[Bioperl-l] Fwd: problem with bioperl (where's the Mus?)

[Hilmar Lapp]

On Aug 23, 2009, at 1:25 PM, Anand C. Patel wrote:

> The other piece of potentially useful information is below -- output  
> from
> SELECT * FROM `biosql`.`taxon_name` WHERE `taxon_id` = 138;
> (taxon_id 138 maps to ncbi_taxon_id 10090)
>
> taxon_id    name                            name_class
> 138         LK3 transgenic mice             includes
> 138         Mus muscaris                    misnomer
> 138         Mus musculus                    scientific name
> 138         Mus sp. 129SV                   includes
> 138         house mouse                     genbank common name
> 138         mice C57BL/6xCBA/CaJ hybrid     misspelling
> 138         mouse                           common name
> 138         nude mice                       includes
> 138         transgenic mice                 includes
>
> The source from the genbank entry NM_017474 is:
> SOURCE Mus musculus (house mouse)
>
> Which is why I think the issue is that the name_class is "genbank  
> common name" rather than common name.

Note that apparently NCBI has decided that the common name is 'mouse',  
not 'house mouse'. Why what they report in the genbank record is  
different from what they decided to be the common name is beyond me.

Note also that the common name in parentheses is optional. If it's  
missing the record is still in valid format.

> What does strike me as odd though is that not even "mouse" shows up  
> -- common_name is empty.

Indeed, that's odd. Can you file this as a bug report and assign to  
the bioperl-db queue?

	-hilmar
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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