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

[Chris Fields]

On Aug 24, 2009, at 12:16 PM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>>>
>>> ...
>> This points to a problem in Bio::Species::scientific_name(), given  
>> that binomial() is correct. Could you file this as a bug report?
>
> What code creates the Bio::Species object here? I suspect this code  
> isn't aware of changes in Bio::Species since BioPerl 1.5.2.

I think it's bioperl-db-related.  You've previously pointed out the  
incongruity bioperl-db has with Bio::Species in a bug report (I  
indicated that in a separate post to this thread).

>>> The common name is missing, despite having loaded it from NCBI  
>>> taxonomy using the provided script.
>>> It is ONLY present as this "genbank common name".
>>> [...]
>>> I could go through and replace all of the instances of "genbank  
>>> common name" with "common name" and see if this fixes it.
>> I think we need to first discuss how we want to treat the 'common  
>> name' versus 'genbank common name' classes in BioPerl.
>> So question for everyone: do we need to have both available (in  
>> which case we need to add an accessor in Bio::Species), or only  
>> 'common name', or should 'genbank common name' override 'common  
>> name' if both are present and have different values.
>
> Bio::Species (via Bio::Taxon) has the common_names() method, for  
> which common_name() is an alias that in scalar context returns the  
> first of possibly many common names, one of which may be the genbank  
> common name.
>
> See:
> http://www.bioperl.org/wiki/Core_1.5.2_new_features#Implementation_changes

Yes, but that method stored names in an array and removes the context,  
presumed or not.  If there are two or more, which names correspond to  
common_name, which to genbank_common_name (and which should we prefer)?

chris