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

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

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