[Bioperl-l] Bio::DB::Taxonomy root not present

[Brian Osborne]

is_root(), or the equivalent?


On Jul 7, 2011, at 11:05 PM, Hilmar Lapp wrote:

> Right, but do you agree that looking for the label 'root' shouldn't be the only way to identify it?
> 
> 	-hilmar
> 
> On Jul 7, 2011, at 10:17 PM, Brian Osborne wrote
> 
>> Hilmar,
>> 
>> Instead of addressing the side issues address what I named as the most salient issue: if we base this module's behaviour on NCBI's taxonomy - and all data says this module should mirror NCBI's taxonomy - then a node called "root" should exist since it exists in NCBI's data files. Right?
>> 
>> BIO
>> 
>> On Jul 7, 2011, at 6:28 PM, Hilmar Lapp wrote:
>> 
>>> 
>>> On Jul 7, 2011, at 3:22 PM, Brian Osborne wrote:
>>> 
>>>> It's also true that having 5 trees instead of 1 is incorrect scientifically
>>> 
>>> That's a strong statement and I'm not sure I agree with this - let's keep in mind that these are taxonomies, not phylogenetic trees of all of life. Not every taxonomy has a node for "all of life" or for LUCA. For example, ITIS, one of the most widely used taxonomies if you're not dealing strictly with molecular data, does not - there is one "tree" for each kingdom of life. (Not that I want to recommend that as a good thing.)
>>> 
>>> I agree with your programming awkwardness argument, though I would add  that looking for a specific label of a node to identify the root is always a bad (because fragile) thing to do. A better way to identify a root node would be parent undefined, or being the same as the node itself. If the code did that for each the 5 or so children of 'root', then the fake root could be removed.
>>> 
>>> At the very least code in Bio::DB::Taxonomy or anywhere else should not assume that there is a single root for a taxonomy. Because there are taxonomies for which this really isn't the case.
>>> 
>>> 	-hilmar
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
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>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
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> 
> 
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