Organism table unique constraint

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Organism table unique constraint

Naama Menda
is there a reason why the unique constraint in the organism table is on (genus, species) ? 
Shouldn't the species name be unique ? (assuming the full species name is loaded e.g. genus = 'Solanum' species = 'Solanum lycopersicum' ) 

thanks!
-naama


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

(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
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Re: Organism table unique constraint

Josh Goodman
Hi Naama,

I believe that the original Chado creators were assuming that the binomial name would be deconstructed when stored in the organism table. 

e.g. genus = 'Solanum' and species = 'lycopersicum'

The constraint then enforces the uniqueness of the scientific name (genus + species).  This makes complete sense from a database design point of view in terms of reducing redundancy.  It is less clear from the biological point of view and I could see where it might lead to different interpretations.

At FlyBase we follow the genus = 'Solanum' and species = 'lycopersicum' model.

$ psql -h flybase.org -U flybase -c "select abbreviation,genus,species from organism where genus='Drosophila' limit 15;" flybase
 abbreviation |   genus    |           species          
--------------+------------+-----------------------------
 Dmel         | Drosophila | melanogaster
              | Drosophila |
 Dere         | Drosophila | erecta
 Dgri         | Drosophila | grimshawi
 Dmoj         | Drosophila | mojavensis
 Dper         | Drosophila | persimilis
 Dsec         | Drosophila | sechellia
 Dwil         | Drosophila | willistoni
 Dyak         | Drosophila | yakuba
 Dpse         | Drosophila | pseudoobscura pseudoobscura
 Dbuz         | Drosophila | buzzatii
 Dsim         | Drosophila | simulans
 Dana         | Drosophila | ananassae
 Dvir         | Drosophila | virilis
 Dtak         | Drosophila | takahashii
 Dleb         | Drosophila | lebanonensis
 Dtsa         | Drosophila | tsacasi


Cheers,
Josh


On Thu, Mar 1, 2012 at 2:41 PM, Naama Menda <[hidden email]> wrote:
is there a reason why the unique constraint in the organism table is on (genus, species) ? 
Shouldn't the species name be unique ? (assuming the full species name is loaded e.g. genus = 'Solanum' species = 'Solanum lycopersicum' ) 

thanks!
-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]

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
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