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

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

Looks great, but I think we do need to have the species in the URL; also we've 
started keeping track of non-coding RNAs, and I think everyone will want to 
soon.  So how about the following elaborations?

 http://your.site/genome/
  leads to index page for species

 http://your.site/genome/Binomial_name/
  leads to index for releases for species
  Binomial_name

 http://your.site/genome/Binomial_name/release_name/
  leads to index for named release

 http://your.site/genome/Binomial_name/current/
  leads to index for current release

 http://your.site/genome/Binomial_name/current/dna
  leads directly to FASTA file containing big DNA fragments
  (e.g. chromosomes)

  http://your.site/genome/Binomial_name/current/mrna
    leads directly to FASTA file containing spliced
  mRNA transcript sequences
  
 http://your.site/genome/Binomial_name/current/ncrna
      leads directly to FASTA file containing non-coding
    RNA sequences

 http://your.site/genome/Binomial_name/current/protein
  leads directly to FASTA file for protein downloads

 http://your.site/genome/Binomial_name/current/feature
  leads directly to GFF3 file for feature downloads

Lincoln


On Wednesday 16 March 2005 10:14 am, Kara Dolinski wrote:
> Works for me!
>
> Is the idea we'd have a page like Don's
> (http://preview.flybase.net/genome/) that would serve as an
> index/description page, then have subdirectories that directly go to
> the data file of interest?
>
> For eg:
> genome/dna/
> directly to download page for chromosomes in fasta format
>
> genome/feature/
> (and/or genome/gff/)
> directly download GFF
>
> genome/protein/
> directly download protein sequences in fasta format
>
> genome/gene/
> (and/or genome/transcript/
> and/or genome/orf/)
> directly download DNA sequences of all genes in fasta format
>
> If this works for everyone, let's implement!
>
> -Kara
>
> On Mar 16, 2005, at 2:39 AM, Don Gilbert wrote:
> > Here is a flybase example
> > http://preview.flybase.net/genome/
> >
> > How close is this to what other MODs think should be a common
> > genome URL?
> >
> > - Don
> > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> > -- gil...@in...--http://marmot.bio.indiana.edu/
>
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-- 
Lincoln Stein
ls...@cs...
Cold Spring Harbor Laboratory
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