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Re: [hcls] Temporal relations, n-ary relations, 4D ontologies

From: Chris Mungall <cjm@fruitfly.org>
Date: Tue, 22 May 2007 09:00:25 -0700
Message-Id: <BF145570-446A-481F-813C-C077C3D71E1B@fruitfly.org>
Cc: public-semweb-lifesci@w3.org
To: samwald@gmx.at


On May 22, 2007, at 8:04 AM, samwald@gmx.at wrote:

>
> I have changed the title of the mail, since the discussion has  
> moved away from the BMC Bioinformatics paper.
>
> First of all, RDF and OWL have no special features for n-ary  
> relations (RDF reification is not practical for that), and in my  
> opinion there is now way that this will change at this point in  
> time. Introducing such features would break the basic triple model,  
> and it seems quite unrealistic to me that such a feature will be  
> introduced to OWL or RDF in the foreseeable future. We should try  
> to make the best of what we have in RDF and OWL, and I think that  
> with some basic, good design choices, the problems might probably  
> be far less severe than it has been portrayed in the recent  
> discussion.
> I also cannot agree that the OWL design patterns described earlier  
> are 'cheating'. Almost every relation can also be viewed as an  
> entity that is comprised of two parts or participants. In most  
> cases, both the 'relation view' and the 'entity view' seem equally  
> plausible to me, and I cannot see why the 'relation view' should  
> win by default.
>
> I think it would be instructive if we would try to go through some  
> real examples where n-ary relations and temporal indexing seem to  
> be necessary, and try to formulate it in standard OWL. Let's try to  
> talk through clear examples and not through references to the  
> history of formal logics -- that would be better understandable to  
> most readers of this mailing list (me included). Then we can  
> compare different approaches and try to find the one that is the  
> most intuitive, consistent, flexible and OWL-DL-compatible.
>
> I will try to express the examples in AFO (http://esw.w3.org/topic/ 
> HCLS/AFO_Foundational_Ontology), a very simple ontology that  
> distinguishes objects, processes and qualities. Objects and  
> processes can have 'full temporal parts' that are made up of the  
> whole object at a certain timespan ('lifetime'). Qualities have the  
> same lifetime as the objects or processes they inhere in.
>
>>>> Organism has_feature SOME (Temperature_Feature THAT
>>>>         has_temporal_extent VALUE temporal_extent_1 AND
>>>>         has_state SOME (has_magnitude VALUE 37 AND has_units VALUE
>>>> degrees_C))
>
> Similar statement in AFO (on the instance-level, just because it is  
> easier to write):
>
> -----
> <Organism> <has_temporal_part> <Organism_at_timespan_1> .
> <Organism_at_timespan_1> <has_quality> <temperature_quality> .
> <temperature_quality> <has_value> "37" .
> -----
>
>
>>> Protein that has_feature SOME (Location_Feature THAT
>>> 	has_temporal_extent VALUE temporal_extent_1 AND
>>> 	has_location SOME cytoplasm)
>
> In AFO:
> -----
> <Protein> <has_temporal_part> <Protein_at_timespan_1> .
> <Protein_at_timespan_1> <located_in> <cytoplasm> .
> -----

Why not cytoplasm_at_timespan_1?

>
> cheers,
> 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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> Der kanns mit allen: http://www.gmx.net/de/go/multimessenger
>
>
Received on Tuesday, 22 May 2007 16:00:39 UTC

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