From: Lincoln S. <ls...@cs...> - 2005-03-23 00:22:13
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I like the idea of elaborators, but let's keep it simple for the time being. I want people to implement this, and I know that if it gets much more complicated, I'll be one of the laggards. Another thing to think about is whether we can use RSS format as an alternative to the index pages. This will let people receive updates on their iPods when new genomic data is available. Lincoln On Tuesday 22 March 2005 04:13 pm, Aaron J. Mackey wrote: > Looks great, count us (ApiDB.org) in too ... > > Do the index pages have a specified (i.e. parsable) format? Perhaps > /format/ can be a generic trailing argument for any url to specify > /xml/ or /fasta/ or /genbank/, etc? > > -Aaron > > 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) > > -- > Aaron J. Mackey, Ph.D. > Dept. of Biology, Goddard 212 > University of Pennsylvania email: am...@pc... > 415 S. University Avenue office: 215-898-1205 > Philadelphia, PA 19104-6017 fax: 215-746-6697 -- Lincoln Stein ls...@cs... Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) |