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

[Diana Jaunzeikare]

On Wed, May 27, 2009 at 2:41 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> 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
>


What about treating "code" element as id, but with type "swiss-prot".


> 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
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