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.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
------------------------------------------------------------------------------
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.
http://www.accelacomm.com/jaw/sfnl/114/51521223/_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Locked
