[Bioperl-l] Bio::*Taxonomy* changes

[Hilmar Lapp]

I don't think we should differ from NCBI in places where the  
connection between a method name and the NCBI data file is obvious or  
otherwise we will confuse people and send them into traps.

$node->scientific_name() should simply report what NCBI reports. For  
simple species this will be identical to what $node->binomial()  
returns, but for others it may not, e.g., strains, varieties, etc or  
the weird world of viri and bacteria.

This will also absolve us from retaining the business logic for how  
to construct the scientific name from genus, species, and possibly  
strain or whatever.

binomial() isn't part of the NCBI taxonomy definition, so you have  
freedom there to report what suits you.

	-hilmar

On Jul 17, 2006, at 5:33 PM, Sendu Bala wrote:

> Chris Fields wrote:
>> There was some interest in getting Bio::Species to delegate to
>> Bio::Taxonomy::Node, so having scientific_name() would help quite  
>> a bit
>> since the name used on the ORGANISM line is the scientific name  
>> (well, is
>> supposed to be; famous last words).
>
> Can you clarify exactly what you mean here? Preferably with an  
> example?
> ORGANISM line of which file format?
> The reason I ask is that I still feel we need to do parsing of the  
> names
> for species rank and lower:
>
> # The 'scientific name' for humans could be considered to be 'Homo  
> sapiens'.
> # Taxid 9606 in the NCBI taxonomy database has rank 'species' and
> ScientificName 'Homo sapiens'.
> # For sanity, Bio::*Taxonomy* likes to interpret this  
> ScientificName as
> 'sapiens' so that the genus is not held redundantly. It provides a
> binomial() method to give you 'Homo sapiens' again if you want it.
> # I plan on maintaining this; scientific_name() would give you the
> non-redundant sibling-unique name 'sapiens'. binomial() on a species
> rank and lower would give you 'Homo sapiens' (presumably grabbing the
> 'Homo' from the parent node with rank 'genus', or similar).
>
> Good, bad or ugly? I would prefer it works like this and we agree to
> differ with NCBI on what the 'scientific name' of a species node  
> should
> be. Bio::Species can still delegate to Bio::Taxonomy::Node by calling
> binomial() (which I propose will actually give the correct answer,  
> even
> for bacteria and viruses).
>
> Perhaps the short-hand (and the classifier used in name()) shouldn't
> mention the word 'scientific' to avoid confusion? But a) what else  
> would
> we call it?, and b) for all ranks above species it /is/ the  
> scientific name.
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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