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Re: Playing with sets in OWL...

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Fri, 8 Sep 2006 21:50:30 -0400
Message-Id: <FAE17943-87B0-41D5-9F24-268907229CCE@gmail.com>
Cc: "Marco Brandizi" <brandizi@ebi.ac.uk>, semantic-web@w3.org, public-semweb-lifesci@w3.org
To: "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com>

Yes. However I don't think I would change anything I wrote. Because  
OWL works  in the open world, we can say that all these things  
exists, but only supply the details that we need. But having the  
framework which explains the meaning of what is supplied is one of  
the points of using ontologies. In this case, if all we know is that  
there was some computation that led to this gene set we could use  
some arbitrary name for it (remembering that if we decided to  
represent it later/ merge it with the experimental run we can use  
owl:sameAs to merge our name with the actual name).

So. with reference to this ontology (generated by Marco, or imported   
from some standard) he could simply state:

Individual(c1 type(Computation)
    value(geneComputedAsExpressed g1)
    value(geneComputedAsExpressed g2)
    value(geneComputedAsExpressed g3)
  )

If he wanted to state that the source was an array experiment (but he  
didn't know the details), he could add to c1

    value(fromExperiment Individual( type(ExpressionProfileExperiment)))

which uses an anonymous individual (blank node) of the appropriate  
type. Now you know that the data originally came from an expression  
profile experiment,  though you haven't needed to add any other  
information other than that.

The pattern that Marco mentions that is closest to this is

>>> set1 isA GeneSet
>>> set1 hasMember g1, g2, g3

in that we are using the property values on an instance to represent  
the set. But the point I wanted to make was that a gene set isn't  
some arbitrary set. It is a choice, chosen for a reason/purpose, and  
that the ontology should explicitly represent those reasons/purposes.

If there are defined kinds of follow up, then he could define define  
an instance to represent that process too.

Finally, I wanted to make the technical point that that he doesn't  
need to use constructs of the form:

>>> set1 derivesFromUnionOf set2, set3

OWL provides the ability to say these things, even when the "set" is  
the property values of an instance, for example, given

Individual(c1 type(Computation)
    value(geneComputedAsExpressed g1)
  )

  Individual(c2 type(Computation)
    value(geneComputedAsExpressed g2)
    value(geneComputedAsExpressed g3)
)

supposing that he wanted to represent a followup list to be verified  
by RT PCR represented by the class RTPCRFollowup.
Let's say that wanted to call the property geneToFollowUp, with  
inverse geneFollowedUpIn

Individual(RTPCRFollowup1  type(RTPCRFollowup))

EquivalentClasses(
   unionOf(
     restriction(GeneExpressedAccordingTo hasValue(c1))
     restriction(GeneExpressedAccordingTo hasValue(c2)))
   restriction(geneFollowedUpIn hasValue(RTPCRFollowup1))))

Now, e.g. Pellet, will conclude that the values of the property  
geneToFollowUp of instance RTPCRFollowup1 is exactly g1, g2, g3

Of course that's not the only way to do it, but it does show that OWL  
reasoning can make it economical to represent and work with sets  
without having to go off and recapitulate set theory.

-Alan

On Sep 8, 2006, at 7:41 PM, Miller, Michael D (Rosetta) wrote:

>
> 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 Saturday, 9 September 2006 01:50:39 UTC

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