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Lang; Use case for URI links w/o importing

From: Jim Hendler <hendler@cs.umd.edu>
Date: Wed, 25 Sep 2002 22:41:30 -0400
Message-Id: <p05111729b9b8228bde1d@[129.2.177.222]>
To: webont <www-webont-wg@w3.org>
In a separate conversation with Chris Welty, he asked me about the 
importing issue and asked if I had an example.  Since I was in the 
middle of writing one up for a scientific publication, I did some 
cutting and pasting to create a realistic use case -- here it is 
(slightly edited so I can use it in public)

>
>Seriously, you catch me at a good time because I'm just in the 
>middle of writing up an example for <name of publication>.  Here's 
>roughly how it goes:
>
>There exists an ontology for cancer that the NCBI (National Center 
>for Bio Informatics) maintains.  They create instances like against 
>an ontology that defines classes like "oncogene"  (note that I 
>haven't fixed the characters to be legal XML - we have a 
>preprocessor that does that in practice)
>
>><Oncogene rdf:ID="Oncogene, MYC">
>>	<Found_In_Organism rdf:ID="Human">
>>	</Found_In_Organism>
>>	<Gene_Has_Function rdf:ID="Gene Transcription">
>>	</Gene_Has_Function>
>>	<Gene_Has_Function rdf:ID="Transcriptional Regulation">
>>	</Gene_Has_Function>
>>	<In_Chromosomal_Location rdf:ID="8q24"/>
>>	<Gene_Associated_With_Disease rdf:ID="Burkitt's Lymphoma">
>>	</Gene_Associated_With_Disease>
>></Oncogene>
>
>
>Other people now link to this - for example, suppose you are writing 
>a paper on "burkitt's lymphoma" - if you link to 
>"http://.../thisdocument#burkitts_lymphoma" then you are agreeing to 
>THIS use of that term.     Meanwhile, someone working on a database 
>has a sequence that is part of gene 8, so he links it to :8q24 (not 
>the English term, the URI).  Turns out another thing linked to :8q24 
>is a locus called PVT1, and the authors of a paper entitled 
>"Rearrangement of a DNA sequence homologous to a cell-virus junction 
>fragment in several Moloney murine leukemia virus-induced rat 
>thymomas" [1] had their paper linked (by someone else actually) to 
>PVT1.
>
>So we now have a chain
>
>MYC -- associated with disease --> Burkitts
>MYC -- chromosomal_location --> 8q24
>PVT1 -- location on --> 8q24
>(paper title) -- paperDescribes --> PVT1
>
>Thus, the research working on Burkitts, can have an agent that finds 
>this paper, even though the words burkitt, lymphoma, 8q24 and PVT1 
>don't appear anywhere in the paper.  A query like "Is anyone working 
>on a paper that describes the locus of the chromosone associated 
>with Burkitt's Lymphoma" becomes realistic solvable, by the magic of 
>web links.
>
>Was the ontology important?  Absolutely, it provided the means by 
>which the person who described MYC got it right, and it provided the 
>vital link between 8q24 and burkitt's lymphoma.  However, the 
>remainder of the work was in the agreements represented by the links 
>- so the person describing the paper didn't have to know about the 
>ontology, nor did the person sequencing 8q24.  Further, maybe this 
>is linked to other ontologies that we don't care about in this 
>example - if we have to import everything to do examples like this 
>we lose scaleability.
>
>BUT REMEMBER "Hendler's Law:" On the Web there is no 'THE'.
>
>Thus, there are many other uses of this same ontology that 
>absolutely requires the semantic entailments and etc. and for those 
>we provide "imports" -  I want to make sure that I can do those 
>without breaking this, and this without breaking those.
>

[1] Proc Natl Acad Sci U S A 1984 Jan;81(1):38-42;
Lemay G, Jolicoeur P. -- see 
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&uid=84119459&Dopt=r
-- 
Professor James Hendler				  hendler@cs.umd.edu
Director, Semantic Web and Agent Technologies	  301-405-2696
Maryland Information and Network Dynamics Lab.	  301-405-6707 (Fax)
Univ of Maryland, College Park, MD 20742	  240-731-3822 (Cell)
http://www.cs.umd.edu/users/hendler
Received on Wednesday, 25 September 2002 22:41:36 GMT

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