[BioRuby] URL Generation in Bioruby

[Pjotr Prins]

Looks fine to me, I can add URLs for NCBI GEO access - Naohisa, what 
do you think?

Pj.

On Tue, Oct 14, 2008 at 03:51:40PM +1100, Ben Woodcroft wrote:
> Thanks for the encouragement. I've made an initial attempt at integrating
> URL generation into BioRuby. I've made it available as my 'url' branch,
> which is available at
> 
> http://github.com/wwood/bioruby/tree/url
> 
> Is this what you had in mind or am I misunderstanding you?
> 
> Thanks,
> ben
> 
> 2008/10/11 Pjotr Prins <pjotr2008 at thebird.nl>
> 
> > We could have a mixin module with methods that generate all different
> > URLs in a central location. I think that is a good idea.
> >
> > Pj.
> >
> > On Sat, Oct 11, 2008 at 09:28:47AM +1100, Ben Woodcroft wrote:
> > > Thanks for your response. I would have thought the fact that they change
> > is
> > > more reason to include it - not less.
> > >
> > > Is that database you speak of freely available? Just as part of the AceDB
> > > download?
> > >
> > > Thanks,
> > > ben
> > >
> > > 2008/10/10 Michael Han <mh6 at sanger.ac.uk>
> > >
> > > >
> > > > On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
> > > >
> > > > Hi list,
> > > >
> > > > A common thing I find myself doing is to 'linkout' to other databases.
> > For
> > > > instance, I have a PDB id and I want to link to the corresponding
> > record in
> > > > pdb.org. Right now, I would have to go to the pdb site and try to
> > reverse
> > > > engineer it. In the past I've even had to email the webmasters for more
> > > > information. It seems to me this is a duplication of effort, and so
> > > > class(es) to collect this information for me might have a place in
> > BioRuby.
> > > >
> > > > Does this sound reasonable to anyone? Is there any precendents out
> > there?
> > > > What might be a good way to structure the code?
> > > >
> > > > Thanks,
> > > > ben
> > > >
> > > > --
> > > > FYI: My email addresses at unimelb, uq and gmail all redirect to the
> > same
> > > > place.
> > > > _______________________________________________
> > > > BioRuby mailing list
> > > > BioRuby at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/bioruby
> > > >
> > > >
> > > > Hi Ben,
> > > >
> > > > what we did is save URL constructors in an database object in a sprintf
> > > > style, which is in turn used by the xref objects linked to
> > > > genes/proteins/etc.
> > > > Anyway I am not sure if it is a good idea to put it in the bioruby
> > library,
> > > > as when you have a couple of dozens of different database, you can be
> > sure
> > > > that one URL will change every few days/weeks, so it is a hassle to
> > keep all
> > > > of them up-to-date.
> > > > Michael
> > > > ---------------------------------------
> > > >   oo Wormbase Group, Sanger Institute
> > > >   |  The Wellcome Trust Genome Campus,
> > > >   |  Hinxton, Cambridge, CB10 1HH, UK.
> > > >   |  Tel.: +44 (0)1223 49 6869
> > > > --'
> > > >
> > > >
> > > >
> > > >
> > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research
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> > company
> > > > registered in England with number 2742969, whose registered office is
> > 215
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> > > >
> > >
> > >
> > >
> > > --
> > > FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> > > place.
> > > _______________________________________________
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> > > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> 
> 
> 
> -- 
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.