Re: Advancing translational research with the Semantic Web

Hi Alan,

Can you give a little more detail on exactly how the evidence is  
linked.  I realize I can go to the OWL ontologies you and others  
created for the demo, but I wondered if you could give a quick review  
of the syntactical constructs you used to represent the evidence here.

You say "annotation property" here - is that an  
owl:AnnotationProperty? If so, do you specify a data type for the  
annotation property value?  If so, that would take you outside the  
OWL DL language species and interfere with your ability to do certain  
things with certain reasoners - no?

If you are using an enumeration class "design pattern" with an  
associated ObjectProperty (e.g., hasEvidence), in making such an  
assertion about Class X, wouldn't you then be forced to make the same  
evidentiary assertion about all the instances, descendant classes,  
and instances of descendant classes - which is certainly not what is  
intended when making an evidentiary statement.

Cheers,
Bill


On May 17, 2007, at 10:56 PM, Alan Ruttenberg wrote:

>
> 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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>>
>
>

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
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Please Note: I now have a new email - William.Bug@DrexelMed.edu