RFC: Chado relase v1.3

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RFC: Chado relase v1.3

Stephen Ficklin-2
Dear Chado User Community,

Representatives from the Tripal (Stephen Ficklin, Lacey Sanderson) and
Chado (Scott Cain) projects have combined efforts to work towards a v1.3
release of Chado.    To do this, we have compiled a list of the
requested changes that we knew about or that were posted to the GMOD
Schema mailing list.   You can find the list on the Google Doc at this link:

https://docs.google.com/document/d/1IZ3VMpIoG1hhpbHYi6rbChImLgrlmbyy7Ewms-EpaeU/edit?usp=sharing

We are requesting comments on the document.   For v1.3 we are proposing
a quick release that will include mostly new linking and property tables
to existing Chado tables (see Google doc for complete list).  If you
have any additional linking tables that you would like to request for
the v1.3 release please make a suggestion so we can add them to the list
for consideration.

Aside from these linking tables we are considering the following changes
to the v1.3 release.

1)  Add a new 'infraspecific' field for the organism table to allow for
storing the names of subspecies, varieties, subvarieties, forma and
subforma.   However, we would like to know.... should the infraspecific
field be used for storing names of strains and cultivars?  If so, then
the recommendation would be to store details about individual strains
and cultivars in the Stock module tables. Alternatively, FlyBase has
suggested a separate set of tables for storing strains.   Please comment
on the Google Doc if you have opinions on the best way to
represent/store strains/cultivars in Chado.

2)  The addition of an 'organism_relationship' table that allows for
storing relationships (not taxonomy) between organisms.  An example use
case would be for storing breeding relationships (e.g. sterile_with,
incompatible_with, fertile_with).

3)  Move the 'db' and 'dbxref' tables into a new module called 'DB'.  
This will not require any SQL changes, just a name change in the
documentation.

4) Change 'feature.seqlen' to a bigint to accommodate longer sequences.

The more complex issues we are reserving for a potential v1.4 release
after more discussion is held.

Thanks for any input!
Stephen






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Re: [Gmod-schema] RFC: Chado relase v1.3

Lukas A. Mueller
HI Stephen,

just to add another totally unrelated request: Could we have timestamps for creation time (maybe also update) in the nd_experiment and stock (possibly project) tables? In breeding programs, people would like to know when and how many things have been added…

cheers
Lukas

> On Mar 9, 2015, at 9:20 AM, Stephen Ficklin <[hidden email]> wrote:
>
> Dear Chado User Community,
>
> Representatives from the Tripal (Stephen Ficklin, Lacey Sanderson) and
> Chado (Scott Cain) projects have combined efforts to work towards a v1.3
> release of Chado.    To do this, we have compiled a list of the
> requested changes that we knew about or that were posted to the GMOD
> Schema mailing list.   You can find the list on the Google Doc at this link:
>
> https://docs.google.com/document/d/1IZ3VMpIoG1hhpbHYi6rbChImLgrlmbyy7Ewms-EpaeU/edit?usp=sharing
>
> We are requesting comments on the document.   For v1.3 we are proposing
> a quick release that will include mostly new linking and property tables
> to existing Chado tables (see Google doc for complete list).  If you
> have any additional linking tables that you would like to request for
> the v1.3 release please make a suggestion so we can add them to the list
> for consideration.
>
> Aside from these linking tables we are considering the following changes
> to the v1.3 release.
>
> 1)  Add a new 'infraspecific' field for the organism table to allow for
> storing the names of subspecies, varieties, subvarieties, forma and
> subforma.   However, we would like to know.... should the infraspecific
> field be used for storing names of strains and cultivars?  If so, then
> the recommendation would be to store details about individual strains
> and cultivars in the Stock module tables. Alternatively, FlyBase has
> suggested a separate set of tables for storing strains.   Please comment
> on the Google Doc if you have opinions on the best way to
> represent/store strains/cultivars in Chado.
>
> 2)  The addition of an 'organism_relationship' table that allows for
> storing relationships (not taxonomy) between organisms.  An example use
> case would be for storing breeding relationships (e.g. sterile_with,
> incompatible_with, fertile_with).
>
> 3)  Move the 'db' and 'dbxref' tables into a new module called 'DB'.  
> This will not require any SQL changes, just a name change in the
> documentation.
>
> 4) Change 'feature.seqlen' to a bigint to accommodate longer sequences.
>
> The more complex issues we are reserving for a potential v1.4 release
> after more discussion is held.
>
> Thanks for any input!
> Stephen
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-schema] RFC: Chado relase v1.3

Sook Jung
Hi,
I recently also realized that it would be really useful to have timestamps in the tables that Lukas mentioned.
Thanks
Sook

On Mon, Mar 9, 2015 at 10:37 AM, Lukas A. Mueller <[hidden email]> wrote:
HI Stephen,

just to add another totally unrelated request: Could we have timestamps for creation time (maybe also update) in the nd_experiment and stock (possibly project) tables? In breeding programs, people would like to know when and how many things have been added…

cheers
Lukas

> On Mar 9, 2015, at 9:20 AM, Stephen Ficklin <[hidden email]> wrote:
>
> Dear Chado User Community,
>
> Representatives from the Tripal (Stephen Ficklin, Lacey Sanderson) and
> Chado (Scott Cain) projects have combined efforts to work towards a v1.3
> release of Chado.    To do this, we have compiled a list of the
> requested changes that we knew about or that were posted to the GMOD
> Schema mailing list.   You can find the list on the Google Doc at this link:
>
> https://docs.google.com/document/d/1IZ3VMpIoG1hhpbHYi6rbChImLgrlmbyy7Ewms-EpaeU/edit?usp=sharing
>
> We are requesting comments on the document.   For v1.3 we are proposing
> a quick release that will include mostly new linking and property tables
> to existing Chado tables (see Google doc for complete list).  If you
> have any additional linking tables that you would like to request for
> the v1.3 release please make a suggestion so we can add them to the list
> for consideration.
>
> Aside from these linking tables we are considering the following changes
> to the v1.3 release.
>
> 1)  Add a new 'infraspecific' field for the organism table to allow for
> storing the names of subspecies, varieties, subvarieties, forma and
> subforma.   However, we would like to know.... should the infraspecific
> field be used for storing names of strains and cultivars?  If so, then
> the recommendation would be to store details about individual strains
> and cultivars in the Stock module tables. Alternatively, FlyBase has
> suggested a separate set of tables for storing strains.   Please comment
> on the Google Doc if you have opinions on the best way to
> represent/store strains/cultivars in Chado.
>
> 2)  The addition of an 'organism_relationship' table that allows for
> storing relationships (not taxonomy) between organisms.  An example use
> case would be for storing breeding relationships (e.g. sterile_with,
> incompatible_with, fertile_with).
>
> 3)  Move the 'db' and 'dbxref' tables into a new module called 'DB'.
> This will not require any SQL changes, just a name change in the
> documentation.
>
> 4) Change 'feature.seqlen' to a bigint to accommodate longer sequences.
>
> The more complex issues we are reserving for a potential v1.4 release
> after more discussion is held.
>
> Thanks for any input!
> Stephen
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-schema


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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-schema] RFC: Chado relase v1.3

adf_ncgr
In reply to this post by Stephen Ficklin-2
Hi Stephen-
it's great to see this moving forward!

here are a couple of additional very minor changes from our ongoing work with the phylogeny module that I think
would fit the spirit of the proposed v1.3 release:

add phylotreeprop table
add index to phylonode.parent_phylonode_id (we had some serious performance issues with tree deletions until
                                                                        the omission of this index was discovered)


Also, unrelated to phylogeny but possibly worth including in the set of linker tables to be added this round:
biomaterial_project

we found this useful when representing BioSample/BioProject info taken from NCBI; but, we also made some associated
changes to existing tables that may be outside the scope of the v1.3 release:
  • project table
    • add dbxref_id => dbxref (supports NCBI BioProject ids, for example)
    • add type_id => cvterm (supports classification of projects, initially using cv derived from NCBI's BioProject vocabulary)
    • ALTER COLUMN description TYPE text (BioProject descriptions can be long)
  • biomaterial table
    • add stock_id => stock (allows tracking cultivar, etc. for samples; but this may be unnecessary if subspecies info is now going to be included in organism)
    • add project_id => project (links samples to primary projects, as is done in NCBI)

hope that is helpful; let us know if you need more info to justify their inclusion or whatever else would make
it easier for you to get the changes incorporated into v 1.3 (DDL, etc).

thanks again

Andrew Farmer




On 3/9/15 7:20 AM, Stephen Ficklin wrote:
Dear Chado User Community,

Representatives from the Tripal (Stephen Ficklin, Lacey Sanderson) and 
Chado (Scott Cain) projects have combined efforts to work towards a v1.3 
release of Chado.    To do this, we have compiled a list of the 
requested changes that we knew about or that were posted to the GMOD 
Schema mailing list.   You can find the list on the Google Doc at this link:

https://docs.google.com/document/d/1IZ3VMpIoG1hhpbHYi6rbChImLgrlmbyy7Ewms-EpaeU/edit?usp=sharing

We are requesting comments on the document.   For v1.3 we are proposing 
a quick release that will include mostly new linking and property tables 
to existing Chado tables (see Google doc for complete list).  If you 
have any additional linking tables that you would like to request for 
the v1.3 release please make a suggestion so we can add them to the list 
for consideration.

Aside from these linking tables we are considering the following changes 
to the v1.3 release.

1)  Add a new 'infraspecific' field for the organism table to allow for 
storing the names of subspecies, varieties, subvarieties, forma and 
subforma.   However, we would like to know.... should the infraspecific 
field be used for storing names of strains and cultivars?  If so, then 
the recommendation would be to store details about individual strains 
and cultivars in the Stock module tables. Alternatively, FlyBase has 
suggested a separate set of tables for storing strains.   Please comment 
on the Google Doc if you have opinions on the best way to 
represent/store strains/cultivars in Chado.

2)  The addition of an 'organism_relationship' table that allows for 
storing relationships (not taxonomy) between organisms.  An example use 
case would be for storing breeding relationships (e.g. sterile_with, 
incompatible_with, fertile_with).

3)  Move the 'db' and 'dbxref' tables into a new module called 'DB'.  
This will not require any SQL changes, just a name change in the 
documentation.

4) Change 'feature.seqlen' to a bigint to accommodate longer sequences.

The more complex issues we are reserving for a potential v1.4 release 
after more discussion is held.

Thanks for any input!
Stephen






------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the 
conversation now. http://goparallel.sourceforge.net/
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-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

------------------------------------------------------------------------------
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things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-schema] RFC: Chado relase v1.3

Karl O. Pinc
In reply to this post by Stephen Ficklin-2
On Mon, 09 Mar 2015 09:20:49 -0400
Stephen Ficklin <[hidden email]> wrote:

> Representatives from the Tripal (Stephen Ficklin, Lacey Sanderson)
> and Chado (Scott Cain) projects have combined efforts to work towards
> a v1.3 release of Chado.

> We are requesting comments...

You could make Papio anubis (baboon) organism_id 13....


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

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