[Gmod-resources] Common MOD URL for genome data?

[Don G. <gil...@bi...>]

Dear MOD folks,

Do you think we should arrange to have a common URL to locate genome
data?   The value to this is making it easier for anyone looking for
dna, protein, feature data for a given genome (or all of them).

Common urls would be something like this:
  my.org/genome?species=x [&version=y]   == dna fasta
  my.org/proteome?species=x ...    == protein fasta
  my.org/transcriptome? ...        == transcript fasta

and I guess add gff or include it as option above ?
  my.org/genomefeatures?...

I would vote for keeping the above options fairly simple, not
necessarily comprehensive for all possible data choices.
Also I'd suggest a common URL for information (e.g. a web page
that lists the particulars for a MOD).
  my.org/genomes/help  or equivalent
  
One can think of variants on the above:
  my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ...
The main thing is some agreement and folks who will
implement this.   

= Don Gilbert

From: Kara Dolinski <ka...@ge...>
| Thanks for the info, and thanks for the reminder about Lincoln's idea; 
| I had totally forgotten about it!  I think it's a great idea--it'd be 
| fabulous to have a standard URL to get these common files that we all 
| provide.  No matter how hard we all try, it is still pretty darn hard 
| to make it easy for people to navigate our ftp sites.  A 
| standard/common URL to get at least the basic files would do wonders.  
| I think beginning with DNA and protein fasta files for all ORFs + a gff 
| file would be a great start.
| 
| Should we send a message to a gmod list and see if we can decide on the 
| URL, then work on implementation?  Should be pretty straightforward to 
| do, I think....
| 
| -Kara

On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote:

>
> Kara,
>
> Find drosophila genome data including gff at 
> http://flybase.net/annot/#Data
> the gff section (for each of two species).
>
> Lincoln Stein thought we (mods) should all be serving bulk genome data 
> sets thru
> a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx,
> yeastgenome.org/genome/...).
> I don't recall what the specific url was, but if we all used the same 
> one, it would
> make it easier to find these things.
>
> Ah, notes help - October GMOD meeting - you were there also?
>  sample standard urls something like this:
>  my.org/genome?species=x [&version=y]   == dna fasta
>  my.org/proteome?species=x ...    == protein fasta
>  my.org/transcriptome? ...        == transcript fasta
>
> and I guess add gff or include it as option above ?
>  my.org/genomefeatures?...
>
> I'm not sure what options we would be expected to all support.