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Re: Re: HCLSig July 6 Teleconference Agenda

From: <samwald@gmx.at>
Date: Thu, 06 Jul 2006 17:03:16 +0200
Message-ID: <20060706150316.120000@gmx.net>
To: AJ Chen <canovaj@gmail.com>, public-semweb-lifesci@w3.org

Some thoughts:

You should consider right from the start how (and if) you are integrating information that is represented in with another RDF/OWL ontology. For example a researcher might want to make his experiments about protein interactions public with your ontology, but he also wants to publish the actual data based on another ontology like BioPAX [1]. How does he connect the descripton of the experiments with the data in BioPAX format?
I would suggest to implement this functionality through a property with unrestricted range. This property points from the description of the experiment (based on your ontology) to a certain instance in the graph that describes the interaction data (in BioPAX format). Lets call this property "yielded-resource" for now.
Of course, the graph describing protein interactions consists of more than one instance, and it would be preferable to agree on some rules that tell us to which of these instances we should point with the "yielded-resource" property. This should be quite intuitive, though.
We could also think about referring to named graphs, but I would prefer the mechanism described above, as it stays 'inside' the RDF/OWL world, while labeled graphs are somewhat exotic from the viewpoint of RDF.

You are probably aware of it, but anyways I want to point out that many of the classes you proposed are already part of the FOAF ontology [2]. Re-using some of the classes and properties of FOAF should really be considered.

>             project
see foaf:Project
>             researcher
see foaf:Person

>             group
see foaf:Group

>             organization
see foaf:Organization

[1] http://www.biopax.org/
[2] http://xmlns.com/foaf/0.1/

kind regards,
Matthias Samwald

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Received on Thursday, 6 July 2006 15:10:03 UTC

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