[BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml support
Diana Jaunzeikare
rozziite at gmail.com
Thu May 28 02:49:58 UTC 2009
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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