- 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
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 23:42:01 UTC