Re: Bioontology.org and Linked Data?

On 7/24/13 7:21 PM, Ray Fergerson wrote:
> 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

Okay! That's a lot clearer :-)

Kingsley
>
> -----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
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