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

[Christian M Zmasek]

Hi:
>
>
>
> I looked at BioPerl and this is what I could extract and understand 
> from documentation (I have almost no experience with Perl)
>
> Bio::Taxonomy:Node
>   * rank (species, genus, order etc)
>   * id (NCBI taxonomy id in most cases)
>   * parent_id (NCBI taxonomy id in most cases)
>   * genetic_code
>   * mitochondrial_genetic_code
>   * create_date (Date this node was created (in the database))
>   * update_date (Get/Set Date this node was updated (in the database))
>   * pub_date (Get/Set Date this node was published (in the database))
>   * scientific_name
>   * common_names []
This is almost a superset of what phyloxml has now.
With the exception that phyloxml has the (useful, but unloved?) "code" 
element for swiss-prot style mnomonics



>
> I don't think the create_date, update_date and pub_date are necessary 
> for our purposes, since it is database specific information, and if 
> you need it, then you can go to database and get it.
>
> I didn't found a taxonomy/taxon class in BioPython.
>
> Here is BioJava. Its taxon class represents taxonomy information at 
> NCBI database. BioSQL has almost identical taxon class.
>
> NCBITaxon Class
>   * acronym
>   * common name
>   * equivalent name
>   * genetic code
>   * hidden
>   * left value
>   * mitogeneticcode
>   * noderank
>   * parent
>   * rightvalue
>   * scientific name
>   * synonym
This seems to invite inconsitent use. What is the difference between 
"equivalent name" and "synonym"?
Similar to the BioPerl Taxonomy:Node, it has fields to store tree-like 
data (parent, rightvalue, etc.)

An interesting question related to this taxonomy issue is how to compare 
them. When are taxonomies considered equal?

--CZ