W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > July 2013

Re: Bioontology.org and Linked Data?

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Tue, 23 Jul 2013 19:28:06 -0400
Message-ID: <51EF1186.3020203@openlinksw.com>
To: public-semweb-lifesci@w3.org
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
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Received on Tuesday, 23 July 2013 23:28:28 UTC

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