From: Kara D. <ka...@ge...> - 2005-03-22 21:05:54
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These elaborations look great to me. Unless there are objections expressed in the next couple of days, I'll put this implementation on the SGD to-do list. On Mar 22, 2005, at 3:44 PM, Lincoln Stein wrote: > 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/ >> >> ------------------------------------------------------- >> SF email is sponsored by - The IT Product Guide >> Read honest & candid reviews on hundreds of IT Products from real >> users. >> Discover which products truly live up to the hype. Start reading now. >> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >> _______________________________________________ >> Gmod-devel mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-devel > > -- > Lincoln Stein > ls...@cs... > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) |