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Re: Advancing translational research with the Semantic Web

From: <samwald@gmx.at>
Date: Fri, 18 May 2007 19:03:23 +0200
Cc: public-semweb-lifesci@w3.org
Message-ID: <20070518170323.281670@gmx.net>
To: Alan Ruttenberg <alanruttenberg@gmail.com>, Eric.Jain@isb-sib.ch

> By a reasonable  definition of process  (following, e.g.,  the BFO  
> papers), if a process happens in a location, then each participant is  
> located in some part of that location. 
> In fact, very few such axioms are currently encoded in the BFO and  
> OBO ontologies

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. That is one of the problems I want to address with the creation of the so-called 'AFO Foundational Ontology' [1]. This issue is also addressed in a recent publication in BMC Bioinformatics by Stefan Schulz et al. [2].

> In the mean time, the approach we tooks for the demo was to add some  
> ability to query over inferred knowledge by precomputing specific  
> pieces of information which we knew would be useful for some of the  
> queries we wanted to do, for example the part_of relations in the GO.

I also think that this approach is the way to go for the immediate future (and maybe even in the long term). Not all of the complexities of OWL inference are actually required when the ontology and the data are deployed to a triple store (altough they ARE needed when the ontology is created and debugged). Huajun Chen and I are working on a proposal on how to make OWL ontologies 'digestable' in this way.

[1] http://esw.w3.org/topic/HCLS/AFO_Foundational_Ontology
[2] http://www.biomedcentral.com/1471-2105/8/134/abstract

Matthias Samwald


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


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Received on Friday, 18 May 2007 17:03:30 UTC

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