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Re: Identity of URIs. WAS: Re: Is there an NCBI taxonomy in OWL ?

From: Andrea Splendiani <andrea.splendiani@bbsrc.ac.uk>
Date: Mon, 2 Mar 2009 22:52:41 +0000
Cc: Kei Cheung <kei.cheung@yale.edu>, Alan Ruttenberg <alanruttenberg@gmail.com>, Chris Mungall <cjm@berkeleybop.org>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, Maryann Martone <maryann@ncmir.ucsd.edu>
Message-Id: <B6B91B2B-AD71-4E84-AFF6-AAA05B21D168@bbsrc.ac.uk>
To: wangxiao@musc.edu
Hi,

I'm not following you 100%. I'm talking about the identity of the URI  
as a symbol. And I was thinking about a declarative approach, rather  
than procedural one (or did I misunderstood ?). Up in this thread,  
I've got an interesting answer by David Booth.

ciao,
Andrea

Il giorno 02/mar/09, alle ore 22:43, Xiaoshu Wang ha scritto:

>
>
> Andrea Splendiani wrote:
>> One thing that I think would be very useful, though it poses some   
>> semantic problem... is the possibility to assert equivalence in rdf.
>> At the moment equivalence can be asserted only in owl (and this   
>> implies a distinction between individuals, properties, classes...).
>>
>> But that is a lower level statement we can make about URI.
>>
>> For instance, I can say that:
>>
>>
>>> http://dbpedia.org/resource/Dopamine_receptor
>>>
>> is the same uri as:
>>
>>> http://dbpedia.org/resource/DopamineReceptor
>>>
>>
>>
>> And I want to say this independently from the interpretation   
>> associated to this URI, as my knowledge about the identity is a- 
>> priori:
>> if this leads to inconsistency, then this is because what is  
>> expressed  is inconsistent, not because of this equivalence.
>>
>> Is there a way to express this in RDF ? Don't think so...
>>
> I am not sure exactly what you intend.  Do you mean that you want to  
> assert the equivalence of the URI as the symbols or you want to  
> assert that the referent of the two URIs are the same?  If your  
> intension is the latter, I don't think RDF offers this kind of  
> vocabulary.  But you can always mint your own terms just as with all  
> other concepts that is not in RDF, right?
>
> If you want to assert the equivalence of two URI, but not the  
> resource that they references.  There isn't a straight-forward  
> answer but there can be work-around.
>
> For instance, you can design a class, say URI, which has a string  
> property that confirms to URI spec.  Of course, if you want, you can  
> also make it several properties according to the URI spec.  Then,  
> you can create instance of this URI class, which URI can be either a  
> b-node or you can designate another URI to it.   This would allow  
> you to make assertions on URI rather than its referent..
>
> Such an inconvenience of describing URI is due to the incomplete  
> syntax of URI.  Among the three essential things of the Web, URI,  
> Representation, and Resource, only Resource is "conveniently* in  
> URI's referential realm.  I have suggested a solution in [1] to  
> offer some syntactic sugar.  In that proposal,
>
> "http://dbpedia.org/resource/Dopamine_receptor?" would by definition  
> denote the URI.  This would greatly simplify the task.
>
> Xiaoshu
> 1. http://dfdf.inesc-id.pt/tr/uri-issues
>> ciao,
>> Andrea
>>
>> Il giorno 27/feb/09, alle ore 03:03, Kei Cheung ha scritto:
>>
>>
>>> I gave the following neuroscience URI examples in my biordf talk  
>>> at  C-SHALS yesterday.
>>>
>>> http://dbpedia.org/resource/Dopamine_receptor
>>> http://purl.org/ycmi/senselab/  
>>> neuron_ontology.owl#Dopaminergic_Receptor
>>> http://purl.org/nif/ontology/NIF-Molecule.owl#nifext_5832
>>>
>>> I pointed out that the last one might be a possible solution.  
>>> There  might be hope. :-)
>>>
>>> -Kei
>>>
>>>
>>> Alan Ruttenberg wrote:
>>>
>>>
>>>> So I count three different sets of URIs for NCBI taxonomy so  
>>>> far. :(
>>>> -Alan
>>>>
>>>> On Fri, Feb 27, 2009 at 11:37 AM, Chris Mungall  <cjm@berkeleybop.org 
>>>> > wrote:
>>>>
>>>>
>>>>> also..
>>>>>
>>>>> part of the NCBI taxonomy is in NIF Organism:
>>>>>
>>>>> http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl
>>>>>
>>>>> See also:
>>>>>
>>>>> https://wiki.neuinfo.org/xwiki/bin/view/Main/NIFSTDoverview
>>>>> http://neuinfo.org
>>>>>
>>>>>
>>>>> On Feb 25, 2009, at 4:17 PM, andrea splendiani (RRes-Roth) wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> It'2 240M, but compressed is only 9.
>>>>>> I wonder whether there is some architecture to transparently   
>>>>>> transfer
>>>>>> compressed ontologies...
>>>>>>
>>>>>> Ciao,
>>>>>> Andrea
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Chris Mungall [mailto:cjm@berkeleybop.org]
>>>>>> Sent: 25 February 2009 20:53
>>>>>> To: andrea splendiani (RRes-Roth)
>>>>>> Cc: public-semweb-lifesci hcls
>>>>>> Subject: Re: Is there an NCBI taxonomy in OWL ?
>>>>>>
>>>>>>
>>>>>> On Feb 25, 2009, at 11:58 AM, Andrea Splendiani wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I was looking for an NCBI Taxnomoy in OWL, but I didn't find  
>>>>>>> it  (or
>>>>>>> better, could find fragment from other projects...)
>>>>>>>
>>>>>>> What is strange though, is that on the obo foundry website
>>>>>>> (berkeleybop.org/ontologies) there are notes on the ncbi  
>>>>>>> taxonomy
>>>>>>> representation in owl... but not the representation itself.
>>>>>>>
>>>>>>>
>>>>>> Temporarily dropped from the summary page but still available  
>>>>>> at  the
>>>>>> usual URL
>>>>>> http://purl.org/obo/owl/NCBITaxon
>>>>>>
>>>>>> (warning: large..)
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Does anybody have some hint about where I can fin an OWL  
>>>>>>> version ?
>>>>>>> Or even an RDF version ? Even better would a sparql endpoint
>>>>>>> containing it...
>>>>>>>
>>>>>>> best,
>>>>>>> Andrea Splendiani
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>
>>
>>
>>
>
Received on Monday, 2 March 2009 22:53:27 UTC

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