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Re: Advancing translational research with the Semantic Web

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Thu, 17 May 2007 22:56:18 -0400
Message-Id: <D7F6CF9C-E46E-44BE-AFA3-F0461923AB0A@gmail.com>
Cc: samwald@gmx.at, public-semweb-lifesci@w3.org
To: Pat Hayes <phayes@ihmc.us>

The example isn't necessarily a disagreement. Both could be true.

I think these really need to be class statements, in any case, to  
make any sense.

In my representation this is (schematically)

Class protein_a_expression_process_located_in_tissue_b
    subclassOf expression and produced some protein_a and located_in  
some tissue b
annotation: has_evidence: traceable author statement, cites evidence  
source: c

Class protein_a_expression_process_located_in_tissue_b
    subclassOf expression and produced some protein_a and located_in  
some tissue e
annotation: has_evidence: traceable author statement, cites evidence  
source: c

No disagreement. But also not so much power.

I have proposed in other mail (on this list, I think) that one may  
strengthen this, either as hypothesis, or by conviction by making the  
"overstatement"

expression and produced some protein_a
equivalentClass protein_a_expression_process_located_in_tissue_b
equivalentClass protein_a_expression_process_located_in_tissue_e

Now if tissue e and tissue b are disjoint, there would be a  
contradiction.

Or we could hypothesize that

expression and produced some protein_a
equivalentClass
    unionOf(protein_a_expression_process_located_in_tissue_b,  
protein_a_expression_process_located_in_tissue_e)

Given what's been said so far, we can't actually tell which of these  
two cases is supposed to be meant.

And even my version  doesn't handle parts very well. In the case of  
cellular components, for example, we want to be able to say that   
it's active in the cell and it's active in the E.R. and not have that  
be inconsistent because the because every E.R. is part of some cell.

-Alan





On May 17, 2007, at 1:00 PM, Pat Hayes wrote:

>
>>  > How would you say e.g. "protein a is expressed in tissue b,  
>> according to
>>>  source c"?
>>
>> through something like
>>
>> <protein_a_expression_process> <has_participant> <protein_a> .
>> <protein_a_expression_process> <located_in> <tissue_b> .
>> <protein_a_expression_process> <described_by> <source_c> .
>
> OK, but suppose source d disagrees, and says that a is expressed in  
> e. Now you have
>
> <protein_a_expression_process> <located_in> <tissue_e> .
> <protein_a_expression_process> <described_by> <source_d> .
>
> and its all about the same process. What now associates d with e,  
> and c with b? You just have five triple all with the same subject.
>
> Pat Hayes.
>
>> -- Matthias Samwald
>>
>>
>> Yale Center for Medical Informatics, New Haven /
>> Section on Medical Expert and Knowledge-Based Systems, Vienna /
>> http://neuroscientific.net
>>
>>
>> .
>> --
>> Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
>> Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer
>
>
> --
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Received on Friday, 18 May 2007 02:56:13 UTC

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