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

From: Xiaoshu Wang <wangxiao@musc.edu>
Date: Mon, 02 Mar 2009 23:15:44 +0000
Message-ID: <49AC68A0.6010302@musc.edu>
To: Andrea Splendiani <andrea.splendiani@bbsrc.ac.uk>
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>


Andrea Splendiani wrote:
> 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.
>   
I am a bit of unsure too. :-)

Let's use the following convention, lower case letter represent URI and 
upper case Resource the URI denotes.  Hence, a denotes A and b denotes 
B. Is your intension to assert something between (1) a and b? Or (2) A 
and B?

I thought your message seems to suggest case (1) ? Is this correct?

Xiaoshu
> 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 23:16:29 UTC

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