An "experiement" table?

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An "experiement" table?

Nicolas Girault
Hi,

Thank you for reading.
I'm building a database to record sequence variations that appear in stem cell cultures.

Here is my problem:
A feature (sequence variation) should be linked to a cell line, a publication, a computational analysis BUT I also would like to link it to an experiment with a protocol.

I can't find any Chado table appropriate for this. I see a "protocol" table but there is no experiment (or equivalent) table directly linked to a feature. The "experiment" table can't be the "pub" table since a publication can present several experiments.

I am considering to add this "experiment" table to the schema but I would like to avoid as much as possible to modify the Chado structure... This is why I would like to know if my way of structuring the data is not Chadoish or if I am missing a table that could help me.

Thank you for your hints,

--------------------------------------
Nicolas GIRAULT
Phone: +33 7 81 83 71 93
--------------------------------------

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Re: An "experiement" table?

Naama Menda
hi Nicolas,

where do you store your cell lines? 
You could store those as 'stocks' and use the Natural Diversity module for the experiments 

-Naama



Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
[hidden email]


On Mon, Jul 29, 2013 at 6:40 AM, Nicolas Girault <[hidden email]> wrote:
Hi,

Thank you for reading.
I'm building a database to record sequence variations that appear in stem cell cultures.

Here is my problem:
A feature (sequence variation) should be linked to a cell line, a publication, a computational analysis BUT I also would like to link it to an experiment with a protocol.

I can't find any Chado table appropriate for this. I see a "protocol" table but there is no experiment (or equivalent) table directly linked to a feature. The "experiment" table can't be the "pub" table since a publication can present several experiments.

I am considering to add this "experiment" table to the schema but I would like to avoid as much as possible to modify the Chado structure... This is why I would like to know if my way of structuring the data is not Chadoish or if I am missing a table that could help me.

Thank you for your hints,

--------------------------------------
Nicolas GIRAULT
Phone: <a href="tel:%2B33%207%2081%2083%2071%2093" value="+33781837193" target="_blank">+33 7 81 83 71 93
--------------------------------------

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Re: An "experiement" table?

Siddhartha Basu
Hi Naama,

On Mon, 29 Jul 2013, Naama Menda wrote:

>    hi Nicolas,
>    where do you store your cell lines?
>    You could store those as 'stocks' and use the Natural Diversity module for
>    the experiments
>    http://gmod.org/wiki/Chado_Natural_Diversity_Module
This is a nice and  interesting suggestion. So,  i went through the
module documentation(very well done), and what i understood so far that
nd_experiment table is for an event/result/outcome which might have
generated/created an entity that we in most cases store in stock
table(pardon my ignorance and lack of detail understanding though).
In that case, it's  mandatory to have a precise geolocation, however how to
model something when i don't have geolocation with it. This is something
i could not figure it out.

And of course, thanks to all for having this nice chado module.

thanks,
-siddhartha



>    -Naama
>    Naama Menda
>    Boyce Thompson Institute for Plant Research
>    Tower Rd
>    Ithaca NY 14853
>    USA
>
>    (607) 254 3569
>    Sol Genomics Network
>    http://solgenomics.net/
>    [hidden email]
>
>    On Mon, Jul 29, 2013 at 6:40 AM, Nicolas Girault <[hidden email]>
>    wrote:
>
>      Hi,
>      Thank you for reading.
>      I'm building a database to record sequence variations that appear in
>      stem cell cultures.
>      Here is my problem:
>      A feature (sequence variation) should be linked to a cell line, a
>      publication, a computational analysis BUT I also would like to link it
>      to an experiment with a protocol.
>      I can't find any Chado table appropriate for this. I see a "protocol"
>      table but there is no experiment (or equivalent) table directly linked
>      to a feature. The "experiment" table can't be the "pub" table since a
>      publication can present several experiments.
>      I am considering to add this "experiment" table to the schema but I
>      would like to avoid as much as possible to modify the Chado structure...
>      This is why I would like to know if my way of structuring the data is
>      not Chadoish or if I am missing a table that could help me.
>      Thank you for your hints,
>      --------------------------------------
>      Nicolas GIRAULT
>      Phone: +33 7 81 83 71 93
>      Email: [hidden email]
>      --------------------------------------
>      ------------------------------------------------------------------------------
>      See everything from the browser to the database with AppDynamics
>      Get end-to-end visibility with application monitoring from AppDynamics
>      Isolate bottlenecks and diagnose root cause in seconds.
>      Start your free trial of AppDynamics Pro today!
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>      _______________________________________________
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>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema

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Re: An "experiement" table?

Naama Menda
yes, nd_experiment is very abstract. you can have a 'stock' associated with experiments, or experiments that create new stocks.
It's up to the user to decide if stock - to - nd_experiment should be one-to-one or one-to-many (as reflected from the number of use cases in the wiki) .
We don't have a geolocation for many experiments. In those cases we use an  generic 'unknown' location, or store the location of the lab (just the name, without coordinates) .


best,
-Naama

 



Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

<a href="tel:%28607%29%20254%203569" value="+16072543569" target="_blank">(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
[hidden email]


On Mon, Jul 29, 2013 at 11:05 AM, Siddhartha Basu <[hidden email]> wrote:
Hi Naama,

On Mon, 29 Jul 2013, Naama Menda wrote:

>    hi Nicolas,
>    where do you store your cell lines?
>    You could store those as 'stocks' and use the Natural Diversity module for
>    the experiments
>    http://gmod.org/wiki/Chado_Natural_Diversity_Module
This is a nice and  interesting suggestion. So,  i went through the
module documentation(very well done), and what i understood so far that
nd_experiment table is for an event/result/outcome which might have
generated/created an entity that we in most cases store in stock
table(pardon my ignorance and lack of detail understanding though).
In that case, it's  mandatory to have a precise geolocation, however how to
model something when i don't have geolocation with it. This is something
i could not figure it out.

And of course, thanks to all for having this nice chado module.

thanks,
-siddhartha



>    -Naama
>    Naama Menda
>    Boyce Thompson Institute for Plant Research
>    Tower Rd
>    Ithaca NY 14853
>    USA
>
>    <a href="tel:%28607%29%20254%203569" value="+16072543569" target="_blank">(607) 254 3569
>    Sol Genomics Network
>    http://solgenomics.net/
>    [hidden email]
>
>    On Mon, Jul 29, 2013 at 6:40 AM, Nicolas Girault <[hidden email]>
>    wrote:
>
>      Hi,
>      Thank you for reading.
>      I'm building a database to record sequence variations that appear in
>      stem cell cultures.
>      Here is my problem:
>      A feature (sequence variation) should be linked to a cell line, a
>      publication, a computational analysis BUT I also would like to link it
>      to an experiment with a protocol.
>      I can't find any Chado table appropriate for this. I see a "protocol"
>      table but there is no experiment (or equivalent) table directly linked
>      to a feature. The "experiment" table can't be the "pub" table since a
>      publication can present several experiments.
>      I am considering to add this "experiment" table to the schema but I
>      would like to avoid as much as possible to modify the Chado structure...
>      This is why I would like to know if my way of structuring the data is
>      not Chadoish or if I am missing a table that could help me.
>      Thank you for your hints,
>      --------------------------------------
>      Nicolas GIRAULT
>      Phone: <a href="tel:%2B33%207%2081%2083%2071%2093" value="+33781837193" target="_blank">+33 7 81 83 71 93
>      Email: [hidden email]
>      --------------------------------------
>      ------------------------------------------------------------------------------
>      See everything from the browser to the database with AppDynamics
>      Get end-to-end visibility with application monitoring from AppDynamics
>      Isolate bottlenecks and diagnose root cause in seconds.
>      Start your free trial of AppDynamics Pro today!
>      http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema

> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
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Re: An "experiement" table?

Nicolas Girault
In reply to this post by Siddhartha Basu
Thank you Naama.

Your solution sounds interesting. I was thinking to store the cell lines in the cell_line module (http://gmod.org/wiki/Chado_Cell_Line_Module) but now I'll consider to store it as stocks.

Best,
Nicolas


2013/7/29 Siddhartha Basu <[hidden email]>
Hi Naama,

On Mon, 29 Jul 2013, Naama Menda wrote:

>    hi Nicolas,
>    where do you store your cell lines?
>    You could store those as 'stocks' and use the Natural Diversity module for
>    the experiments
>    http://gmod.org/wiki/Chado_Natural_Diversity_Module
This is a nice and  interesting suggestion. So,  i went through the
module documentation(very well done), and what i understood so far that
nd_experiment table is for an event/result/outcome which might have
generated/created an entity that we in most cases store in stock
table(pardon my ignorance and lack of detail understanding though).
In that case, it's  mandatory to have a precise geolocation, however how to
model something when i don't have geolocation with it. This is something
i could not figure it out.

And of course, thanks to all for having this nice chado module.

thanks,
-siddhartha



>    -Naama
>    Naama Menda
>    Boyce Thompson Institute for Plant Research
>    Tower Rd
>    Ithaca NY 14853
>    USA
>
>    (607) 254 3569
>    Sol Genomics Network
>    http://solgenomics.net/
>    [hidden email]
>
>    On Mon, Jul 29, 2013 at 6:40 AM, Nicolas Girault <[hidden email]>
>    wrote:
>
>      Hi,
>      Thank you for reading.
>      I'm building a database to record sequence variations that appear in
>      stem cell cultures.
>      Here is my problem:
>      A feature (sequence variation) should be linked to a cell line, a
>      publication, a computational analysis BUT I also would like to link it
>      to an experiment with a protocol.
>      I can't find any Chado table appropriate for this. I see a "protocol"
>      table but there is no experiment (or equivalent) table directly linked
>      to a feature. The "experiment" table can't be the "pub" table since a
>      publication can present several experiments.
>      I am considering to add this "experiment" table to the schema but I
>      would like to avoid as much as possible to modify the Chado structure...
>      This is why I would like to know if my way of structuring the data is
>      not Chadoish or if I am missing a table that could help me.
>      Thank you for your hints,
>      --------------------------------------
>      Nicolas GIRAULT
>      Phone: +33 7 81 83 71 93
>      Email: [hidden email]
>      --------------------------------------
>      ------------------------------------------------------------------------------
>      See everything from the browser to the database with AppDynamics
>      Get end-to-end visibility with application monitoring from AppDynamics
>      Isolate bottlenecks and diagnose root cause in seconds.
>      Start your free trial of AppDynamics Pro today!
>      http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema

> ------------------------------------------------------------------------------
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Re: An "experiement" table?

Stephen Ficklin-2
Hi All,

Storing the cell lines in the stock table makes sense and works and the stock.type_id can be used to indicate that the record is a cell line.  But, since the cell_line tables exist I think it may be best to use them to preserve the ability for intuitive data exchange.

We often use custom linker tables when we need to associate two data types. For example, we use a stock_library to link a stock to a genomic library derived from it.  It's not a current table in the Chado schema but it's such a simple addition and follows the style of other Chado linking tables that I think it's quite benign.

What if Nicholas used the cell_line tables to store details about his cell lines and created a custom 'nd_experiment_cell_line' table modeled after the 'nd_experiment_stock' table.  This allows him to uses the cell_line module as it was intended but adds the benefits for using the ND tables?

Stephen

On 7/29/2013 11:18 AM, Nicolas Girault wrote:
Thank you Naama.

Your solution sounds interesting. I was thinking to store the cell lines in the cell_line module (http://gmod.org/wiki/Chado_Cell_Line_Module) but now I'll consider to store it as stocks.

Best,
Nicolas


2013/7/29 Siddhartha Basu <[hidden email]>
Hi Naama,

On Mon, 29 Jul 2013, Naama Menda wrote:

>    hi Nicolas,
>    where do you store your cell lines?
>    You could store those as 'stocks' and use the Natural Diversity module for
>    the experiments
>    http://gmod.org/wiki/Chado_Natural_Diversity_Module
This is a nice and  interesting suggestion. So,  i went through the
module documentation(very well done), and what i understood so far that
nd_experiment table is for an event/result/outcome which might have
generated/created an entity that we in most cases store in stock
table(pardon my ignorance and lack of detail understanding though).
In that case, it's  mandatory to have a precise geolocation, however how to
model something when i don't have geolocation with it. This is something
i could not figure it out.

And of course, thanks to all for having this nice chado module.

thanks,
-siddhartha



>    -Naama
>    Naama Menda
>    Boyce Thompson Institute for Plant Research
>    Tower Rd
>    Ithaca NY 14853
>    USA
>
>    (607) 254 3569
>    Sol Genomics Network
>    http://solgenomics.net/
>    [hidden email]
>
>    On Mon, Jul 29, 2013 at 6:40 AM, Nicolas Girault <[hidden email]>
>    wrote:
>
>      Hi,
>      Thank you for reading.
>      I'm building a database to record sequence variations that appear in
>      stem cell cultures.
>      Here is my problem:
>      A feature (sequence variation) should be linked to a cell line, a
>      publication, a computational analysis BUT I also would like to link it
>      to an experiment with a protocol.
>      I can't find any Chado table appropriate for this. I see a "protocol"
>      table but there is no experiment (or equivalent) table directly linked
>      to a feature. The "experiment" table can't be the "pub" table since a
>      publication can present several experiments.
>      I am considering to add this "experiment" table to the schema but I
>      would like to avoid as much as possible to modify the Chado structure...
>      This is why I would like to know if my way of structuring the data is
>      not Chadoish or if I am missing a table that could help me.
>      Thank you for your hints,
>      --------------------------------------
>      Nicolas GIRAULT
>      Phone: +33 7 81 83 71 93
>      Email: [hidden email]
>      --------------------------------------
>      ------------------------------------------------------------------------------
>      See everything from the browser to the database with AppDynamics
>      Get end-to-end visibility with application monitoring from AppDynamics
>      Isolate bottlenecks and diagnose root cause in seconds.
>      Start your free trial of AppDynamics Pro today!
>      http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema

> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
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Re: An "experiement" table?

Bob MacCallum
Just to second Naama's point about nd_geolocations - we also use a placeholder description="laboratory" (everything else null) for many nd_experiments.


On Mon, Jul 29, 2013 at 4:46 PM, Stephen Ficklin <[hidden email]> wrote:
Hi All,

Storing the cell lines in the stock table makes sense and works and the stock.type_id can be used to indicate that the record is a cell line.  But, since the cell_line tables exist I think it may be best to use them to preserve the ability for intuitive data exchange.

We often use custom linker tables when we need to associate two data types. For example, we use a stock_library to link a stock to a genomic library derived from it.  It's not a current table in the Chado schema but it's such a simple addition and follows the style of other Chado linking tables that I think it's quite benign.

What if Nicholas used the cell_line tables to store details about his cell lines and created a custom 'nd_experiment_cell_line' table modeled after the 'nd_experiment_stock' table.  This allows him to uses the cell_line module as it was intended but adds the benefits for using the ND tables?

Stephen


On 7/29/2013 11:18 AM, Nicolas Girault wrote:
Thank you Naama.

Your solution sounds interesting. I was thinking to store the cell lines in the cell_line module (http://gmod.org/wiki/Chado_Cell_Line_Module) but now I'll consider to store it as stocks.

Best,
Nicolas


2013/7/29 Siddhartha Basu <[hidden email]>
Hi Naama,

On Mon, 29 Jul 2013, Naama Menda wrote:

>    hi Nicolas,
>    where do you store your cell lines?
>    You could store those as 'stocks' and use the Natural Diversity module for
>    the experiments
>    http://gmod.org/wiki/Chado_Natural_Diversity_Module
This is a nice and  interesting suggestion. So,  i went through the
module documentation(very well done), and what i understood so far that
nd_experiment table is for an event/result/outcome which might have
generated/created an entity that we in most cases store in stock
table(pardon my ignorance and lack of detail understanding though).
In that case, it's  mandatory to have a precise geolocation, however how to
model something when i don't have geolocation with it. This is something
i could not figure it out.

And of course, thanks to all for having this nice chado module.

thanks,
-siddhartha



>    -Naama
>    Naama Menda
>    Boyce Thompson Institute for Plant Research
>    Tower Rd
>    Ithaca NY 14853
>    USA
>
>    (607) 254 3569
>    Sol Genomics Network
>    http://solgenomics.net/
>    [hidden email]
>
>    On Mon, Jul 29, 2013 at 6:40 AM, Nicolas Girault <[hidden email]>
>    wrote:
>
>      Hi,
>      Thank you for reading.
>      I'm building a database to record sequence variations that appear in
>      stem cell cultures.
>      Here is my problem:
>      A feature (sequence variation) should be linked to a cell line, a
>      publication, a computational analysis BUT I also would like to link it
>      to an experiment with a protocol.
>      I can't find any Chado table appropriate for this. I see a "protocol"
>      table but there is no experiment (or equivalent) table directly linked
>      to a feature. The "experiment" table can't be the "pub" table since a
>      publication can present several experiments.
>      I am considering to add this "experiment" table to the schema but I
>      would like to avoid as much as possible to modify the Chado structure...
>      This is why I would like to know if my way of structuring the data is
>      not Chadoish or if I am missing a table that could help me.
>      Thank you for your hints,
>      --------------------------------------
>      Nicolas GIRAULT
>      Phone: <a href="tel:%2B33%207%2081%2083%2071%2093" value="+33781837193" target="_blank">+33 7 81 83 71 93
>      Email: [hidden email]
>      --------------------------------------
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Re: An "experiement" table?

Nicolas Girault
The negative point with the natural diversity module is that it proposes much more things than I need. It does not matches very well my situation. For example I won't use the nd_geolocations.

Stephen highlighted the possibility to add linking tables. Thus my problem would be solved if I create a "study_feature" table to link the "study" table to the "feature" table. The "study" table corresponds well to the representation I need of an experiment.

Thank you for this very helpful discussion.
Nicolas


2013/7/29 Bob MacCallum <[hidden email]>
Just to second Naama's point about nd_geolocations - we also use a placeholder description="laboratory" (everything else null) for many nd_experiments.


On Mon, Jul 29, 2013 at 4:46 PM, Stephen Ficklin <[hidden email]> wrote:
Hi All,

Storing the cell lines in the stock table makes sense and works and the stock.type_id can be used to indicate that the record is a cell line.  But, since the cell_line tables exist I think it may be best to use them to preserve the ability for intuitive data exchange.

We often use custom linker tables when we need to associate two data types. For example, we use a stock_library to link a stock to a genomic library derived from it.  It's not a current table in the Chado schema but it's such a simple addition and follows the style of other Chado linking tables that I think it's quite benign.

What if Nicholas used the cell_line tables to store details about his cell lines and created a custom 'nd_experiment_cell_line' table modeled after the 'nd_experiment_stock' table.  This allows him to uses the cell_line module as it was intended but adds the benefits for using the ND tables?

Stephen


On 7/29/2013 11:18 AM, Nicolas Girault wrote:
Thank you Naama.

Your solution sounds interesting. I was thinking to store the cell lines in the cell_line module (http://gmod.org/wiki/Chado_Cell_Line_Module) but now I'll consider to store it as stocks.

Best,
Nicolas


2013/7/29 Siddhartha Basu <[hidden email]>
Hi Naama,

On Mon, 29 Jul 2013, Naama Menda wrote:

>    hi Nicolas,
>    where do you store your cell lines?
>    You could store those as 'stocks' and use the Natural Diversity module for
>    the experiments
>    http://gmod.org/wiki/Chado_Natural_Diversity_Module
This is a nice and  interesting suggestion. So,  i went through the
module documentation(very well done), and what i understood so far that
nd_experiment table is for an event/result/outcome which might have
generated/created an entity that we in most cases store in stock
table(pardon my ignorance and lack of detail understanding though).
In that case, it's  mandatory to have a precise geolocation, however how to
model something when i don't have geolocation with it. This is something
i could not figure it out.

And of course, thanks to all for having this nice chado module.

thanks,
-siddhartha



>    -Naama
>    Naama Menda
>    Boyce Thompson Institute for Plant Research
>    Tower Rd
>    Ithaca NY 14853
>    USA
>
>    (607) 254 3569
>    Sol Genomics Network
>    http://solgenomics.net/
>    [hidden email]
>
>    On Mon, Jul 29, 2013 at 6:40 AM, Nicolas Girault <[hidden email]>
>    wrote:
>
>      Hi,
>      Thank you for reading.
>      I'm building a database to record sequence variations that appear in
>      stem cell cultures.
>      Here is my problem:
>      A feature (sequence variation) should be linked to a cell line, a
>      publication, a computational analysis BUT I also would like to link it
>      to an experiment with a protocol.
>      I can't find any Chado table appropriate for this. I see a "protocol"
>      table but there is no experiment (or equivalent) table directly linked
>      to a feature. The "experiment" table can't be the "pub" table since a
>      publication can present several experiments.
>      I am considering to add this "experiment" table to the schema but I
>      would like to avoid as much as possible to modify the Chado structure...
>      This is why I would like to know if my way of structuring the data is
>      not Chadoish or if I am missing a table that could help me.
>      Thank you for your hints,
>      --------------------------------------
>      Nicolas GIRAULT
>      Phone: <a href="tel:%2B33%207%2081%2083%2071%2093" value="+33781837193" target="_blank">+33 7 81 83 71 93
>      Email: [hidden email]
>      --------------------------------------
>      ------------------------------------------------------------------------------
>      See everything from the browser to the database with AppDynamics
>      Get end-to-end visibility with application monitoring from AppDynamics
>      Isolate bottlenecks and diagnose root cause in seconds.
>      Start your free trial of AppDynamics Pro today!
>      http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema

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Re: An "experiement" table?

Siddhartha Basu
In reply to this post by Naama Menda
On Mon, 29 Jul 2013, Naama Menda wrote:

>    yes, nd_experiment is very abstract. you can have a 'stock' associated
>    with experiments, or experiments that create new stocks.
>    It's up to the user to decide if stock - to - nd_experiment should be
>    one-to-one or one-to-many (as reflected from the number of use cases in
>    the wiki) .
>    We don't have a geolocation for many experiments. In those cases we use an
>     generic 'unknown' location, or store the location of the lab (just the
>    name, without coordinates) .
Really appreciate you clarification, however i wonder isn't it might be easier
to have the nd_geolocation_id column(nd_experiment table) be less restrictive
and allow NULL values.

thanks once again,
-siddhartha


>    best,
>    -Naama
>    
>    Naama Menda
>    Boyce Thompson Institute for Plant Research
>    Tower Rd
>    Ithaca NY 14853
>    USA
>
>    (607) 254 3569
>    Sol Genomics Network
>    http://solgenomics.net/
>    [hidden email]
>
>    On Mon, Jul 29, 2013 at 11:05 AM, Siddhartha Basu <[hidden email]>
>    wrote:
>
>      Hi Naama,
>      On Mon, 29 Jul 2013, Naama Menda wrote:
>
>      >    hi Nicolas,
>      >    where do you store your cell lines?
>      >    You could store those as 'stocks' and use the Natural Diversity
>      module for
>      >    the experiments
>      >    http://gmod.org/wiki/Chado_Natural_Diversity_Module
>      This is a nice and  interesting suggestion. So,  i went through the
>      module documentation(very well done), and what i understood so far that
>      nd_experiment table is for an event/result/outcome which might have
>      generated/created an entity that we in most cases store in stock
>      table(pardon my ignorance and lack of detail understanding though).
>      In that case, it's  mandatory to have a precise geolocation, however how
>      to
>      model something when i don't have geolocation with it. This is something
>      i could not figure it out.
>
>      And of course, thanks to all for having this nice chado module.
>
>      thanks,
>      -siddhartha
>
>      >    -Naama
>      >    Naama Menda
>      >    Boyce Thompson Institute for Plant Research
>      >    Tower Rd
>      >    Ithaca NY 14853
>      >    USA
>      >
>      >    (607) 254 3569
>      >    Sol Genomics Network
>      >    http://solgenomics.net/
>      >    [hidden email]
>      >
>      >    On Mon, Jul 29, 2013 at 6:40 AM, Nicolas Girault
>      <[hidden email]>
>      >    wrote:
>      >
>      >      Hi,
>      >      Thank you for reading.
>      >      I'm building a database to record sequence variations that appear
>      in
>      >      stem cell cultures.
>      >      Here is my problem:
>      >      A feature (sequence variation) should be linked to a cell line, a
>      >      publication, a computational analysis BUT I also would like to
>      link it
>      >      to an experiment with a protocol.
>      >      I can't find any Chado table appropriate for this. I see a
>      "protocol"
>      >      table but there is no experiment (or equivalent) table directly
>      linked
>      >      to a feature. The "experiment" table can't be the "pub" table
>      since a
>      >      publication can present several experiments.
>      >      I am considering to add this "experiment" table to the schema but
>      I
>      >      would like to avoid as much as possible to modify the Chado
>      structure...
>      >      This is why I would like to know if my way of structuring the
>      data is
>      >      not Chadoish or if I am missing a table that could help me.
>      >      Thank you for your hints,
>      >      --------------------------------------
>      >      Nicolas GIRAULT
>      >      Phone: +33 7 81 83 71 93
>      >      Email: [hidden email]
>      >      --------------------------------------
>      >    
>       ------------------------------------------------------------------------------
>      >      See everything from the browser to the database with AppDynamics
>      >      Get end-to-end visibility with application monitoring from
>      AppDynamics
>      >      Isolate bottlenecks and diagnose root cause in seconds.
>      >      Start your free trial of AppDynamics Pro today!
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>       http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
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>
>      >
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