[Gmod-resources] Re: [GMOD-devel] Common MOD URL for genome data?

[Aaron J. M. <am...@pc...>]

FYI, if/when a consensus is reached, the ApiDB databases (PlasmoDB, 
ToxoDB, CryptoDB, etc.) will follow suit.

I'd be happy with the virtual path based solution, and even happier if 
it was extended to include the possibility for different formats:

my.org/genome      # dna fasta, current version
my.org/genome/v4.4 # dna fasta, version 4.4

my.org/proteome/v4.3     # protein fasta, version 4.3
my.org/proteome/v4.3/gff # GFF of protein-encoding (CDS) features
my.org/proteome/gff/v4.3 # same, order shouldn't matter
my.org/v4.3/gff/proteome # same, ditto

I'd argue that "v4.3" and such strings be very "weakly typed", i.e. 
they're just tags that represent different instances of the dataset. 
This way I can also get:

my.org/proteome/gff/glimmerM/v4.3
my.org/proteome/gff/twinscan/v4.4

While this last bit looks hard, it actually isn't with the right Apache 
configuration ... but maybe this is overkill?  And it leaves open the 
problem of how would one find out what possible datasets/tags/formats 
are available (besides a separate download index HTML page) ... should 
my.org/proteome/list provide a flat list of available URLs?

-Aaron

Don Gilbert wrote:
> 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.
> 
> 
> 
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