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Nine eukaryote proteomes have been aligned to the D. pulex genome, with help from Daphnia Genomics Consortium, TeraGrid and Generic Model Organism Database projects. A focus of this is to assess feasibility of using shared cyberinfrastructure like TeraGrid for the genome database community. So far the stumbling blocks seem surmountable, and the question will be to see if we can make this easy and compelling enough so that genomicists from such as Daphnia Genomics Consortium can pick a new genome data set to run their BLAST (or other) analysis using TeraGrid. My question for the GMOD group: is this the sort of shared-need that new and old organism genome databases would like tools and support for? E.g., a Teragrid Science Gateway project http://www.teragrid.org/programs/sci_gateways/ could offer scheduled times to run large cross-species comparisons, grid-aware bioinformatics tools, and provide access to shared genome data sets for analyses. ..................... The D.pulex genome is a 4x preliminary assembly available to Daphnia Genomics Consortium. The nine proteomes, with 217,006 total protein sequences, are drawn from organism genome databases, Ensembl and NCBI. Alignment is done using NCBI tBLASTn, with a Grid-aware version of NCBI software developed at IU, and run on the TeraGrid. The TeraGrid run for this took 12 hours using 64 processors. Blast output is converted to scaffold locations, and displayed for browsing and seaching in GMOD GBrowse genome maps. Find sample map snapshots at http://wfleabase.org/maps/dpgenomesample/ The full genome annotation map is available to DGC members, and to everyone at public release of this genome. - Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gil...@in...--http://marmot.bio.indiana.edu/
On Sat, 2005年05月14日 at 12:48 -0500, Don Gilbert wrote: > Scott, > > This looks good. I have a small set of software for this that I'd add if you > like, see at http://preview.flybase.net/genome/server-software/ > > However, I lack the karma: > **** Access denied: Insufficient Karma (dongilbert|standard-urls/genomeurl-sample|) Whoops! Typo: I had a _ instead of a -. Should be fixed now. > > -- Don -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory
Scott, This looks good. I have a small set of software for this that I'd add if you like, see at http://preview.flybase.net/genome/server-software/ However, I lack the karma: **** Access denied: Insufficient Karma (dongilbert|standard-urls/genomeurl-sample|) -- Don
Hello, I created a new gmod cvs reposotory call standard-urls for tools written by Todd Harris for easily setting up the standard download URLs discussed on these lists over the last few months. It is fairly straight forward and should be generic, as well as having documentation. Please check it out and let's hear about your experiences: cvs -d:ext:use...@cv...:/cvsroot/gmod co standard-urls or anonymously: cvs -d:pserver:ano...@cv...:/cvsroot/gmod login cvs -d:pserver:ano...@cv...:/cvsroot/gmod co standard-urls Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory
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年04月11日 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
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
> 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.
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
Lincoln, This standard_urls.txt looks good to me. On the question of species spelling variants, this is where I don't see an answer that is best for all, esp. for being easy to figure out/guess by the people who will use this (including people not conversant in species spellings, taxonomy ids, etc., and lazy programmers like myself :). My suggestion for a species-less variant is what would make more sense to me, to keep it very simple, but I'm agreeable to whatever you all prefer. - Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gil...@in...--http://marmot.bio.indiana.edu/
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
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>
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.
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.
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.
Hi subscribers to the gmod resources mailing list, Sorry about the backlog of mail that was hung up waiting for me to approve it. Either sourceforge has decided to stop sending messages that there are things waiting or the were getting caught up in a spam filter somewhere. Hopefully I've rectified it by changing the address that the messages should go to. Meanwhile, enjoy the 12 tardy messages that came in this morning :-) Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory
On Tue, 2005年03月22日 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
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ドル 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
> > 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
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)
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
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)
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)
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/
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/
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.