[BioRuby] A Rails application with BioRuby

[Yen-Ju Chen]

On 12/19/07, Toshiaki Katayama <ktym at hgc.jp> wrote:
>
> Hi Yen-Ju,
>
> On 2007/12/19, at 6:54, Yen-Ju Chen wrote:
>
> > Hi,
> >  I am working on a rails application using BioRuby to collect references
> > and database entries.
> >  You can find the application (not source code yet) at
> > journalclub.reciprocallattice.com
>
> Cool.
>
>
> >  It is still at early stage. I use it personally and figure it would be
> > interesting to have more users.
> >  If you want to join, please write to me in private so that it will not
> > pollute BioRuby maillist.
> >  I don't know how many users the application can take. Please see the
> > website for more details.
> >
> >  These are things related to BioRuby,
> >  * The output from Reference to BibTex format lacks abstract.
> >  * It would be nice to be able to output to RIS format for EndNote and
> > ReferenceManager.
>
>
> If you could provide a patch for them, I'll include it in BioRuby.


  I will look at the RIS format and supply a patch later.

>  * Is it possible to get DOI from PubMed ?
>
>   entry = Bio::PubMed.query(16946072)
>   doi = entry[/AID - (\S+) \[doi\]/, 1]
>
>
> or you can extend the Bio::MEDLINE class to add the doi method



  Is it possible to have this feature in BioRuby ?
  I found DOI becomes more common recently, even PDB has DOI number.
  And it seems the only way to have a unique id on an article.
  For example, PubMed and Goggle Scholar may return the same article with
their own id (PMID and Google Scholar ID).
  I found it is only possible to compare the DOI to ensure two entries refer
to the same article.

  [snip]



> >  * BioRuby can get information from many databases through biofetch,
> >    but not processing them, like Pfam, Prosite, etc.
>
> You can process them by appropriate corresponding classes. For example,
>
>   cyclins = Bio::Fetch.query('prosite', 'PS00292')
>   prosite = Bio::PROSIE.new(cyclins)



  Thanx. I didn't notice PROSITE from BioRuby API before.
  Pfam is still missing.
  I will see what I can do about it.


>
>
> >  * it is not clear what's the database from biofetch, for example: rn,
> rp,
> > str, pr.
> >    I am in structural biology. Many of these abbreviation is not
> obvious.
>
> In BioRuby, the default BioFetch server is implemented as a proxy for the
> DBGET system through KEGG API.
> So, please refer to the abbreviation field in the DBGET manual at
>
>   http://www.genome.jp/dbget/



  That's a good tip.
  It would also be user-friendly to show them from BioRuby.

  Thanx for these information.

  Yen-Ju

and also note that the DBGET service for GenBank (gb) database is no longer
> available.
>
>
> Regards,
> Toshiaki Katayama
>
>
>
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