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Re: [rdf] Re: proposal for standard NCBI database URI

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Tue, 9 May 2006 13:25:47 -0400
Message-Id: <9A29E51F-6399-422D-A58F-A04A304309F5@gmail.com>
Cc: markw@illuminae.com, larry.hunter@uchsc.edu
To: public-semweb-lifesci@w3.org

Thanks, I like this proposal, Larry. You are right - it works now and  
satisfies the requirement.

I amend my proposal to be:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=  
DATABASE_GOES_HERE>&<IDENTIFIER_GOES_HERE

e.g.

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=596
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? 
db=protein&id=NP_000624

RDF tools might not present this too prettily, but they can be fixed.

-Alan

On May 9, 2006, at 1:12 PM, Mark Wilkinson wrote:

> I stand corrected :-)
>
> Are there limits on the number of retrievals that can be done in a day
> on these URLs?  i.e. will my domain get blacklisted if I pull in 100K
> records every hour?

Yes. Don't do that. (you don't need to for the purposes I outlined).

>
> M
>
>
> On Tue, 2006-05-09 at 10:58 -0600, Larry Hunter wrote:
>> On Tue, 2006-05-09 at 09:16 -0700, Mark Wilkinson wrote:
>>> Hmmmm.... yeah, that's true... but my "gut" does a back-flip when  
>>> I am
>>> forced to use a URI that refers to a web page, complete with  
>>> fancy NCBI
>>> decorations and menu's
>>
>> You're mistaken about that.  If you don't want the decorations,  
>> then use
>> the efetch URL:
>>
>>   http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
>>
>> which just brings back the raw data.  Details here:
>>
>>   http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
>>
>> Format the query to return XML or ASN.1, and there you are.
>>
>> Look, I don't think these are very pretty interfaces, either, but  
>> it is
>> possible to do what Alan wanted to do with no additional work.
>>
>> Larry
>>
> -- 
>
> --
> Mark Wilkinson
> Asst. Professor, Dept. of Medical Genetics
> University of British Columbia
> PI in Bioinformatics, iCAPTURE Centre
> St. Paul's Hospital, Rm. 166, 1081 Burrard St.
> Vancouver, BC, V6Z 1Y6
> tel: 604 682 2344 x62129
> fax: 604 806 9274
>
> "For most of this century we have viewed communications as a conduit,
>        a pipe between physical locations on the planet.
> What's happened now is that the conduit has become so big and  
> interesting
>       that communication has become more than a conduit,
>        it has become a destination in its own right..."
>
>                 Paul Saffo - Director, Institute for the Future
>
Received on Tuesday, 9 May 2006 17:26:01 GMT

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