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

Re: Advancing translational research with the Semantic Web

From: <samwald@gmx.at>
Date: Wed, 30 May 2007 16:44:27 +0200
Message-ID: <20070530144427.83350@gmx.net>
To: public-semweb-lifesci@w3.org, obo-relations@lists.sourceforge.net

Matthias wrote:
> > The specific difficulties with the location of objects and  
> > processes are to some degree inherent in the current OWL versions  
> > of BFO and the Relation Ontology. They make it a bit difficult to  
> > create statements that relate processes to certain locations and  
> > force you to make statements about the participants of the process  
> > instead.

Alan wrote:
> Could you elaborate on this? My understanding is that according to  
> BFO, pretty much everything about a process is determined by the  
> participants (the process is existentially dependent on the  
> participants). 

Yes. But there are some situations where we might prefer to talk about the 'location' of the process directly, without explicitly talking about its participants.

Let me introduce the relation <is_location_of_process> as an example.
<A> <is_location_of_process> <B> means that <A> contains all of the participants that make up process <B>.
A concrete example for the use of this property would be

<Human_organism> <is_location_of_process> <blood_circulation> .

The property would have two main advantages:
1) It does not force us to make statements about the participants of a process when we are unsure what the actual participants are. In the example above, we would probably be forced to introduce a fiat part of the human organism like 'human_organism_circulatory_system' that is not very clearly defined. We had a similar problem in our ontology of neuronal morphology with the localization of the process of ionic currents.
2) It gives us the possibility to say that the physical extent of a process is CONFINED to the extent of a certain object. Normally, the process of blood_circulation is confined to the spatial extent of the human_organism, unless you are undergoing blood dialysis. This property would allow us to state this fact a bit more easily in OWL with its open world assumption.

This problem is probably not significant enough to warrant the introduction of such a new relation, but at least it is a little difficulty that many people working with the Relation Ontology will encounter. Maybe it should be addressed in the documentation of the ontology.

Matthias Samwald


Yale Center for Medical Informatics, New Haven /
Section on Medical Expert and Knowledge-Based Systems, Vienna /

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Received on Wednesday, 30 May 2007 14:44:51 UTC

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