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
.
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