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

[Chris Fields]

That is a good point, actually (as well as your earlier one re: how to determine whether a node is root or not), and is likely the reasoning Sendu used for doing this in the first place.  At the very least this behavior should be documented, though, as it is a little unexpected.

chris

On Jul 7, 2011, at 10:05 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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