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RE: Playing with sets in OWL...

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Fri, 8 Sep 2006 16:41:35 -0700
To: "Alan Ruttenberg" <alanruttenberg@gmail.com>, "Marco Brandizi" <brandizi@ebi.ac.uk>
cc: semantic-web@w3.org, public-semweb-lifesci@w3.org
Message-ID: <E1GLpyp-0000tE-Jn@aji.w3.org>

Hi Alan,

What you are describing is described in MAGE-OM/MAGE-ML, as a UML model
to capture the real world aspects of running a microarray experiment.

Typically at the end of this process a set of genes is identified as
being interesting for some reason and one wants to know more about this
set of genes beyond the microarray experiment that has been performed.

I might be wrong but I think that is where Marco is starting, at the end
of the experiment for follow-up.

cheers,
Michael

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Alan Ruttenberg
> Sent: Friday, September 08, 2006 3:07 PM
> To: Marco Brandizi
> Cc: semantic-web@w3.org; public-semweb-lifesci@w3.org
> Subject: Re: Playing with sets in OWL...
> 
> 
> 
> Hi Marco,
> 
> There are a number of ways to work with sets, but I don't think I'd  
> approach this problem from that point of view.
> Rather,  I would start by thinking about what my domain instances  
> are, what their properties are, and what kinds of questions I 
> want to  
> be able to ask based on the representation. I'll sketch this out a  
> bit, though the fact that I name an object or property doesn't mean  
> that you have to supply it (remember OWL is open-world) - still  
> listing these make the ontology makes your intentions clearer  and  
> the ontology easier to work with by others.
> 
> The heading in each of these is a class, of which you would make one  
> or more instances to represent your results.
> The indented names are properties on instances of that class.
> 
> An expression technology:
>     Vendor:
>     Product: e.g. array name
>     Name of spots on the array
>     Mappings:  (maps of spot to gene - you might use e.g. 
> affymetrix,  
> or you might compute your own)
> 
> ExpressionTechnologyMap
>    SpotMapping: (each value a spot mapping)
> 
> Spot mapping:
>    SpotID:
>    GeneID:
> 
> An expression profile experiment (call yours exp0)
>     When done:
>     Who did it:
>     What technology was used: (an expression technology)
>     Sample: (a sample)
>     Treatment: ...
>     Levels: A bunch of pairs of spot name, intensity
> 
> Spot intensity
>    SpotID:
>    Intensity:
> 
> A  computation of which spots/genes are "expressed" (call yours c1)
>     Name of the method : e.g. mas5 above threshold
>     Parameter of the method: e.g. the threshold
>     Experiment: exp0
>     Spot Expressed: spots that were over threshold
>     Gene Computed As Expressed: genes that were over threshold
> 
> And maybe:
> 
> Conclusion
>     What was concluded:
>     By who:
>     Based on: c1
> 
> All of what you enter for your experiment are instances (so 
> there are  
> no issues of OWL Full)
> 
> Now, The gene set you wanted can be expressed as a class:
> 
> Let's define an inverse property of   
> "GeneComputedAsExpressed", call  
> it "GeneExpressedAccordingTo"
> 
> Class(Set1 partial restriction(GeneExpressedAccordingTo hasValue(c1))
> 
> Instances of Set1 will be those genes. You may or may not want to  
> actually define this class. However I don't think that youneed
> to add any properties to it. Everything you would want to say  
> probably wants to be said on one of the instances - the experiment,  
> the computation, the conclusion, etc.
> 
> Let me know if this helps/hurts - glad to discuss this some more
> 
> -Alan
> 
> 
> 
> 
> 2)
> 
> On Sep 8, 2006, at 11:58 AM, Marco Brandizi wrote:
> 
> >
> > Hi all,
> >
> > sorry for the possible triviality of my questions, or the 
> messed-up  
> > mind
> > I am possibly showing...
> >
> > I am trying to model the grouping of individuals into sets. In my
> > application domain, the gene expression, people put 
> together, let's  
> > say
> > genes, associating a meaning to the sets.
> >
> > For instance:
> >
> > Set1 := { gene1, gene2, gene3 }
> >
> > is the set of genes that are expressed in experiment0
> >
> > (genei and exp0 are OWL individuals)
> >
> >
> > I am understanding that this may be formalized in OWL by:
> >
> > - declaring Set1 as owl:subClassOf Gene
> > - using oneOf to declare the membership of g1,2,3
> > (or simpler: (g1 type Set1), (g2 type Set1), etc. )
> > - using hasValue with expressed and exp0
> >
> > (right?)
> >
> > Now, I am trying to build an application which is like a semantic  
> > wiki.
> >
> > Hence users have a quite direct contact with the underline  
> > ontology, and
> > they can write, with a simplified syntax, statements about a subject
> > they are describing (subject-centric approach).
> >
> > Commiting to the very formal formalism of OWL looks a bit 
> too much...
> > formal... ;-) and hard to be handled with a semantic wiki-like  
> > application.
> >
> > Another problem is that the set could have properties on 
> its own, for
> > instance:
> >
> > Set1 hasAuthor Jhon
> >
> > meaning that John is defining it. But hasAuthor is 
> typically used for
> > individuals, and I wouldn't like to fall in OWL-Full, by 
> making an OWL
> > reasoner to interpret Set1 both as an individual and a class.
> >
> > Aren't there more informal (although less precise) methods to model
> > sets, or list of individuals?
> >
> > An approach could be modeling some sort of set-theory over  
> > individuals:
> >
> > set1 isA GeneSet
> > set1 hasMember g1, g2, g3
> > ...
> >
> > set1 derivesFromUnionOf set2, set3
> >
> > ...
> >
> > But I am not sure it would be a good approach, or if someone else
> > already tried that.
> >
> > Any suggestion?
> >
> >
> > Thanks in advance for a reply.
> >
> > Cheers.
> >
> > -- 
> >
> > 
> ==============================================================
> ======== 
> > =========
> > Marco Brandizi <brandizi@ebi.ac.uk>
> > http://gca.btbs.unimib.it/brandizi
> >
> >
> 
> 
> 
> 
Received on Friday, 8 September 2006 23:42:03 UTC

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