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

[Raoul JP Bonnal]

Christian M Zmasek ha scritto:
> I agree it is better to extend existing classes, as opposed to change 
> them drastically.
> One thing to keep in mind, is that many attributes are composed of 
> multiple fields themselves, i.e. you would need to create a class for 
> them (if such a class not already exists).
> The most important element besides sequence, is the taxonomy class.
>
> Since BioRuby does not contain a general purpose taxonomy class at 
> this point, it might be worth spending some time in designing such a 
> class.
>
> 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)
>
> What do people think about this?
How other langs represent that class ? I think that having the chance to 
define a new class there is the opportunity to define a similar api 
among bio-languages.
Then, taxonomy class could be used by biosequences objects 
representing/grabbing data from biosql for example.
http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/biosql-ERD.pdf

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Ra