[BioRuby] Bio::Fetch and EBI dbfetch

[Hamish McWilliam]

Hi folks,

The recent update to the EBI's dbfetch service
<http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010>
adds support for the BioRuby biofetch meta-information methods and
means that the Bio::Fetch documentation
<http://bioruby.org/rdoc/classes/Bio/Fetch.html> needs to be updated.
The databases(), formats() and maxids() methods are now supported by
the EBI service as well as biofetch. For full details of the extended
syntax supported by dbfetch see
http://www.ebi.ac.uk/Tools/dbfetch/syntax.jsp.

Another thing I notice is that Bio::Fetch does not set a user-agent,
so no trace of BioRuby appears in the service logs. I'm not sure what
the most appropriate user-agent would be, something like
"BioRuby/1.1.0 Ruby/1.8.6" would probably do, but the maybe a module
specific style user-agent as used by BioPerl would be better (e.g.
"Bio::DB::RefSeq/0.8" or "bioperl-Bio_DB_RefSeq/1.4")?

All the best,

Hamish
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