[BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml support
Christian M Zmasek
czmasek at burnham.org
Wed May 27 18:29:24 UTC 2009
Hi:
> (BTW you will also notice that there is
> nothing even close to the Swissprot "mnemonic" - nobody does this
> except Swissprot - whose chief business is protein annotation, not
> taxonomy - so you may want to consider how much significance you want
> to give this in your object model.)
>
Again, agreed. But in practice this "mnemonic" is very, very useful.
For example, it is a very handy way to create short protein
names/identifiers which still contain human readable species information
but are short enough the be used in a variety of alignment/phylogeny
reconstruction programs.
> As an aside, the name of a taxon really is a proxy for a taxon
> concept, whether that is a species or not, except that typically a
> taxon name isn't given in full (i.e., with author, year, and
> publication) to allow unambiguous identification. That's one of the
> reasons why taxon identifiers are key.
Indeed.
And the taxon concept is a "science" in itself....
> BTW NCBI taxon IDs are just one
> kind of taxon IDs. There are also Catalog of Life, ITIS, IPNI, and
> others.
>
Definitely. That's why the phyloxml taxonomy has a typed id.
Like so: <id type="ITIS">594569</id>.
--CZ
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