W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2007

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

From: Alan Rector <rector@cs.man.ac.uk>
Date: Wed, 23 May 2007 10:05:35 +0100
Message-Id: <76CC82E5-B2A9-4505-AF49-134AD0D19A49@cs.man.ac.uk>
Cc: samwald@gmx.at, public-semweb-lifesci@w3.org
To: Chris Mungall <cjm@fruitfly.org>


On 22 May 2007, at 17:00, Chris Mungall wrote:

>
>
> On May 22, 2007, at 8:04 AM, samwald@gmx.at wrote:
>
>>
>> I h
>>
>> 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" .


Other than syntax - and indices for the individuals and typographic  
conventions, how is this different from

anOrganism has_temporal_part VALUE organiism_1_at_timespan_1
Organism_at_timespan_1 has_quality VALUE aTemperature_quality
aTemperature_quality has_value VALUE 37.

which would classify to be as of type

	Organism THAT has_temporal_part SOME
		(Organism_temporal_part THAT has_quality SOME
			(Temperature_quality THAT has_value VALUE 37))

which could be written more simply if the correct domains etc were in  
place as

	Organism THAT has_temporal_part SOME (has_quality SOME  
Temperature_quality THAT has_value VALUE 37))

And how does this relate to histories?


(There is a separate issue about the use of numbers rather than  
quantities as values - but that's for a different email.)


>> -----
>>
>>
>>>> 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
>>
>>
>>
>> .
>> -- 
>> Psssst! Schon vom neuen GMX MultiMessenger gehört?
>> Der kanns mit allen: http://www.gmx.net/de/go/multimessenger
>>
>>
>
>

-----------------------
Alan Rector
Professor of Medical Informatics
School of Computer Science
University of Manchester
Manchester M13 9PL, UK
TEL +44 (0) 161 275 6149/6188
FAX +44 (0) 161 275 6204
www.cs.man.ac.uk/mig
www.clinical-esciences.org
www.co-ode.org
Received on Wednesday, 23 May 2007 09:05:36 UTC

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