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Re: Advancing translational research with the Semantic Web

From: Alan Rector <rector@cs.man.ac.uk>
Date: Sat, 19 May 2007 11:36:20 +0100
Message-Id: <DAF64C08-4DF0-48ED-B348-30A5DC869C16@cs.man.ac.uk>
To: chris mungall <cjm@fruitfly.org>, public-semweb-lifesci <public-semweb-lifesci@w3.org>, Pat Hayes <phayes@ihmc.us>, Bijan Parsia <bparsia@cs.man.ac.uk>, Alan Ruttenberg <alanruttenberg@gmail.com>

Chris, Bijan, Pat, All

Coming into this late, it seems to me that there are a series of use- 
cases / requirements / wishes that people are trying to accommodate  
made worse by real difficulties of the "use vs mention" variety.  I  
think there is a need of a high level document setting out the issues  
separate, insofar as possible, from the nitty gritty of RDF or OWL.

Pat or others can probably help get these clearer, but s a start...   
Most of this is expressed in a more OWL than RDF way because that's  
how I work.


*	Reference to the specific symbols (triples) in a specific ontology  
in a specific version in a specific document - required for  
provenance.  I have lots of requirements for tracking the changes to  
reference documents at this level, where it is the symbols in the  
document of a particular document that are of concern.

*	Reference to the statement represented by those symbols on the  
authority represented.  The same statement on might have been made  
elsewhere on the web with physically different symbols.  Who made the  
statement, etc.  The symbols may change, e.g. with versioning, but  
the statement persist.

*	Reference to the fact asserted in the statement - e.g. whether or  
not it is true, supported by sufficient evidence for a given purpose,  
believed by Chris, etc.



*	Is the class a sufficient level of granularity.  In OWL I often  
need to refer to specific axioms and even to conjuncts within a  
definition.  For example in Alan's query.

>> There is a subclass of gene expression processes, during each  
>> instance of which some instance of protein a is the participant  
>> which is "the thing produced", and which is located_in some  
>> instance of tissue b.

Is it sufficient to refer to the entire construct? or do I need to  
refer to the provenance of the claim that the protein is then located  
in some issue of tissue b (rather than some tissue c)? (And is this a  
"definition" in the sense of a set of jointly sufficient and  
individually necessary conditions, or just a group of necessary  

In modular OWL ontologies, the ability to annotate individual axioms  
is an absolute requirement to know where they came from and should be  
edited.  I think I have cases for annotation and provenance where it  
is needed for individual conjuncts in necessary and sufficient  

*	Annotation of removal/exclusion of axioms.  That an axiom is absent  
is frequently as important as that it is present.  When after a long  
controversy an assertion is removed, I want to record that  
information to help avoid somebody adding it back later.


*	For OWL ontologies, we need a standard way to annotate whether a  
given "statement" in OWL has been asserted or inferred.  (and whether  
an ontology is being provided in with all standard inferences already  
performed).   If it has been inferred, then we need to know the  
overall scope of the inference - i.e. the set of all ontologies  
imported and accessible to the reasoner during the inference.  In  
this case, whether or not an statement has been inferred or asserted  
(by someone at some time...) is just another form of provenance  


Received on Sunday, 20 May 2007 01:56:31 UTC

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