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Re: SemWeb BOF @ ISMB 04

From: john wilbanks <jwilbanks@rcn.com>
Date: Tue, 03 Aug 2004 10:53:44 -0400
Message-ID: <410FA6F8.3090705@rcn.com>
To: public-semweb-lifesci@w3.org

How did the BOF go?  And the bio-ontologies meeting?

Enquiring minds (without travel budgets) want to know!

jtw

wangxiao wrote:

>>If I have understood you correctly, you are describing one of 
>>the use cases for the Life Sciences URN identifier. A single 
>>LSID can describe and give remote programatic access to both 
>>your data (the gel data in the format you invented or some 
>>other standard format appropriate to that data if one exists) 
>>and  any amount of metadata in RDF that describes that data 
>>and its cross-relationships with other entities. 
>>    
>>
>
>What I want is perhap something similar to a "context".  Let's use a very
>simple hypothetical peptide sequence as an example.  If I have two peptides:
>"MYLH" and "LEDA".  Each of them is a resource, so does each of the amino
>acid that composed them.  Of course, if I want, I can assign each amino acid
>a URI, but that will make the sequence data too verbose.  But if I don't
>assign each AA a URI, how can I use RDF to describe the special property of
>a particular amino acid within the peptide.  In other words, how can I
>distinguish the Leucine of the first peptide from the one in second peptide.
>
>Yes, theoretically we could invent an ontology to describe a protein
>sequence so that each aimino acid could have a URI.  But then, to extend it,
>why shouldn't we go further to the atomic level?  In that case, not many
>people could even write a protein sequence without some professional help.
>:-)
>
>I roughly knows the idea of LSID (but will look in more detail).  But I am
>not sure if LSID can sovle that problem.  But perhaps, one solution is to
>register some sub protocol so that a URI can be implicitly assigned to
>"part" of a resource. In a way similar to the MIME type where a program
>knows how to deal with an application according to type, LSID might be able
>to allow the implicit assignment of URI to fragment of a resource of a
>particular type.  If this can be achieved, it will solve a lot of problem,
>don't you agree? 
>
>Xiaoshu  
>
>
>  
>
Received on Tuesday, 3 August 2004 10:53:52 GMT

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