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

[Todd H. <ha...@cs...>]

Hi Don - 

I definitely think the MODs should implement this as discussed at the last
meeting.  Currently, WormBase uses an Apache handler to map URLs to files --
or if need be, database dump scripts.

Currently, we have
    /genome
    /proteome
    /transcriptome
    /laboratories   // a list of labs and IDs, admittedly worm specific

When appropriate, URLs also accept a "species=" parameter.

I'd also like to suggest two additional URLs:

    /version   // The current version or release of the MOD
    /defaults  //  A key=value listing of appropriate defaults for the MOD

These last two options are used by my Bio::GMOD module which aims to provide
a unified perl API to the MODs.  (I haven't officially announced the module
yet while I polish some details and add some documentation).

Todd


> On 3/3/05 12:38 PM, 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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