[Gmod-resources] Re: [GMOD-devel] Common MOD URL for genome data?

[Lincoln S. <ls...@cs...>]

Hi Folks,

Enclosed are my ideas about standard MOD URLs -- I think I wrote this 
way back in September 2004 and distributed it to the wormbase and 
gmod lists.

I like the various proposed extensions under genome/ (feature/dna, 
etc) .  I'm not so happy with providing both singular and plural 
forms, though.  It's a good principle to enforce a direct 
correspondence between a URL-based ID and the data content.

Lincoln

On Monday 07 March 2005 04:32 pm, Aaron J. Mackey wrote:
> in your example URL's, "my.org/genome(s)/..."
>
> Is this just to denote the special "data dump" section of the
> website? And if so, isn't there a more specific word to be used
> (e.g. "data" or "access" or "download" or such)?
>
> Also, I think the whole must/may criteria is moot.  Everything is
> "may", there's nothing I "must" do ;)
>
> some additional paths to possibly provide:
>
> /help    # Don's suggested default "index" page
> /version # Todd's suggestion of current release version
> /listing # a tab-delim list of available data, in various versions,
>           # species and formats
>
> My vote for common options:
>    version
>    species (by scientific name, by taxon id, ?)
>    format (default FASTA or GFF, as apropos)
>
> And I realize my URL path syntax for specifying options is just
> candy coating over the CGI GET syntax, but I think that cleaner
> URLs are generally more humanly robust for memorization and
> publication.  We'll follow the community "spec" (whatever it is),
> but will likely implement the URL path syntax also (if necessary).
>
> I also agree that we should provide both singular and plural forms
> of URL paths for convenience.
>
> -Aaron
>
> Don Gilbert wrote:
> > Todd, others,
> >
> > Sounds like there is general support.  For specifics, my own
> > quick thoughts are it would be easier, maybe better, to start
> > with one top level folder, and put the options off of that, with
> > some "MUST" options, and many "MAY" options.  I would probably
> > prefer this sort of organization:
> >
> >   my.org/genome{s}/
> >     -- return information/help page with links, MUST offer
> >    { plurals are tricky - do people remember them? }
> >   my.org/genome/dna  == return full genome dna in fasta format
> >          genome/genome == alias to /dna
> >   my.org/genome/protein{s} == return " proteins in fasta
> >          genome/proteome  == alias to proteins
> >   my.org/genome/transcript{s} ==  transcripts in fasta
> > 	 genome/transcriptome  == alias to transcripts
> >   my.org/genome/feature{s} ==  features in GFF
> >          genome/gff  == alias to features
> >
> >    -- other options as people want to support them
> >        genome/versions/ ...
> >        genome/species/ ..
> >    -- and/or use CGI options for these "?species=x&version=y"
> >
> > But we should decide what good common terms above and option
> > names are.
> >
> > -- Don
> >
> >
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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