W3C home > Mailing lists > Public > public-lod@w3.org > February 2012

Re: How do OBO ontologies work on the LOD?

From: Peter DeVries <pete.devries@gmail.com>
Date: Thu, 23 Feb 2012 17:58:07 -0500
Message-ID: <CAE0MQeHhG-H1RjPe8+f43BKeJ_MnH3fyuyQjtn-=z6hfs+WhdQ@mail.gmail.com>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Cc: public-lod@w3.org
Here is another example.

If I take this HAO URI

http://purl.obolibrary.org/obo/HAO_0000512

And plug it into the Sindice Inspector Tool on this page http://sindice.com/

It it interprets it as a web page, not an owl class.

If I take the URI as it exists in the ontology
http://purl.org/obo/owl/HAO#HAO_0000512

It does see it as an information source but with a number of blank nodes -
which it does not know how to interpret.

They could have followed the pattern that a lot of LOD sites do and have
something like this:

The URI
http://api.hymao.org/projects/32/public/ontology_class/show/1033#item
The HTML http://api.hymao.org/projects/32/public/ontology_class/show/1033

It seems that RDFa would work for this (here is a beta RDFa example
http://lod.taxonconcept.org/odes/thomas_say_1823_culex.html )

Which would allow them have the RDF markup in the .html page, rather than a
separate .rdf document.

That would give them a separate but more LOD friendly ontology.

An ontology which operates in the way LOD sites and services expect.

Respectfully,

- Pete



On Thu, Feb 23, 2012 at 5:18 PM, Alan Ruttenberg
<alanruttenberg@gmail.com>wrote:

> Hi Kinglsey,
>
> We don't do content negotiation. I've written concerning why, in the past,
> to some of the W3C groups.  I don't like the practice because it muddies up
> what exactly the URI means. So we use a not uncommon technique of
> responding to requests uniformly, with RDF/XML, and providing a stylesheet
> for rendering in the browser.
>
> As far as I know this is consistent with the aims of LOD. The underlying
> information is in RDF but if you put a URL into your browser you get back
> human readable information. Is the issue here that some computer wants
> human readable information? In my prototypes I had a foaf:page link to
> html. I will ask that this be added to Ontobee and the computers can use
> that.
>
> -Alan
>
> On Thu, Feb 23, 2012 at 3:40 PM, Kingsley Idehen <kidehen@openlinksw.com>wrote:
>
>> On 2/23/12 1:32 PM, Peter DeVries wrote:
>>
>>> However, I think testing using the Vapour Validator is easier to
>>> understand.
>>>
>>> This might best be shown in comparison to a LOD OWL class that works
>>> correctly,
>>>
>>> OBO Ontology URI http://purl.org/obo/owl/HAO#**HAO_0000000<http://purl.org/obo/owl/HAO#HAO_0000000>
>>>
>>> Mapped URI http://purl.obolibrary.org/**obo/HAO_0000000<http://purl.obolibrary.org/obo/HAO_0000000>
>>>
>>> HTML Page http://api.hymao.org/public/**ontology_class/show_expanded/**
>>> 4048 <http://api.hymao.org/public/ontology_class/show_expanded/4048>
>>>
>>> Check in the Vapour Validator http://validator.linkeddata.**org/vapour<http://validator.linkeddata.org/vapour>
>>>
>>> For comparison
>>>
>>> URI for the Species Apis mellifera http://lod.taxonconcept.org/**
>>> ses/z9oqP#Species <http://lod.taxonconcept.org/ses/z9oqP#Species>
>>>
>>> Human Page http://lod.taxonconcept.org/**ses/z9oqP.html<http://lod.taxonconcept.org/ses/z9oqP.html>
>>>
>>> Check the URI using the  Vapour Validator
>>>
>>> It is my opinion that this ontology could have been (and could still be
>>> modified to) implemented in a way that followed LOD best practices.
>>>
>>> My concern is that other groups like the beetle people
>>> (Coleopterologists) etc. would see the HAO ontology and assume that they
>>> should also use OBO.
>>>
>>
>> How about using URI Debugger [1] to iron out the Linked Data principles
>> concerns.
>>
>> Start here:
>> http://linkeddata.informatik.**hu-berlin.de/uridbg/index.php?**
>> url=http%3A%2F%2Fpurl.org%**2Fobo%2Fowl%2FHAO%23HAO_**
>> 0000000&useragentheader=&**acceptheader=<http://linkeddata.informatik.hu-berlin.de/uridbg/index.php?url=http%3A%2F%2Fpurl.org%2Fobo%2Fowl%2FHAO%23HAO_0000000&useragentheader=&acceptheader=>
>>
>> Follow the 302 response "Location:" value, note what's returned compared
>> to actual mime type in response headers.
>>
>> Example:
>>
>> HTTP/1.1 200 OK
>> Date: Thu, 23 Feb 2012 20:11:06 GMT
>> Server: Apache/2.2.14 (Ubuntu)
>> Last-Modified: Wed, 22 Feb 2012 20:53:47 GMT
>> ETag: "10c0630-4bfb71-4b993b94cecc0"
>> Accept-Ranges: bytes
>> Content-Length: 4979569
>> Content-Type: text/plain; charset=UTF-8
>> Vary: Accept-Encoding
>>
>> But the actual content is RDF/XML .
>>
>> Play around with different mime types via "Accept:" when alternative
>> representation requests etc.. Example re. Turtle request:
>>
>> HTTP/1.1 200 OK
>> Date: Thu, 23 Feb 2012 20:11:46 GMT
>> Server: Apache/2.2.14 (Ubuntu)
>> Last-Modified: Wed, 22 Feb 2012 20:53:47 GMT
>> ETag: "10c0630-4bfb71-4b993b94cecc0"
>> Accept-Ranges: bytes
>> Content-Length: 4979569
>> Content-Type: text/plain; charset=UTF-8
>> Vary: Accept-Encoding
>>
>> But actual content is RDF/XML .
>>
>>
>> I think this is the place where Linked Data problems are arising.
>>
>> Links:
>>
>> 1. http://linkeddata.informatik.**hu-berlin.de/uridbg/<http://linkeddata.informatik.hu-berlin.de/uridbg/>-- URI Debugger .
>>
>> --
>>
>> Regards,
>>
>> Kingsley Idehen
>> Founder&  CEO
>>
>> OpenLink Software
>> Company Web: http://www.openlinksw.com
>> Personal Weblog: http://www.openlinksw.com/**blog/~kidehen<http://www.openlinksw.com/blog/~kidehen>
>> Twitter/Identi.ca handle: @kidehen
>> Google+ Profile: https://plus.google.com/**112399767740508618350/about<https://plus.google.com/112399767740508618350/about>
>> LinkedIn Profile: http://www.linkedin.com/in/**kidehen<http://www.linkedin.com/in/kidehen>
>>
>>
>>
>>
>>
>>
>>
>


-- 
------------------------------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries@wisc.edu
TaxonConcept <http://www.taxonconcept.org/>  &
GeoSpecies<http://about.geospecies.org/> Knowledge
Bases
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
--------------------------------------------------------------------------------------
Received on Thursday, 23 February 2012 22:58:36 UTC

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