[BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml support

[Christian M Zmasek]

Hi:

It's a great idea to look at TDWG's standards.
But to me, these standards seem designed specifically for collections in museums and, not surprisingly, biodiversity applications. For the purposes of comparative genomics and related fields, these taxonomy concepts seem a little bit overkill.
In my experience, taxonomy objects which can contain a scientific name, a common name, a mnemonic, and a (typed) identifier (which could be a Uniform Resource Name (URN) or a NCBI taxonomy id) are sufficient for most applications. This is pretty much what phyloXML's taxon element contains now. 
Of course, this does not mean that a potential taxonomy class in BioRuby has to follow the concept for phyloXML.

What do you think?

Christian





Hilmar Lapp wrote:
> On May 25, 2009, at 6:16 PM, Christian M Zmasek wrote:
>
>   
>> I propose a taxonomy class with the following elements:
>> -scientific name (e.g. Nematostella vectensis)
>> -common name (e.g. starlet sea anemone)
>> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
>> -rank (e.g. species)
>>
>> phyloxml also has a URI for taxonomies, but I am not sure if this is
>> important for a general taxonomy class.
>>
>> On the other hand, a general taxonomy class might also have
>> - authority (e.g. Stephenson, 1935)
>> - aliases []
>>
>> (if these elements are considered important, they of course could be
>> added to the next version of phyloxml)
>>     
>
>
> Note that there is the Taxonomic Concepts Transfer Schema as a  
> ratified TDWG standard, so if you really want to have a rich  
> representation of taxonomic entities or concepts I wouldn't try to  
> roll my own.
>
> http://www.tdwg.org/standards/117/
>
> For lightweight taxonomic designation, there are taxonomic elements in  
> Darwin Core:
>
> http://wiki.tdwg.org/DarwinCore
>
> 	-hilmar
>