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From: Don G. <gil...@bi...> - 2005-03-07 20:54:16
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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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From: Don G. <gil...@bi...> - 2005-03-16 07:39:44
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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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From: Kara D. <ka...@ge...> - 2005-03-16 15:14:44
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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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From: Lincoln S. <ls...@cs...> - 2005-03-22 20:45:09
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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)
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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) |
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From: Aaron J. M. <am...@pc...> - 2005-03-22 21:13:25
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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 |
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From: Lincoln S. <ls...@cs...> - 2005-03-23 00:22:15
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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) |
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From: Aaron J. M. <am...@pc...> - 2005-03-23 13:35:15
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I agree completely. But I thought that "compliance" with any of this spec was purely optional; that is, nobody guarantees to support all datatypes/indices/formats (punishable by ... ?) Thus, I was merely trying to flesh out the likely areas of feature creep. Any unsupported URLs should probably return 404 Not Found. And yes, RSS for the index is exactly what I had in mind. For ApiDB-umbrella databases, Don's default genome/dna url may be difficult to do right (e.g. for PlasmoDB, there are 5 species; you might argue falciparum is the "default", but in other cases this might not be so clear). I advocate that the "spec" should specify the binomial name (as defined by the NCBI Taxonomy scientific name, e.g. Giardia intestinalis, not Giardia lamblia or Giardia duodenalis). Talk about feature creep, if /xml/ was a valid elaborator for features, you could then imagine further appended XPath queries to filter the dataset, leading to a technologically cheap queryable data warehouse (given an agreeable DTD, presumably ChadoXML ??) -Aaron On Mar 22, 2005, at 7:21 PM, Lincoln Stein wrote: > 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) > > > ------------------------------------------------------- > This SF.net email is sponsored by: 2005 Windows Mobile Application > Contest > Submit applications for Windows Mobile(tm)-based Pocket PCs or > Smartphones > for the chance to win $25,000 and application distribution. Enter > today at > http://ads.osdn.com/?ad_id=6882&alloc_id=15148&op=click > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel > -- 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 |
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From: Scott C. <ca...@cs...> - 2005-03-23 13:50:10
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On Tue, 2005-03-22 at 19:21 -0500, Lincoln Stein wrote: > This will let people receive updates on their > iPods when new genomic data is available. > Excellent Idea :-) -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Lincoln S. <ls...@cs...> - 2005-03-23 15:19:38
Attachments:
standard_urls.txt
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Ok, how does this look as the basis for a document that we can post at the Sequence Ontology and/or GMOD web sites? Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen <mic...@cs...> on all emails regarding scheduling and other time-critical topics. |
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From: Kara D. <ka...@ge...> - 2005-03-23 16:04:19
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Looks great to me, and I like the B_name idea (vs. Binomial_name). Less tricky typing is good. One suggestion on the doc, from a previous point on this thread: we might want to explicitly have a note for MODs that do not yet provide all file types, something like: If your MOD does not yet provide a particular file type in this specification, then the URL for the unsupported file type should return a 404 Not Found (or text that states "This file is not yet available for this MOD" or whatever behavior people think is most useful).... I think this will be a common question that will come up. On Mar 23, 2005, at 10:19 AM, Lincoln Stein wrote: > Ok, how does this look as the basis for a document that we can post at > the Sequence Ontology and/or GMOD web sites? > > Lincoln > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > > NOTE: Please copy Sandra Michelsen <mic...@cs...> on > all emails regarding scheduling and other time-critical topics. > <standard_urls.txt> |
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From: Aaron J. M. <am...@pc...> - 2005-03-23 16:13:00
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I like B_name too, but I'd suggest it might be a synonym for the
Binomial_name; NCBI Taxonomy IDs might also be valid synonyms.
Also, we're going to run into subspecies/isolate issues, e.g.
Plasmodium_falciparum_3D7 vs. Plasmodium_falciparum_DD2. In this case,
I'd think that
http://your.site/genome/P_falciparum/releases/
might provide the index/RSS for all isolates, pointing to fully-named
directories:
http://your.site/genome/P_falciparum_3D7/v4.4/dna
And perhaps 501 Not Implemented is better than 404 Not Found?
Todd, are you planning on implementing these handlers as part of the
Bio::GMOD toolkit?
-Aaron
On Mar 23, 2005, at 11:02 AM, Kara Dolinski wrote:
> Looks great to me, and I like the B_name idea (vs. Binomial_name).
> Less tricky typing is good.
>
> One suggestion on the doc, from a previous point on this thread: we
> might want to explicitly have a note for MODs that do not yet provide
> all file types, something like:
>
> If your MOD does not yet provide a particular file type in this
> specification, then the URL for the unsupported file type should
> return a 404 Not Found
> (or text that states "This file is not yet available for this MOD" or
> whatever behavior people think is most useful)....
>
> I think this will be a common question that will come up.
>
> On Mar 23, 2005, at 10:19 AM, Lincoln Stein wrote:
>
>> Ok, how does this look as the basis for a document that we can post at
>> the Sequence Ontology and/or GMOD web sites?
>>
>> Lincoln
>>
>> --
>> Lincoln D. Stein
>> Cold Spring Harbor Laboratory
>> 1 Bungtown Road
>> Cold Spring Harbor, NY 11724
>>
>> NOTE: Please copy Sandra Michelsen <mic...@cs...> on
>> all emails regarding scheduling and other time-critical topics.
>> <standard_urls.txt>
>
>
--
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
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From: Adrian R. T. <ar...@sa...> - 2005-03-23 19:46:41
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Lincoln Stein wrote: >Ok, how does this look as the basis for a document that we can post at >the Sequence Ontology and/or GMOD web sites? > >Lincoln > > Hi, We'd be happy to implement this for GeneDB. A few comments: a) I'd agree with Aaron J. Mackey that we need to be able to distinguish between different strains/isolates. b) Presumably binomial name extends to trinomial name as necessary ie we need to distinguish Trypanosoma_brucei_gambiense from our other trypanosoma species. c) I'll admit to no detailed knowledge of writing RSS but it sounds a confusing world (The myth of RSS compatibility, http://diveintomark.org/archives/2004/02/04/incompatible-rss)! Is it worth specifying a version sooner rather than later, or are the differences not great in practice? Adrian |
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From: Lincoln S. <ls...@cs...> - 2005-04-05 16:49:42
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> b) Presumably binomial name extends to trinomial name as necessary > ie we need to distinguish Trypanosoma_brucei_gambiense from our > other trypanosoma species. Sure, let's extend the convention to subspecies, strains and isolates. =20 I still like shortening the genus name. What do you think? T_brucei_gambiense_gambiense_isolate0392 > c) I'll admit to no detailed knowledge of writing RSS but it sounds > a confusing world (The myth of RSS compatibility, > http://diveintomark.org/archives/2004/02/04/incompatible-rss)! Is > it worth specifying a version sooner rather than later, or are the > differences not great in practice? RSS version 1 is easier to deal with and seems to be more broadly=20 supported. Lincoln =2D-=20 Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen <mic...@cs...> on all emails regarding scheduling and other time-critical topics. |
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From: Adrian R. T. <ar...@sa...> - 2005-04-11 13:40:04
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Lincoln Stein wrote: >>b) Presumably binomial name extends to trinomial name as necessary >>ie we need to distinguish Trypanosoma_brucei_gambiense from our >>other trypanosoma species. >> >> > >Sure, let's extend the convention to subspecies, strains and isolates. >I still like shortening the genus name. What do you think? > > T_brucei_gambiense_gambiense_isolate0392 > > > Sorry, I've been on holiday. Yep, sounds fine to us. Adrian |
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From: Scott C. <ca...@cs...> - 2005-04-11 14:36:26
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Hi All, I'm glad Adrian sent this because it reminded me: would anybody be willing to summarize what has been agreed to and what outstanding issues there are with this for the GMOD meeting next month? Thanks, Scott On Mon, 2005-04-11 at 14:39 +0100, Adrian Roy Tivey wrote: > Lincoln Stein wrote: > > >>b) Presumably binomial name extends to trinomial name as necessary > >>ie we need to distinguish Trypanosoma_brucei_gambiense from our > >>other trypanosoma species. > >> > >> > > > >Sure, let's extend the convention to subspecies, strains and isolates. > >I still like shortening the genus name. What do you think? > > > > T_brucei_gambiense_gambiense_isolate0392 > > > > > > > Sorry, I've been on holiday. Yep, sounds fine to us. > > Adrian > > > > > > ------------------------------------------------------- > 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 > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
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From: Don G. <gil...@bi...> - 2005-03-23 02:27:34
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> > http://your.site/genome/Binomial_name/current/dna > > leads directly to FASTA file To be clear, I take this to mean it should always be a http stream of FastA data, not a redirect to ftp:// file or other http:path, for programmability. Likewise for other endpoints. I assume gzip compression is allowed when browser/client accepts that. This sounds good to me. I'd also like to ask if we should also support the simpler case which will work for many people who want the primary species, most current data: http://your.site/genome/dna Not as critical if everyone supports a /genome/ index page. - Don |
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From: Lincoln S. <ls...@cs...> - 2005-03-23 15:00:35
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Hi, Actually, I don't see any reason that it can't be a redirect to an=20 ftp:// URL. Most Java and Perl client libraries that I'm aware of=20 will automatically follow the redirects. Lincoln On Tuesday 22 March 2005 09:27 pm, Don Gilbert wrote: > > > http://your.site/genome/Binomial_name/current/dna > > > leads directly to FASTA file > > To be clear, I take this to mean it should always be a http > stream of FastA data, not a redirect to ftp:// file or other > http:path, for programmability. Likewise for other > endpoints. I assume gzip compression is allowed when > browser/client accepts that. > > This sounds good to me. I'd also like to ask if we should > also support the simpler case which will work for many > people who want the primary species, most current data: > > http://your.site/genome/dna > > Not as critical if everyone supports a /genome/ index page. > > - Don =2D-=20 Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen <mic...@cs...> on all emails regarding scheduling and other time-critical topics. |
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From: Lincoln S. <ls...@cs...> - 2005-03-23 15:04:31
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One last question before we "go gold" on the first phase of this=20 scheme. What do people think about replacing full Binomial_name with=20 B_name, e.g.: D_melanogaster G_intestinalis I bring this up only because my favorite organism, Caenorhabditis, is=20 hard to spell! Lincoln On Tuesday 22 March 2005 09:27 pm, Don Gilbert wrote: > > > http://your.site/genome/Binomial_name/current/dna > > > leads directly to FASTA file > > To be clear, I take this to mean it should always be a http > stream of FastA data, not a redirect to ftp:// file or other > http:path, for programmability. Likewise for other > endpoints. I assume gzip compression is allowed when > browser/client accepts that. > > This sounds good to me. I'd also like to ask if we should > also support the simpler case which will work for many > people who want the primary species, most current data: > > http://your.site/genome/dna > > Not as critical if everyone supports a /genome/ index page. > > - Don =2D-=20 Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen <mic...@cs...> on all emails regarding scheduling and other time-critical topics. |
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From: Aaron J. M. <am...@pc...> - 2005-03-07 21:34:02
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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 > > > ------------------------------------------------------- > 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 |
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From: Lincoln S. <ls...@cs...> - 2005-03-07 23:03:37
Attachments:
standard_urls.txt
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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 > > > > > > ------------------------------------------------------- > > 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 > > ------------------------------------------------------- > 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 D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen <mic...@cs...> on all emails regarding scheduling and other time-critical topics. |
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