Interspecific genetic maps

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Interspecific genetic maps

Cannon, Ethalinda K [COM S]

Hello,


We are storing genetic maps at PeanutBase that are created from multiple species. Our favorite option at the moment is to attach the multiple species to the stock record for the mapping population via a new stock_organism linker table and leaving the field, stock.organism_id blank.


Alternatively, we have considered creating a genus-level organism record and using that for stock.organism_id (and potentially feature.organism_id, which is a required field), then attaching multiple species via our new stock_organism table.


Any better suggestions? Has anyone else out there had to deal with interspecific crosses?


Ethy



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Re: Interspecific genetic maps

Sook Jung
Hi Ethy,

Our databases (GDR, CGD, CottonGen,etc) stores genetic maps from interspecific crosses and we just use featuremap_organism table (which is one of our custom tables that we recently submitted to Scott to be included in the next version of Chdo). For the interspecific population stored in stock table, we just use organism id for 'spp.' as species. 'spp.' is commonly used for multispecies and 'sp.' is for single species (when exact species not known)..

I think we need to do something to directly store interspecific crosses to multiple species. We could create stock_organism table to store individual species and then store .spp for stock.organism_id but it could be confusing..

Cheers
Sook



On Wed, Mar 18, 2015 at 10:19 AM, Cannon, Ethalinda K [E CPE] <[hidden email]> wrote:

Hello,


We are storing genetic maps at PeanutBase that are created from multiple species. Our favorite option at the moment is to attach the multiple species to the stock record for the mapping population via a new stock_organism linker table and leaving the field, stock.organism_id blank.


Alternatively, we have considered creating a genus-level organism record and using that for stock.organism_id (and potentially feature.organism_id, which is a required field), then attaching multiple species via our new stock_organism table.


Any better suggestions? Has anyone else out there had to deal with interspecific crosses?


Ethy



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Re: Interspecific genetic maps

Cannon, Ethalinda K [COM S]

Hi Sook,


Thanks for the information!


I had originally planned to attach the multiple organisms to featuremap as you describe, but then decided it made more sense to attach it to the stock record for the mapping population, particularly for the synthetic crosses which come with lengthy descriptions.


But having both stock.organism_id and a stock_organism table seems confusing to me as well, hence our thought of creating a genus-level organism (perhaps similar to your .spp organism) for that field. But that is also confusing. 


We don't want to create organism records for each inter-species cross because they are often synthetic crosses between double haploids, so two different crosses between the same two parent species are likely to produce very different progeny. Also, there is no organism_relationship table, so there's currently no way to link the inter-species crosses back to their parent species. For these cases it makes more sense to have a 'derives-from' relationship between the mapping population and parent species.


Maybe store one species in stock.organism_id and additional ones in stock_organism? I'm not sure if I like that either....


Ethy



From: Sook Jung <[hidden email]>
Sent: Wednesday, March 18, 2015 9:56 AM
To: Cannon, Ethalinda K [E CPE]
Cc: [hidden email]
Subject: Re: [Gmod-schema] Interspecific genetic maps
 
Hi Ethy,

Our databases (GDR, CGD, CottonGen,etc) stores genetic maps from interspecific crosses and we just use featuremap_organism table (which is one of our custom tables that we recently submitted to Scott to be included in the next version of Chdo). For the interspecific population stored in stock table, we just use organism id for 'spp.' as species. 'spp.' is commonly used for multispecies and 'sp.' is for single species (when exact species not known)..

I think we need to do something to directly store interspecific crosses to multiple species. We could create stock_organism table to store individual species and then store .spp for stock.organism_id but it could be confusing..

Cheers
Sook



On Wed, Mar 18, 2015 at 10:19 AM, Cannon, Ethalinda K [E CPE] <[hidden email]> wrote:

Hello,


We are storing genetic maps at PeanutBase that are created from multiple species. Our favorite option at the moment is to attach the multiple species to the stock record for the mapping population via a new stock_organism linker table and leaving the field, stock.organism_id blank.


Alternatively, we have considered creating a genus-level organism record and using that for stock.organism_id (and potentially feature.organism_id, which is a required field), then attaching multiple species via our new stock_organism table.


Any better suggestions? Has anyone else out there had to deal with interspecific crosses?


Ethy



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Re: Interspecific genetic maps

Sook Jung
More thoughts below..

On Wed, Mar 18, 2015 at 11:58 AM, Cannon, Ethalinda K [E CPE] <[hidden email]> wrote:

Hi Sook,


Thanks for the information!


I had originally planned to attach the multiple organisms to featuremap as you describe, but then decided it made more sense to attach it to the stock record for the mapping population, particularly for the synthetic crosses which come with lengthy descriptions.

I think storing organism information for featuremap as well as for stock is useful since then we can query directly for genetic map or population that are associated with a specific species. 


But having both stock.organism_id and a stock_organism table seems confusing to me as well, hence our thought of creating a genus-level organism (perhaps similar to your .spp organism) for that field. But that is also confusing. 


We don't want to create organism records for each inter-species cross because they are often synthetic crosses between double haploids, so two different crosses between the same two parent species are likely to produce very different progeny. Also, there is no organism_relationship table, so there's currently no way to link the inter-species crosses back to their parent species. For these cases it makes more sense to have a 'derives-from' relationship between the mapping population and parent species.


I don't think I would create organism records for each inter-species cross but spp. is pretty commonly used to describe the situation (when we know it's cross-species but don't know exact parental species).  We name population with germplasm name, not species name (we use species name if germplasm name is not known), so we can trace back their parent using stock_relationship table. Citrus mapping population has quite complicated structure and we also use a naming scheme, used by breeders, that tells the cross scheme (e.g. Thong Dee/Pomeroy//Pomeroy-BC1). 


Maybe store one species in stock.organism_id and additional ones in stock_organism? I'm not sure if I like that either....


I don't know what else we can do... even though I don't really like it either :)
With type_id perhaps - to store the relationship like 'derives_from'??

Ethy



From: Sook Jung <[hidden email]>
Sent: Wednesday, March 18, 2015 9:56 AM
To: Cannon, Ethalinda K [E CPE]
Cc: [hidden email]
Subject: Re: [Gmod-schema] Interspecific genetic maps
 
Hi Ethy,

Our databases (GDR, CGD, CottonGen,etc) stores genetic maps from interspecific crosses and we just use featuremap_organism table (which is one of our custom tables that we recently submitted to Scott to be included in the next version of Chdo). For the interspecific population stored in stock table, we just use organism id for 'spp.' as species. 'spp.' is commonly used for multispecies and 'sp.' is for single species (when exact species not known)..

I think we need to do something to directly store interspecific crosses to multiple species. We could create stock_organism table to store individual species and then store .spp for stock.organism_id but it could be confusing..

Cheers
Sook



On Wed, Mar 18, 2015 at 10:19 AM, Cannon, Ethalinda K [E CPE] <[hidden email]> wrote:

Hello,


We are storing genetic maps at PeanutBase that are created from multiple species. Our favorite option at the moment is to attach the multiple species to the stock record for the mapping population via a new stock_organism linker table and leaving the field, stock.organism_id blank.


Alternatively, we have considered creating a genus-level organism record and using that for stock.organism_id (and potentially feature.organism_id, which is a required field), then attaching multiple species via our new stock_organism table.


Any better suggestions? Has anyone else out there had to deal with interspecific crosses?


Ethy



------------------------------------------------------------------------------
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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