44 PM, Mara Kim <[hidden email]> wrote:
Hello all,

The conference call today went very well!  The general consensus seems to be to implement a generic "group" table, with linker tables to each relevant member type (ex. organism_group, feature_group, stock_group).

I have updated the proposal schematic on the wiki (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL implementation, and added use cases that were discussed during the call.


A few discussion points:

Which modules should be responsible for their respective linker tables?  For example, should the "feature_group" table be part of the Comparative module or the Sequence module?  Currently I'm leaning towards the latter, and this is reflected in the schematic.

Perhaps we should consider an alternative name for the "group" table?  As it is a SQL keyword (ie. GROUP BY), it requires all references to the table to quote the name (ex. SELECT * FROM "group";).  Of course, Chado already has this problem in PostgreSQL with the "identity" column in analysisfeature (see http://www.postgresql.org/docs/8.4/static/sql-truncate.html).


On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]> wrote:
I am still missing the contact info from Stephen Finklin and Ethy.


On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]> wrote:
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
>      >>         >
>      >>
>       ------------------------------------------------------------------------------
>      >>         >            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/)
>      >>         <a href="tel:216-392-3087" value="+12163923087" target="_blank">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.
>      >>
>      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
>      >
>      >
>      ------------------------------------------------------------------------------
>      > 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.
> 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



--
Mara Kim

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



--
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



------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

adf_ncgr
Hi Andy-
not speaking on behalf of Mara, but from my own not-terribly-mature perspective on these issues:

My 2cents on your first discussion point.  I personally would  go with adding the linking tables (and presumably their respective prop tables) to the group module itself.  One reason is group_feature suggests to me that you have a bunch of features with membership in a group, while feature_group sounds to me like you would be more likely to have many groups associated with one feature (which is certainly possible but not the spirit of the usage).  And the same would apply to other linking tables.  This is just an argument of convention and not one that has been strictly enforced in chado.  Reason 2 is that it may be less painful to extend the grouping concept by adding the linking tables to the group module as needed rather than having to extend the individual modules i.e. if you decide you want to group interactions being able to add the group_interaction and group_interactionprop table to the group module rather than having to add interaction_group and the interaction_groupprop tables to the interaction module.  But if you have a good argument for the latter implementation then I could be convinced..
wouldn't piling all these linker tables into the group module mean that anyone who wanted (for example) a feature grouping functionality
would acquire dependencies on all the other modules for which grouping linkers had been added to the group module? Whereas by putting feature_group into the sequence module, users of the latter would depend on the group module, but would not acquire any other dependencies. We were also thinking
that grouping would be comparable in some sense to the classes defined by cvterms, but with no semantic obligations implied by membership;
by analogy, this would seem to imply feature_group in the Sequence module like feature_cvterm has been defined.

also, I do think the intention was for features (and other entities) to belong to as many groups as necessary/useful (ie a fully many-to-many
relationship); not sure whether feature_group or group_feature is more suggestive in that regard (although the Chado naming conventions
described at http://gmod.org/wiki/Chado_Manual#Table_names don't seem to give a basis for preference)? If the analogy with cvterm seems
reasonable, then I guess that would lean toward feature_group.

Also in your diagram can you explain the group_group table?  Why not relate groups through the group_relationship table?  It seems that group_group could potentially introduce redundancy?

Good point. We didn't really talk in the first call about what sorts of relationships groups would have to one another. Seems likely that
typical set relationships (disjointness, superset/subset, overlap) would be the obvious candidates, but maybe others had something else
in mind? I can imagine some cases in which it might be helpful to make explicit at a set-wise level relationships between groups containing
objects of different types, for example, the set of genes that are the members of a given set of trees (for example, the set of trees containing
only genes from a single species).

In any case, it does seem to me that you are right that group_group is probably not needed and could imagine arguments that it is potentially
a bad idea (bringing to mind sets containing themselves as members and such logical minefields).

just adding a few more 2c to yours, and looking forward to hearing what you and others think...

Andrew Farmer





cheers,
Andy


On Mon, Jan 27, 2014 at 6:44 PM, Mara Kim <[hidden email]> wrote:
Hello all,

The conference call today went very well!  The general consensus seems to be to implement a generic "group" table, with linker tables to each relevant member type (ex. organism_group, feature_group, stock_group).

I have updated the proposal schematic on the wiki (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL implementation, and added use cases that were discussed during the call.


A few discussion points:

Which modules should be responsible for their respective linker tables?  For example, should the "feature_group" table be part of the Comparative module or the Sequence module?  Currently I'm leaning towards the latter, and this is reflected in the schematic.

Perhaps we should consider an alternative name for the "group" table?  As it is a SQL keyword (ie. GROUP BY), it requires all references to the table to quote the name (ex. SELECT * FROM "group";).  Of course, Chado already has this problem in PostgreSQL with the "identity" column in analysisfeature (see http://www.postgresql.org/docs/8.4/static/sql-truncate.html).


On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]> wrote:
I am still missing the contact info from Stephen Finklin and Ethy.


On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]> wrote:
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
>      >>         >
>      >>
>       ------------------------------------------------------------------------------
>      >>         >            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/)
>      >>         <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">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.
>      >>
>      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
>      >
>      >
>      ------------------------------------------------------------------------------
>      > 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.
> 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



--
Mara Kim

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



--
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




------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable 
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk


_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Karl O. Pinc
On 01/28/2014 06:15:30 PM, Andrew Farmer wrote:

> Hi Andy-
> not speaking on behalf of Mara, but from my own not-terribly-mature
> perspective on these issues:
> >
> > My 2cents on your first discussion point.  I personally would  go
> with
> > adding the linking tables (and presumably their respective prop
> > tables) to the group module itself.  One reason is group_feature
> > suggests to me that you have a bunch of features with membership in
> a
> > group, while feature_group sounds to me like you would be more
> likely
> > to have many groups associated with one feature (which is certainly
> > possible but not the spirit of the usage).  And the same would
> apply
>
> > to other linking tables.  This is just an argument of convention
> and
>
> > not one that has been strictly enforced in chado.  Reason 2 is that
> it
> > may be less painful to extend the grouping concept by adding the
> > linking tables to the group module as needed rather than having to
> > extend the individual modules i.e. if you decide you want to group
> > interactions being able to add the group_interaction and
> > group_interactionprop table to the group module rather than having
> to
> > add interaction_group and the interaction_groupprop tables to the
> > interaction module.  But if you have a good argument for the latter
> > implementation then I could be convinced..
> wouldn't piling all these linker tables into the group module mean
> that
> anyone who wanted (for example) a feature grouping functionality
> would acquire dependencies on all the other modules for which
> grouping
>
> linkers had been added to the group module? Whereas by putting
> feature_group into the sequence module, users of the latter would
> depend
> on the group module, but would not acquire any other dependencies. We
> were also thinking
> that grouping would be comparable in some sense to the classes
> defined
>
> by cvterms, but with no semantic obligations implied by membership;
> by analogy, this would seem to imply feature_group in the Sequence
> module like feature_cvterm has been defined.


I have only the most shallow impression of the issues, but why
have dependencies?  If the group module adds extra
functionality then it can depend on any _one_ of the other
modules being installed, but the other modules need not
depend on the group module.  

This suggestion assumes that the
dependency system allows any one of a number of modules
to satisfy any given dependency.  If not, then either
extend the dependency system with this feature or
have the group module depend upon nothing.  If you
install only the group module you just can't do much.


To have the, e.g., feature_group table in the feature
module seems to me to just clutter up the feature module
with stuff that does nothing without the group module,
which itself might not be wanted but (presumably)
would have to be installed because the feature
module would depend on the group module.


I assume here that chado works just fine without
a group module, which would exist to add extra
goodness when necessary.


No need to respond if this analysis contains
fundamental mis-understandings and simply
muddies the waters.


Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Siddhartha Basu
In reply to this post by Mara Kim-2
Hi,

On Mon, 27 Jan 2014, Mara Kim wrote:

>    Hello all,
>
>    The conference call today went very well!  The general consensus seems to
>    be to implement a generic "group" table, with linker tables to each
>    relevant member type (ex. organism_group, feature_group, stock_group).
>    I have updated the proposal schematic on the wiki
>    (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL
>    implementation, and added use cases that were discussed during the call.


>
>    A few discussion points:
>
>    Which modules should be responsible for their respective linker tables?
>    For example, should the "feature_group" table be part of the Comparative
>    module or the Sequence module?  Currently I'm leaning towards the latter,
>    and this is reflected in the schematic.
I think it depends where it would go and this stage its hardly clear. To
get a clear idea i believe we have to define where the group module
stands. If it stands out to be a core and very dependent module then put
the linkers in others. Then it would make sense to pull group module as
an dependency to others.
On the other hand, for early adoption and low barrier of entry i would
make it standalone and let it be pulled when it is needed. Though it is
not in line with loosely connected design however it somehow reduces
burden on existing toolset that works on core schema modules. I would
prefer to see it getting matured with good toolchain support before it
get adopted in core and i start changing my core softwares.

>
>    Perhaps we should consider an alternative name for the "group" table?  As
>    it is a SQL keyword (ie. GROUP BY), it requires all references to the
>    table to quote the name (ex. SELECT * FROM "group";).  
I have a very very strong opinion against the *group* name. Having
experienced conflicts between oracle(reserved keywords) and chado schema over and over
again we should absolutely avoid clashing of keywords. Any code that
needs to use that table have to always account for this exception. This
might seems trivial at this point, however maintaining a complicated
codebase with inter-dependencies that runs on live system along with
revolving developers it would become a possible nightmare.
Now at this point i really don't have a good alternate name, however in
short i would prefer not to invest in this module if the name stays though.
I sincerely hope there are enough smart and savy people in this group to
come up with an alternate though.


> Of course, Chado
>    already has this problem in PostgreSQL with the "identity" column in
>    analysisfeature (see
>    http://www.postgresql.org/docs/8.4/static/sql-truncate.html).
It great to know that. How big of a problem it is. How many gmod tools are broken because of
this ? So, far my code that touches analysisfeature haven't thrown any
error. And i haven't seen any error been reported. If it only appears in
case issuing TRUNCATE then it is somehow contained. Could you give some
details.

thanks,
-sidd



>
>    On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]>
>    wrote:
>
>      I am still missing the contact info from Stephen Finklin and Ethy.
>
>      On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]>
>      wrote:
>
>        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
>          >      >>         >
>          >      >>
>          >      
>          ------------------------------------------------------------------------------
>          >      >>         >            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.
>          >      >>
>          >    
>           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
>          >      >
>          >      >
>          >    
>           ------------------------------------------------------------------------------
>          >      > 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.
>          >
>          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
>
>      --
>      Mara Kim
>
>      Ph.D. Candidate
>      Computational Biology
>      Vanderbilt University
>      Nashville, TN
>
>    --
>    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


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Siddhartha Basu
One more things, as far as i recall, the last module to be integrated in
chado was natural diversity. And as far as i understand it seems to
standalone in spite having bunch of linker tables. Maybe we could borrow
ideas from their design principles in the design of group module. Even
better, if we could ask them(Naama/Sook/Seth/Rob, pardon me if i missed
any of their name) to join our next call and shed some lights on those.
If they also share their thoughts in this discussion that would also be
appreciated.

thanks,
-sidd

On Wed, 29 Jan 2014, Siddhartha Basu wrote:

> Hi,
>
> On Mon, 27 Jan 2014, Mara Kim wrote:
>
> >    Hello all,
> >
> >    The conference call today went very well!  The general consensus seems to
> >    be to implement a generic "group" table, with linker tables to each
> >    relevant member type (ex. organism_group, feature_group, stock_group).
> >    I have updated the proposal schematic on the wiki
> >    (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL
> >    implementation, and added use cases that were discussed during the call.
>
>
> >
> >    A few discussion points:
> >
> >    Which modules should be responsible for their respective linker tables?
> >    For example, should the "feature_group" table be part of the Comparative
> >    module or the Sequence module?  Currently I'm leaning towards the latter,
> >    and this is reflected in the schematic.
> I think it depends where it would go and this stage its hardly clear. To
> get a clear idea i believe we have to define where the group module
> stands. If it stands out to be a core and very dependent module then put
> the linkers in others. Then it would make sense to pull group module as
> an dependency to others.
> On the other hand, for early adoption and low barrier of entry i would
> make it standalone and let it be pulled when it is needed. Though it is
> not in line with loosely connected design however it somehow reduces
> burden on existing toolset that works on core schema modules. I would
> prefer to see it getting matured with good toolchain support before it
> get adopted in core and i start changing my core softwares.
>
> >
> >    Perhaps we should consider an alternative name for the "group" table?  As
> >    it is a SQL keyword (ie. GROUP BY), it requires all references to the
> >    table to quote the name (ex. SELECT * FROM "group";).  
> I have a very very strong opinion against the *group* name. Having
> experienced conflicts between oracle(reserved keywords) and chado schema over and over
> again we should absolutely avoid clashing of keywords. Any code that
> needs to use that table have to always account for this exception. This
> might seems trivial at this point, however maintaining a complicated
> codebase with inter-dependencies that runs on live system along with
> revolving developers it would become a possible nightmare.
> Now at this point i really don't have a good alternate name, however in
> short i would prefer not to invest in this module if the name stays though.
> I sincerely hope there are enough smart and savy people in this group to
> come up with an alternate though.
>
>
> > Of course, Chado
> >    already has this problem in PostgreSQL with the "identity" column in
> >    analysisfeature (see
> >    http://www.postgresql.org/docs/8.4/static/sql-truncate.html).
> It great to know that. How big of a problem it is. How many gmod tools are broken because of
> this ? So, far my code that touches analysisfeature haven't thrown any
> error. And i haven't seen any error been reported. If it only appears in
> case issuing TRUNCATE then it is somehow contained. Could you give some
> details.
>
> thanks,
> -sidd
>
>
>
> >
> >    On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]>
> >    wrote:
> >
> >      I am still missing the contact info from Stephen Finklin and Ethy.
> >
> >      On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]>
> >      wrote:
> >
> >        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
> >          >      >>         >
> >          >      >>
> >          >      
> >          ------------------------------------------------------------------------------
> >          >      >>         >            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.
> >          >      >>
> >          >    
> >           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
> >          >      >
> >          >      >
> >          >    
> >           ------------------------------------------------------------------------------
> >          >      > 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.
> >          >
> >          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
> >
> >      --
> >      Mara Kim
> >
> >      Ph.D. Candidate
> >      Computational Biology
> >      Vanderbilt University
> >      Nashville, TN
> >
> >    --
> >    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
>

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Siddhartha Basu
As i have mentioned in the call P-POD is a tool that leverages chado to
manage analysis from comparative genomics pipeline.
Publication:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000766
Schema usage: http://ppod.princeton.edu/help.html#schema
Another related tool that popped up
http://sybil.sourceforge.net/documentation.html
I don't know how active it is currently though.

If i get a chance would like to test drive P-POD datasets in the
group module. Any idea about how to re-model this datasets(particuraly
the grouping part) and/or any existing software to load this data would
be highly welcome.

thanks,
-siddhartha

On Wed, 29 Jan 2014, Siddhartha Basu wrote:

> One more things, as far as i recall, the last module to be integrated in
> chado was natural diversity. And as far as i understand it seems to
> standalone in spite having bunch of linker tables. Maybe we could borrow
> ideas from their design principles in the design of group module. Even
> better, if we could ask them(Naama/Sook/Seth/Rob, pardon me if i missed
> any of their name) to join our next call and shed some lights on those.
> If they also share their thoughts in this discussion that would also be
> appreciated.
>
> thanks,
> -sidd
>
> On Wed, 29 Jan 2014, Siddhartha Basu wrote:
>
> > Hi,
> >
> > On Mon, 27 Jan 2014, Mara Kim wrote:
> >
> > >    Hello all,
> > >
> > >    The conference call today went very well!  The general consensus seems to
> > >    be to implement a generic "group" table, with linker tables to each
> > >    relevant member type (ex. organism_group, feature_group, stock_group).
> > >    I have updated the proposal schematic on the wiki
> > >    (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL
> > >    implementation, and added use cases that were discussed during the call.
> >
> >
> > >
> > >    A few discussion points:
> > >
> > >    Which modules should be responsible for their respective linker tables?
> > >    For example, should the "feature_group" table be part of the Comparative
> > >    module or the Sequence module?  Currently I'm leaning towards the latter,
> > >    and this is reflected in the schematic.
> > I think it depends where it would go and this stage its hardly clear. To
> > get a clear idea i believe we have to define where the group module
> > stands. If it stands out to be a core and very dependent module then put
> > the linkers in others. Then it would make sense to pull group module as
> > an dependency to others.
> > On the other hand, for early adoption and low barrier of entry i would
> > make it standalone and let it be pulled when it is needed. Though it is
> > not in line with loosely connected design however it somehow reduces
> > burden on existing toolset that works on core schema modules. I would
> > prefer to see it getting matured with good toolchain support before it
> > get adopted in core and i start changing my core softwares.
> >
> > >
> > >    Perhaps we should consider an alternative name for the "group" table?  As
> > >    it is a SQL keyword (ie. GROUP BY), it requires all references to the
> > >    table to quote the name (ex. SELECT * FROM "group";).  
> > I have a very very strong opinion against the *group* name. Having
> > experienced conflicts between oracle(reserved keywords) and chado schema over and over
> > again we should absolutely avoid clashing of keywords. Any code that
> > needs to use that table have to always account for this exception. This
> > might seems trivial at this point, however maintaining a complicated
> > codebase with inter-dependencies that runs on live system along with
> > revolving developers it would become a possible nightmare.
> > Now at this point i really don't have a good alternate name, however in
> > short i would prefer not to invest in this module if the name stays though.
> > I sincerely hope there are enough smart and savy people in this group to
> > come up with an alternate though.
> >
> >
> > > Of course, Chado
> > >    already has this problem in PostgreSQL with the "identity" column in
> > >    analysisfeature (see
> > >    http://www.postgresql.org/docs/8.4/static/sql-truncate.html).
> > It great to know that. How big of a problem it is. How many gmod tools are broken because of
> > this ? So, far my code that touches analysisfeature haven't thrown any
> > error. And i haven't seen any error been reported. If it only appears in
> > case issuing TRUNCATE then it is somehow contained. Could you give some
> > details.
> >
> > thanks,
> > -sidd
> >
> >
> >
> > >
> > >    On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]>
> > >    wrote:
> > >
> > >      I am still missing the contact info from Stephen Finklin and Ethy.
> > >
> > >      On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]>
> > >      wrote:
> > >
> > >        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
> > >          >      >>         >
> > >          >      >>
> > >          >      
> > >          ------------------------------------------------------------------------------
> > >          >      >>         >            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.
> > >          >      >>
> > >          >    
> > >           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
> > >          >      >
> > >          >      >
> > >          >    
> > >           ------------------------------------------------------------------------------
> > >          >      > 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.
> > >          >
> > >          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
> > >
> > >      --
> > >      Mara Kim
> > >
> > >      Ph.D. Candidate
> > >      Computational Biology
> > >      Vanderbilt University
> > >      Nashville, TN
> > >
> > >    --
> > >    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
> >

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Cannon, Steven
This paper is intriguing to me. I would love to see these methods revisited – but applied in the context of plant data sets (since that is the space where I have interest and funding). There are various other gene family databasing and curation projects, e.g. http://www.pantherdb.org , PlantTribes, etc. – but I think it would be very valuable to see solid solutions and momentum in the GMOD family.

I will mention that Andrew Farmer and I have funds for a two-year postdoc to work on these problems – i.e. methods gene family construction, maintenance, improvement, database, and exploration. If any of you know of potential candidates, please have them contact us, or apply directly here: http://www.orise.orau.gov/usda-ars/applicants/description.aspx?JobId=14490

- Steven ([hidden email])


From: Siddhartha Basu <[hidden email]>
Date: Thursday, January 30, 2014 at 11:01 AM
To: "[hidden email]" <[hidden email]>
Subject: Re: [Gmod-schema] [GMOD-devel] Chado Comparative Module

As i have mentioned in the call P-POD is a tool that leverages chado to
manage analysis from comparative genomics pipeline.
Publication:
Another related tool that popped up
I don't know how active it is currently though.

If i get a chance would like to test drive P-POD datasets in the
group module. Any idea about how to re-model this datasets(particuraly
the grouping part) and/or any existing software to load this data would
be highly welcome.

thanks,
-siddhartha

On Wed, 29 Jan 2014, Siddhartha Basu wrote:

One more things, as far as i recall, the last module to be integrated in
chado was natural diversity. And as far as i understand it seems to
standalone in spite having bunch of linker tables. Maybe we could borrow
ideas from their design principles in the design of group module. Even
better, if we could ask them(Naama/Sook/Seth/Rob, pardon me if i missed
any of their name) to join our next call and shed some lights on those.
If they also share their thoughts in this discussion that would also be
appreciated.
thanks,
-sidd
On Wed, 29 Jan 2014, Siddhartha Basu wrote:
> Hi,
>
> On Mon, 27 Jan 2014, Mara Kim wrote:
>
> >    Hello all,
> >
> >    The conference call today went very well!  The general consensus seems to
> >    be to implement a generic "group" table, with linker tables to each
> >    relevant member type (ex. organism_group, feature_group, stock_group).
> >    I have updated the proposal schematic on the wiki
> >    (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL
> >    implementation, and added use cases that were discussed during the call.
>
>
> >
> >    A few discussion points:
> >
> >    Which modules should be responsible for their respective linker tables?
> >    For example, should the "feature_group" table be part of the Comparative
> >    module or the Sequence module?  Currently I'm leaning towards the latter,
> >    and this is reflected in the schematic.
> I think it depends where it would go and this stage its hardly clear. To
> get a clear idea i believe we have to define where the group module
> stands. If it stands out to be a core and very dependent module then put
> the linkers in others. Then it would make sense to pull group module as
> an dependency to others.
> On the other hand, for early adoption and low barrier of entry i would
> make it standalone and let it be pulled when it is needed. Though it is
> not in line with loosely connected design however it somehow reduces
> burden on existing toolset that works on core schema modules. I would
> prefer to see it getting matured with good toolchain support before it
> get adopted in core and i start changing my core softwares.
>
> >
> >    Perhaps we should consider an alternative name for the "group" table?  As
> >    it is a SQL keyword (ie. GROUP BY), it requires all references to the
> >    table to quote the name (ex. SELECT * FROM "group";).  
> I have a very very strong opinion against the *group* name. Having
> experienced conflicts between oracle(reserved keywords) and chado schema over and over
> again we should absolutely avoid clashing of keywords. Any code that
> needs to use that table have to always account for this exception. This
> might seems trivial at this point, however maintaining a complicated
> codebase with inter-dependencies that runs on live system along with
> revolving developers it would become a possible nightmare.
> Now at this point i really don't have a good alternate name, however in
> short i would prefer not to invest in this module if the name stays though.
> I sincerely hope there are enough smart and savy people in this group to
> come up with an alternate though.
>
>
> > Of course, Chado
> >    already has this problem in PostgreSQL with the "identity" column in
> >    analysisfeature (see
> It great to know that. How big of a problem it is. How many gmod tools are broken because of
> this ? So, far my code that touches analysisfeature haven't thrown any
> error. And i haven't seen any error been reported. If it only appears in
> case issuing TRUNCATE then it is somehow contained. Could you give some
> details.
>
> thanks,
> -sidd
>
>
>
> >
> >    On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]>
> >    wrote:
> >
> >      I am still missing the contact info from Stephen Finklin and Ethy.
> >
> >      On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]>
> >      wrote:
> >
> >        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...
> >          >      >>
> >          >    
> >          >      >>
> >          >    
> >          >      >>
> >          >      >>         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.
> >          >      >>         >
> >          >      >>         >          
> >          >      >>         >            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.
> >          >      >>         >
> >          >      >>
> >          >      
> >          >      >>         >          
> >           _______________________________________________
> >          >      >>         >            Gmod-schema mailing list
> >          >      >>         >            [hidden email]
> >          >      >>         >
> >          >      >>         >
> >          >      >>         >        --
> >          >      >>         >        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.
> >          >      >>         >
> >          >      >>
> >          >      
> >          >      >>         >      
> >           _______________________________________________
> >          >      >>         >        Gmod-schema mailing list
> >          >      >>         >        [hidden email]
> >          >      >>         >
> >          >      >>         >
> >          >      >>         >
> >          >      >>
> >          >      
> >          ------------------------------------------------------------------------------
> >          >      >>         >      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.
> >          >      >>         >
> >          >      >>
> >          >      
> >          >      >>         >    
> >           _______________________________________________
> >          >      >>         >      Gmod-devel mailing list
> >          >      >>         >      [hidden email]
> >          >      >>         >
> >          >      >>         >
> >          >      >>         >    --
> >          >      >>         >
> >          >      >>
> >          >      
> >          ------------------------------------------------------------------------
> >          >      >>         >    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.
> >          >      >>         >
> >          >      >>
> >          >    
> >          >      >>
> >          >      >>         > _______________________________________________
> >          >      >>         > Gmod-schema mailing list
> >          >      >>         > [hidden email]
> >          >      >>         >
> >          >      >>
> >          >      >>
> >          >    
> >           ------------------------------------------------------------------------------
> >          >      >>         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.
> >          >      >>
> >          >    
> >          >      >>         _______________________________________________
> >          >      >>         Gmod-schema mailing list
> >          >      >>         [hidden email]
> >          >      >>        
> >          >      >>
> >          >      >>       --
> >          >      >>       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.
> >          >      >>
> >          >    
> >          >      >>
> >          >      >>   _______________________________________________
> >          >      >>   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.
> >          >      >>
> >          >    
> >          >      >> _______________________________________________
> >          >      >> 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.
> >          >      >
> >          >    
> >          >      > _______________________________________________
> >          >      > Gmod-schema mailing list
> >          >      > [hidden email]
> >          >
> >          >    
> >           ------------------------------------------------------------------------------
> >          >      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.
> >          >    
> >          >      _______________________________________________
> >          >      Gmod-schema mailing list
> >          >      [hidden email]
> >          >
> >          >    --
> >          >    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.
> >          >
> >
> >          > _______________________________________________
> >          > Gmod-schema mailing list
> >          > [hidden email]
> >
> >          ------------------------------------------------------------------------------
> >          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.
> >          _______________________________________________
> >          Gmod-schema mailing list
> >          [hidden email]
> >
> >        --
> >        Mara Kim
> >
> >        Ph.D. Candidate
> >        Computational Biology
> >        Vanderbilt University
> >        Nashville, TN
> >
> >      --
> >      Mara Kim
> >
> >      Ph.D. Candidate
> >      Computational Biology
> >      Vanderbilt University
> >      Nashville, TN
> >
> >    --
> >    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.
>
> > _______________________________________________
> > Gmod-schema mailing list
>

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
_______________________________________________
Gmod-schema mailing list






This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Cannon, Ethalinda K [COM S]
Hello All,

A few thoughts before we begin our call:

1. When I suggested the table "group_group" I was thinking of the usual x_relationship table, but had forgotten the appropriate chadoesque naming. I vote to drop group_group and use group_relationship to create groups of groups.

2. While there's an analysisfeature table, that's in the analysis module, so I'm thinking the table named analysisgroup in the schema should be analysis_group (very minor nitpicking) to match the other group linker tables, and be in the analysis module rather than the group module.

3. I agree this module should not be called "group". Here are a few words to prime the naming discussion: classification, category, association, organization, aggregation, collection...

Ethy

________________________________________
From: Cannon, Steven [[hidden email]]
Sent: Thursday, January 30, 2014 11:21 AM
To: Siddhartha Basu; [hidden email]
Subject: Re: [Gmod-schema] [GMOD-devel] Chado Comparative Module

This paper is intriguing to me. I would love to see these methods revisited – but applied in the context of plant data sets (since that is the space where I have interest and funding). There are various other gene family databasing and curation projects, e.g. http://www.pantherdb.org , PlantTribes, etc. – but I think it would be very valuable to see solid solutions and momentum in the GMOD family.

I will mention that Andrew Farmer and I have funds for a two-year postdoc to work on these problems – i.e. methods gene family construction, maintenance, improvement, database, and exploration. If any of you know of potential candidates, please have them contact us, or apply directly here: http://www.orise.orau.gov/usda-ars/applicants/description.aspx?JobId=14490

- Steven ([hidden email])


From: Siddhartha Basu <[hidden email]<mailto:[hidden email]>>
Date: Thursday, January 30, 2014 at 11:01 AM
To: "[hidden email]<mailto:[hidden email]>" <[hidden email]<mailto:[hidden email]>>
Subject: Re: [Gmod-schema] [GMOD-devel] Chado Comparative Module

As i have mentioned in the call P-POD is a tool that leverages chado to
manage analysis from comparative genomics pipeline.
Publication:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000766
Schema usage: http://ppod.princeton.edu/help.html#schema
Another related tool that popped up
http://sybil.sourceforge.net/documentation.html
I don't know how active it is currently though.

If i get a chance would like to test drive P-POD datasets in the
group module. Any idea about how to re-model this datasets(particuraly
the grouping part) and/or any existing software to load this data would
be highly welcome.

thanks,
-siddhartha

On Wed, 29 Jan 2014, Siddhartha Basu wrote:

One more things, as far as i recall, the last module to be integrated in
chado was natural diversity. And as far as i understand it seems to
standalone in spite having bunch of linker tables. Maybe we could borrow
ideas from their design principles in the design of group module. Even
better, if we could ask them(Naama/Sook/Seth/Rob, pardon me if i missed
any of their name) to join our next call and shed some lights on those.
If they also share their thoughts in this discussion that would also be
appreciated.
thanks,
-sidd
On Wed, 29 Jan 2014, Siddhartha Basu wrote:

> Hi,
>
> On Mon, 27 Jan 2014, Mara Kim wrote:
>
> >    Hello all,
> >
> >    The conference call today went very well!  The general consensus seems to
> >    be to implement a generic "group" table, with linker tables to each
> >    relevant member type (ex. organism_group, feature_group, stock_group).
> >    I have updated the proposal schematic on the wiki
> >    (http://gmod.org/wiki/Chado_Comparative_Module), uploaded a putative SQL
> >    implementation, and added use cases that were discussed during the call.
>
>
> >
> >    A few discussion points:
> >
> >    Which modules should be responsible for their respective linker tables?
> >    For example, should the "feature_group" table be part of the Comparative
> >    module or the Sequence module?  Currently I'm leaning towards the latter,
> >    and this is reflected in the schematic.
> I think it depends where it would go and this stage its hardly clear. To
> get a clear idea i believe we have to define where the group module
> stands. If it stands out to be a core and very dependent module then put
> the linkers in others. Then it would make sense to pull group module as
> an dependency to others.
> On the other hand, for early adoption and low barrier of entry i would
> make it standalone and let it be pulled when it is needed. Though it is
> not in line with loosely connected design however it somehow reduces
> burden on existing toolset that works on core schema modules. I would
> prefer to see it getting matured with good toolchain support before it
> get adopted in core and i start changing my core softwares.
>
> >
> >    Perhaps we should consider an alternative name for the "group" table?  As
> >    it is a SQL keyword (ie. GROUP BY), it requires all references to the
> >    table to quote the name (ex. SELECT * FROM "group";).
> I have a very very strong opinion against the *group* name. Having
> experienced conflicts between oracle(reserved keywords) and chado schema over and over
> again we should absolutely avoid clashing of keywords. Any code that
> needs to use that table have to always account for this exception. This
> might seems trivial at this point, however maintaining a complicated
> codebase with inter-dependencies that runs on live system along with
> revolving developers it would become a possible nightmare.
> Now at this point i really don't have a good alternate name, however in
> short i would prefer not to invest in this module if the name stays though.
> I sincerely hope there are enough smart and savy people in this group to
> come up with an alternate though.
>
>
> > Of course, Chado
> >    already has this problem in PostgreSQL with the "identity" column in
> >    analysisfeature (see
> >    http://www.postgresql.org/docs/8.4/static/sql-truncate.html).
> It great to know that. How big of a problem it is. How many gmod tools are broken because of
> this ? So, far my code that touches analysisfeature haven't thrown any
> error. And i haven't seen any error been reported. If it only appears in
> case issuing TRUNCATE then it is somehow contained. Could you give some
> details.
>
> thanks,
> -sidd
>
>
>
> >
> >    On Mon, Jan 27, 2014 at 11:53 AM, Mara Kim <[hidden email]<mailto:[hidden email]>>
> >    wrote:
> >
> >      I am still missing the contact info from Stephen Finklin and Ethy.
> >
> >      On Fri, Jan 24, 2014 at 3:15 PM, Mara Kim <[hidden email]<mailto:[hidden email]>>
> >      wrote:
> >
> >        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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[hidden email]>
> >          https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
> >        --
> >        Mara Kim
> >
> >        Ph.D. Candidate
> >        Computational Biology
> >        Vanderbilt University
> >        Nashville, TN
> >
> >      --
> >      Mara Kim
> >
> >      Ph.D. Candidate
> >      Computational Biology
> >      Vanderbilt University
> >      Nashville, TN
> >
> >    --
> >    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]<mailto:[hidden email]>
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/gmod-schema






This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

Stephen Ficklin-2
In reply to this post by adf_ncgr
Hi All,

In regards to storing co-expression network data in the new Group module...  For the Implementation I have for storing co-expression data, I  created a custom set of chado-esque tables.  After today's call, I took a look at those custom tables to see what I could port to the Group module as we had defined.  I believe I could scrap all of my custom tables and use this new Group module  (if we have an intermediary group member table).  Networks, edges, and modules could all be stored as groups with the appropriate ancillary tables describing the the network, edges, modules and their respective annotations.  I would be happy to write up a use statement for how I would represent the data if the consensus is that we're settling on a good draft set of tables.  I have a Tripal module for display of co-expression networks which needs a bit more fine-tuning before being made public.  I could potentially convert it (if time permits) to use the new Group tables if it gets folded into the next release of Chado.

Stephen

On 1/17/2014 6:00 PM, Andrew Farmer wrote:
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

------------------------------------------------------------------------------
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/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [GMOD-devel] Chado Comparative Module

McGary, Kris L
Stephen,

Networks are now ubiquitous enough that supporting them in Chado would probably attract a new set of users.

Personally, I would really appreciate seeing what you've done to extend Chado and Tripal, since utilizing networks is a substantial part of our long-term agenda. In particular, the network view of genes on chromosomes is very nice.

Kris
________________________________________
From: Stephen Ficklin [[hidden email]]
Sent: Thursday, January 30, 2014 4:23 PM
To: [hidden email]
Subject: Re: [Gmod-schema] [GMOD-devel]  Chado Comparative Module

Hi All,

In regards to storing co-expression network data in the new Group module...  For the Implementation I have for storing co-expression data, I  created a custom set of chado-esque tables.  After today's call, I took a look at those custom tables to see what I could port to the Group module as we had defined.  I believe I could scrap all of my custom tables and use this new Group module  (if we have an intermediary group member table).  Networks, edges, and modules could all be stored as groups with the appropriate ancillary tables describing the the network, edges, modules and their respective annotations.  I would be happy to write up a use statement for how I would represent the data if the consensus is that we're settling on a good draft set of tables.  I have a Tripal module for display of co-expression networks which needs a bit more fine-tuning before being made public.  I could potentially convert it (if time permits) to use the new Group tables if it gets folded into the next release of Chado.

Stephen

On 1/17/2014 6:00 PM, Andrew Farmer wrote:
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]<mailto:[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]<mailto:[hidden email]>> wrote:
Ah, yes, the fake feature solution!


On Fri, Jan 17, 2014 at 11:45 AM, Robert Buels <[hidden email]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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<tel:216-392-3087>
Ontario Institute for Cancer Research



--
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]<mailto:[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]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/gmod-schema



------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
12