Re: biontology.org Linked Data URIs?

On May 28, 2013, at 6:23 PM, Kingsley Idehen <kidehen@openlinksw.com> wrote:

> On 5/28/13 5:04 PM, Richard Boyce wrote:
>> I think this helps bioportal keep track of usage (to justify its existence) and reduce annoying bots. Also, I get updates from bioportal for having registered an account. -R
> 
> Bots are annoying, but they are part of the ecosystem.
> API keys are archaic and quite contradictory an RDF based Linked Data realm. 

Yup. There are more clever ways of accomplishing the desired goals outside inconveniencing every user with an api key. Seems to me the goals also have to do with tracking the usage of the URIs and the users of the resource.

I have tried to advise the Bioportal team about the basic of linked data norms and etiquette in the past, but they seem to be slow to progress along the learning curve. Kingsley, may I suggest that you give specific advise on where changes would be desirable. I would start by paying particular attention to cases where bioportal URIs duplicate authoritative URIs given by the authors of the resources they aggregate. For example, Chris points out that OBO Foundry URIs are intended to be linked data friendly, and certainly Bioportal should not be rewriting these. But I'm sure you can give plenty of other advise that might help them learn the finer points.

I remain, as always, at their disposal.

Regards,
Alan

> 
> RDF is about structured data enhanced with entity relationship semantics. If one actually looks to dog-food RDF you end up with  solution to this broadly exposed problem. All that's required here is the construct RDF based data access policies that are driven by entity relationship semantics. 
> 
> Links:
> 
> 1. http://www.w3.org/wiki/WebAccessControl -- Web Access Controls
> 2. http://bit.ly/M7hd4T -- protecting SPARQL endpoints using RDF based entity relationship semantics
> 3. http://bit.ly/UuWZSI -- collection of posts about ACLs and Data Access policies.
> 
> 
> 
> Kingsley 
>> 
>> On 05/28/2013 04:54 PM, Jim McCusker wrote:
>>> I can see asking for an API key for working with computational resources (like Annotator and Ontology Recommender), but we don't need an API key to see those classes in HTML, why should we need one to see them in RDF?
>>> 
>>> Jim
>>> 
>>> 
>>> On Tue, May 28, 2013 at 4:07 PM, Peter Ansell <ansell.peter@gmail.com> wrote:
>>> Hi Kingsley,
>>> 
>>> I think you may need an API key to work with them? [1]
>>> 
>>> Cheers,
>>> 
>>> Peter
>>> 
>>> [1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services
>>> 
>>> 
>>> On 29 May 2013 05:55, Kingsley Idehen <kidehen@openlinksw.com> wrote:
>>> All,
>>> 
>>> Who are the folks responsible for URIs such as:
>>> 
>>> 1. <http://purl.bioontology.org/ontology/NCIM/C0144157> ?
>>> 2. <http://purl.bioontology.org/ontology/MSH/C010843> ?
>>> 
>>> I ask due to the following curl output:
>>> 
>>> HTTP/1.1 302 Moved Temporarily
>>> Date: Tue, 28 May 2013 19:46:48 GMT
>>> Server: 1060 NetKernel v3.3 - Powered by Jetty
>>> Location: http://bioportal.bioontology.org/virtual/1499/C0144157
>>> Content-Type: text/html; charset=iso-8859-1
>>> X-Purl: 2.0; http://localhost:8080
>>> Expires: Thu, 01 Jan 1970 00:00:00 GMT
>>> Content-Length: 287
>>> Connection: close
>>> 
>>> HTTP/1.1 404
>>> Date: Tue, 28 May 2013 19:46:48 GMT
>>> Server: Apache/2.2.15 (Red Hat)
>>> X-Powered-By: Phusion Passenger (mod_rails/mod_rack) 3.0.18
>>> Cache-Control: no-cache
>>> Set-Cookie: _bp_session=61cc2ee75b3abf041d7df4ada339ce68; domain=.bioontology.org; path=/; HttpOnly
>>> Content-Length: 6468
>>> Status: 404
>>> Connection: close
>>> Content-Type: */*; charset=utf-8
>>> 
>>> And:
>>> 
>>> curl -ILH "Accept: text/turtle" http://purl.bioontology.org/ontology/MSH/C010843
>>> HTTP/1.1 302 Moved Temporarily
>>> Date: Tue, 28 May 2013 19:54:21 GMT
>>> Server: 1060 NetKernel v3.3 - Powered by Jetty
>>> Location: http://bioportal.bioontology.org/virtual/1351/C010843
>>> Content-Type: text/html; charset=iso-8859-1
>>> X-Purl: 2.0; http://localhost:8080
>>> Expires: Thu, 01 Jan 1970 00:00:00 GMT
>>> Content-Length: 286
>>> Connection: close
>>> 
>>> HTTP/1.1 302
>>> Date: Tue, 28 May 2013 19:54:21 GMT
>>> Server: Apache/2.2.15 (Red Hat)
>>> X-Powered-By: Phusion Passenger (mod_rails/mod_rack) 3.0.18
>>> Cache-Control: no-cache
>>> X-Runtime: 12
>>> Set-Cookie: _bp_session=9889b1bed12d58172331ce1bbf42d516; domain=.bioontology.org; path=/; HttpOnly
>>> Location: http://bioportal.bioontology.org/visualize/46836/?conceptid=C010843
>>> Content-Length: 133
>>> Status: 302
>>> Vary: Accept-Encoding
>>> Connection: close
>>> Content-Type: text/html; charset=utf-8
>>> 
>>> HTTP/1.1 301
>>> Date: Tue, 28 May 2013 19:54:21 GMT
>>> Server: Apache/2.2.15 (Red Hat)
>>> X-Powered-By: Phusion Passenger (mod_rails/mod_rack) 3.0.18
>>> Cache-Control: no-cache
>>> X-Runtime: 17
>>> Set-Cookie: _bp_session=17e1fddfad5145ef1b6217dc6a76570c; domain=.bioontology.org; path=/; HttpOnly
>>> Location: http://bioportal.bioontology.org/ontologies/46836?p=terms&conceptid=C010843
>>> Content-Length: 145
>>> Status: 301
>>> Vary: Accept-Encoding
>>> Connection: close
>>> Content-Type: text/html; charset=utf-8
>>> 
>>> HTTP/1.1 200
>>> Date: Tue, 28 May 2013 19:54:21 GMT
>>> Server: Apache/2.2.15 (Red Hat)
>>> X-Powered-By: Phusion Passenger (mod_rails/mod_rack) 3.0.18
>>> X-Runtime: 149
>>> ETag: "2d0e7a20547ae7fa0b9fd221222016e6"
>>> Cache-Control: private, max-age=0, must-revalidate
>>> Set-Cookie: _bp_session=0770e84c6238dfdcc24bb8e0f65a8faf; domain=.bioontology.org; path=/; HttpOnly
>>> Content-Length: 93664
>>> Status: 200
>>> Vary: Accept-Encoding
>>> Connection: close
>>> Content-Type: text/html; charset=utf-8
>>> 
>>> 
>>> 
>>> -- 
>>> 
>>> Regards,
>>> 
>>> Kingsley Idehen 
>>> Founder & CEO
>>> OpenLink Software
>>> Company Web: http://www.openlinksw.com
>>> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
>>> Twitter/Identi.ca handle: @kidehen
>>> Google+ Profile: https://plus.google.com/112399767740508618350/about
>>> LinkedIn Profile: http://www.linkedin.com/in/kidehen
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Jim McCusker
>>> Programmer Analyst
>>> Krauthammer Lab, Pathology Informatics
>>> Yale School of Medicine
>>> james.mccusker@yale.edu | (203) 785-4436
>>> http://krauthammerlab.med.yale.edu
>>> 
>>> PhD Student
>>> Tetherless World Constellation
>>> Rensselaer Polytechnic Institute
>>> mccusj@cs.rpi.edu
>>> http://tw.rpi.edu
>> 
>> 
>> -- 
>> Richard D Boyce, PhD
>> Assistant Professor of Biomedical Informatics
>> Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research and Training Program
>> Scholar, Comparative Effectiveness Research Program
>> University of Pittsburgh
>> rdb20@pitt.edu
>> Office: 412-648-9219
>> Twitter: @bhaapgh
> 
> 
> -- 
> 
> Regards,
> 
> Kingsley Idehen	      
> Founder & CEO 
> OpenLink Software     
> Company Web: http://www.openlinksw.com
> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
> Twitter/Identi.ca handle: @kidehen
> Google+ Profile: https://plus.google.com/112399767740508618350/about
> LinkedIn Profile: http://www.linkedin.com/in/kidehen
> 
> 
> 
>

Received on Tuesday, 28 May 2013 22:51:52 UTC