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Questions about SPE ontology

From: Marco Brandizi <brandizi@ebi.ac.uk>
Date: Tue, 29 Aug 2006 09:03:20 +0100
Message-ID: <44F3F4C8.9050109@ebi.ac.uk>
To: public-semweb-lifesci@w3.org

Sorry, I meant to send the message below to the mailing list... not only 
to the sender...

Thanks to AJ for the prompt reply.

AJ Chen wrote:
> I uploaded one mock example for each of the class (object) of the SPE 
> ontology to the wiki at 
> http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce.  Hope these 
> The examples are created from the demo application at 
> http://web2express.org/demo/. You can take a look at the demo to see how 
> easy it is to publish experiment data and research tool information.

Hi all,

I've been following the developments of SPE ontology and applications
for a while, since my PhD Project is related to the idea of formal
representation of experiments and the knowledge belonging to experiment
cycle (hyphotesis, conclusions, people and their interests, etc.).

I'd like to ask some questions about the SPE project.

- So far there are similar ongoing projects:
   - http://swan.mindinformatics.org/
   - http://expo.sourceforge.net/

I'd like some words of comparison of the above projects (expecially from
the respective authors) and about possible plans for joining the
efforts. What are the differences in main entities, relations, contexts
and communities in which the projects have started?

- Is SPE defined in RDF or is OWL used as well, so that some inference
capabilities of OWL could be exploited?

- Concerning SPE, I guess that Hypothesis and Conclusion are still under
development (they're mentioned in Requirements document but not in 0.2
specification), what shape would these entities have? I read from

> Note: Hypothesis, Dada and Conclusion may be simply represented by
> string or literal, which is sufficient for search engine application.
> But, it may offer advantages for some applications if they are
> represented as object. If anyone has an application that requires
> object representation for Hypothesis, Dada and Conclusion of an
> experiment, please contribute a use case and define the objects

I'd like to exchange opinions about this point. Having a simple text,
plus some meta-data, as an hypothesis or a conclusion ("claims" in the
follow), is simple and may be somehow useful. However, having further
formalization could be even more useful, particularly modeling a claim,
as a triple/statement would allow to re-use such pieces of knowledge in
a semantic-web fashion (machine-readable knowledge, inference etc.).

But I'm feeling that handling statements in RDF world is not so easy,
expecially if ones wants to do something at the level of OWL and
inference. I am attempting to at least trace who is claiming what and
why, by means of named graphs and the good NG4J library for Jena [1]. It
is somehow useful and allows selection of sub-sets of statements [2],
however, it is not so much clear how the idea of quadlets could be
integrated with the upstream layers of OWL and layers, and of course
with the DL theory (C-OWL? Modal DL? Simple filters that, at the level
of named graphs and RDF define what is "true" and can be used upstream
with OWL? Is there some standardization effort?).

Opinions and suggestions welcome.


[1] http://www.wiwiss.fu-berlin.de/suhl/bizer/ng4j/


Marco Brandizi <brandizi@ebi.ac.uk>
Received on Tuesday, 29 August 2006 08:04:42 UTC

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