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RE: Bioontology.org and Linked Data?

From: Ray Fergerson <ray.fergerson@stanford.edu>
Date: Wed, 24 Jul 2013 16:21:37 -0700 (PDT)
To: "'Kingsley Idehen'" <kidehen@openlinksw.com>, <public-semweb-lifesci@w3.org>
Message-ID: <c3fa2b8a.0000275c.0000000e@BMIR-MSOB-245.stanford.edu>
Kingsley,

I think that I may have conveyed the wrong impression in my previous
message. We are not revising our API primarily to better support LOD. We
are implementing the BioPortal backend to use a triple-store. We are doing
this work for a variety of reasons. As part of this backend work we are
revising our REST API to be more regular, consistent, and properly
REST-full. Since we are doing all of this work anyway, we are also trying
to make sure that the revised system works better for linked data access
where it makes sense for us to do so. This includes:

1) a public SPARQL endpoint
2) dereferencable URI's
3) content negotiation, and
4) REST access to all resources

Ray

-----Original Message-----
From: Kingsley Idehen [mailto:kidehen@openlinksw.com] 
Sent: Tuesday, July 23, 2013 4:28 PM
To: public-semweb-lifesci@w3.org
Subject: Re: Bioontology.org and Linked Data?

On 7/23/13 6:51 PM, Ray Fergerson wrote:
> Yes you are correct that our existing REST API does not support the LOD
> model very well. Our new API, still in alpha, should be much better in
> this respect. The draft alpha documentation for this is often available
> at:
>
> http://stagedata.bioontology.org/documentation

If you implement Linked Data principles you would actually get more out 
of this entire endeavor for a fraction of the costs.

I've just looked through your API and I can't understand why you are 
taking this route. It's too much work for too little gain, in a nutshell.

You can publish Linked Data and control its access using authentication 
protocols that also leverage Linked Data. The same applies to CRUD 
operations too :-)

Kingsley
>
> Ray
>
> -----Original Message-----
> From: Kingsley Idehen [mailto:kidehen@openlinksw.com]
> Sent: Monday, July 22, 2013 9:10 AM
> To: HCLS
> Subject: Bioontology.org and Linked Data?
>
> All,
>
> I continue to struggle with the notion that Bioontology.org is a point
> of presence on the Web for Linked Data. The URIs associated with this
> data space don't adhere to Linked Data principles as far as I can tell.
>
> Examples:
>
> Vapour Analysis:
>
> Link:
>
http://linkeddata.uriburner.com:8000/vapour?uri=http%3A%2F%2Fpurl.bioontol
>
ogy.org%2Fontology%2FSNOMEDCT&defaultResponse=dontmind&userAgent=vapour.so
> urceforge.net
>
>
> CURL dump:
>
> curl -IL http://purl.bioontology.org/ontology/SNOMEDCT
> HTTP/1.1 302 Moved Temporarily
> Date: Mon, 22 Jul 2013 16:07:41 GMT
> Server: 1060 NetKernel v3.3 - Powered by Jetty
> Location: http://bioportal.bioontology.org/virtual/1353
> 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: 278
> Connection: close
>
> HTTP/1.1 302
> Date: Mon, 22 Jul 2013 16:07:42 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: 16
> Set-Cookie: _bp_session=99d9609355614f6a360069e5f39c239c;
> domain=.bioontology.org; path=/; HttpOnly
> Location: http://bioportal.bioontology.org/visualize/46896
> Content-Length: 114
> Status: 302
> Vary: Accept-Encoding
> Connection: close
> Content-Type: text/html; charset=utf-8
>
> HTTP/1.1 301
> Date: Mon, 22 Jul 2013 16:07:43 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: 38
> Set-Cookie: _bp_session=8822d00fdb21e317cc987fcab42aa36b;
> domain=.bioontology.org; path=/; HttpOnly
> Location: http://bioportal.bioontology.org/ontologies/46896?p=terms
> Content-Length: 123
> Status: 301
> Vary: Accept-Encoding
> Connection: close
> Content-Type: text/html; charset=utf-8
>
> HTTP/1.1 200
> Date: Mon, 22 Jul 2013 16:07:43 GMT
> Server: Apache/2.2.15 (Red Hat)
> X-Powered-By: Phusion Passenger (mod_rails/mod_rack) 3.0.18
> X-Runtime: 242
> ETag: "0f524114ff5c5e8750df09fd898272aa"
> Cache-Control: private, max-age=0, must-revalidate
> Set-Cookie: _bp_session=b6f2b348269c8540cb63d4cc3721c854;
> domain=.bioontology.org; path=/; HttpOnly
> Content-Length: 87778
> Status: 200
> Vary: Accept-Encoding
> Connection: close
> Content-Type: text/html; charset=utf-8
>
> Macintosh-96:downloads kidehen$ curl -ILH "Accept: text/turtle"
> http://purl.bioontology.org/ontology/SNOMEDCT
> HTTP/1.1 302 Moved Temporarily
> Date: Mon, 22 Jul 2013 16:08:14 GMT
> Server: 1060 NetKernel v3.3 - Powered by Jetty
> Location: http://bioportal.bioontology.org/virtual/1353
> 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: 278
> Connection: close
>
> HTTP/1.1 302
> Date: Mon, 22 Jul 2013 16:08:14 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: 44
> Set-Cookie: _bp_session=0c4cf299a4588d56d4f2500a0a655d13;
> domain=.bioontology.org; path=/; HttpOnly
> Location: http://bioportal.bioontology.org/visualize/46896
> Content-Length: 114
> Status: 302
> Vary: Accept-Encoding
> Connection: close
> Content-Type: text/html; charset=utf-8
>
> HTTP/1.1 301
> Date: Mon, 22 Jul 2013 16:08:15 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: 13
> Set-Cookie: _bp_session=77c17bae2f459c01a3f03a849b820a7f;
> domain=.bioontology.org; path=/; HttpOnly
> Location: http://bioportal.bioontology.org/ontologies/46896?p=terms
> Content-Length: 123
> Status: 301
> Vary: Accept-Encoding
> Connection: close
> Content-Type: text/html; charset=utf-8
>
> HTTP/1.1 200
> Date: Mon, 22 Jul 2013 16:08:15 GMT
> Server: Apache/2.2.15 (Red Hat)
> X-Powered-By: Phusion Passenger (mod_rails/mod_rack) 3.0.18
> X-Runtime: 190
> ETag: "e851734fe4a58319c13adfde5a28d825"
> Cache-Control: private, max-age=0, must-revalidate
> Set-Cookie: _bp_session=7607b39fe6788d1a2ad1401e8fe85d43;
> domain=.bioontology.org; path=/; HttpOnly
> Content-Length: 87778
> Status: 200
> Vary: Accept-Encoding
> Connection: close
> Content-Type: text/html; charset=utf-8
>
> Macintosh-96:downloads kidehen$ curl -ILH "Accept: application/rdf+xml"
> http://purl.bioontology.org/ontology/SNOMEDCT
> HTTP/1.1 302 Moved Temporarily
> Date: Mon, 22 Jul 2013 16:08:32 GMT
> Server: 1060 NetKernel v3.3 - Powered by Jetty
> Location: http://bioportal.bioontology.org/virtual/1353
> 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: 278
> Connection: close
>
> HTTP/1.1 302
> Date: Mon, 22 Jul 2013 16:08:32 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=f40903a37df9f53d14b22c866ebc56d0;
> domain=.bioontology.org; path=/; HttpOnly
> Location: http://bioportal.bioontology.org/visualize/46896
> Content-Length: 114
> Status: 302
> Vary: Accept-Encoding
> Connection: close
> Content-Type: text/html; charset=utf-8
>
> HTTP/1.1 301
> Date: Mon, 22 Jul 2013 16:08:34 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: 10
> Set-Cookie: _bp_session=36b560642ed8da07ab12f1eab2bfb0b1;
> domain=.bioontology.org; path=/; HttpOnly
> Location: http://bioportal.bioontology.org/ontologies/46896?p=terms
> Content-Length: 123
> Status: 301
> Vary: Accept-Encoding
> Connection: close
> Content-Type: text/html; charset=utf-8
>
> HTTP/1.1 500
> Date: Mon, 22 Jul 2013 16:08:34 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=f7fa9dcb15b8a9e6c3da2e48f76c0e53;
> domain=.bioontology.org; path=/; HttpOnly
> Status: 500
> 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
Received on Wednesday, 24 July 2013 23:22:06 UTC

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