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

[Chris Fields]

Hence the reason to have it be a hybrid of Bio::Species and  
Tax::Node.  Bio::SeqIO::genbank works very happily with the current  
Bio::Taxonomy::Node now; if we intend to remove most of the method we  
need to have a similar DB-aware module to house the flatfile data  
(like Bio::Species) yet be capable of working with Bio::Taxonomy  
(like Tax::Node).

As for organelle(), that could be made into something else  
(Bio::Annotation::SimpleValue or similar) but as it's always been  
included with the tax data, that's where it has been.  The TaxID in  
the 'source' seqfeature doesn't refer to the organelle but the organism.

Chris

On Jul 24, 2006, at 7:31 AM, Hilmar Lapp wrote:

> Sounds good to me, except there is no Bio::TaxonomyI yet, and also
> Bio::Species shouldn't fully depend on an internet connection or flat
> file to do anything meaningful.
>
> I.e., it should take advantage of a lookup database if there is one,
> but in the absence of that one should also be able to statically set
> attribute values to whatever one thinks can be gleaned from a parsed
> text or whatever.
>
> 	-hilmar
>
> On Jul 24, 2006, at 4:21 AM, Sendu Bala wrote:
>
>>> I think this would be the way to go. I.e.,
>>>
>>>
>>>           |------Node
>>> NodeI----|
>>>           |-|
>>>             |----SpeciesNode
>>> Species----|
>>
>> Actually, if we're changing the name of the module that Species
>> interacts with, any existing code needs to be re-written. So why not
>> just do it properly and have Bio::Species interact with  
>> Bio::Taxonomy?
>>
>>                    |----Bio::Taxonomy
>> Bio::TaxonomyI----|
>>                    |----Bio::Species
>>
>> Or
>>
>> Bio::TaxonomyI----|----Bio::Taxonomy----|----Bio::Species
>>
>> Leaving Node completely free to be just a node. This way we don't
>> have a
>> crufty SpeciesNode there simply for the sake of Bio::Species.
>> Bio::Species itself provides all the legacy stuff it needs for  
>> itself,
>> while interacting with Nodes via TaxonomyI methods in the 'correct'
>> way
>> only.
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign