Late post...
there may be a limit in RDF/OWL here... in that microarray (as other
information) is not "digital". That is, it doesn't really fit the
assumption that everything you are talking about has a true/false
property.
In this thread, talking about gene sets, there is always the prope
All
I forwarded the email to Ian Horrocks, he of reasoner fame, and his
answer is below.
Envelope-to: [EMAIL PROTECTED]
Cc: Dmitry Tsarkov <[EMAIL PROTECTED]>
From: Ian Horrocks <[EMAIL PROTECTED]>
Subject: Re: Performance issues with OWL Reasoners (Was RE: Playing
with
On Thu, 14 Sep 2006, Kashyap, Vipul wrote:
OWL reasoners support two types of reasoning:
1. ABox reasoning (reasoning about instance data). Scalability here is being
achieved here by leveraging relational database technology (which is
acknowledged to be scalable) and mapping OWL instance
blic-semweb-lifesci-
> [EMAIL PROTECTED] On Behalf Of Alan Ruttenberg
> Sent: Monday, September 11, 2006 7:35 PM
> To: William Bug
> Cc: Miller, Michael D (Rosetta); Marco Brandizi; [EMAIL PROTECTED];
> public-semweb-lifesci@w3.org
> Subject: Re: Playing with sets in OWL...
>
&
Robert.
00:24 12/09/2006, Alan Ruttenberg wrote:
On Sep 10, 2006, at 8:21 AM, Marco Brandizi wrote:
- ...how much are RDF and OWL scalable? Let's take a small data set
of 100 microarray experiments, with 10k probe sets x 10
hybridiazations. We would have (at least) 10 millions numbers to
han
On Sep 8, 2006, at 11:39 PM, William Bug wrote:
3) Re:anonymous classes/individuals of the type Alan describes:
These are essentially "blank nodes" in the RDF sense - "unnamed"
nodes based on a collection of necessary restrictions, if I
understand things correctly. Please pardon the nai
On Sep 10, 2006, at 8:21 AM, Marco Brandizi wrote:
- ...how much are RDF and OWL scalable? Let's take a small data set
of 100 microarray experiments, with 10k probe sets x 10
hybridiazations. We would have (at least) 10 millions numbers to
handle, plus several annotations, plus inference,
Marco,
> 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 b
Hi all,
First, thank you all very much for all the interesting replies. I am not
sure I am understanding all of them, anyway...
> 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
:[EMAIL PROTECTED]
*Sent:* Friday, September 08, 2006 8:39 PM
*To:* Alan Ruttenberg
*Cc:* Miller, Michael D (Rosetta); Marco Brandizi;
[EMAIL PROTECTED]; public-semweb-lifesci@w3.org
*Subject:* Re: Playing with sets in OWL...
I think Alan is making a very important general po
One of the possible modeling options is to express a gene g1 as a subclass
of the Gene class. Consider the model given be Alan below:
> Individual(c1 type(Computation)
> value(geneComputedAsExpressed g1)
> value(geneComputedAsExpressed g2)
> value(geneComputedAsExpressed g3)
> )
H
at
the end
of the experiment for follow-up.
cheers,
Michael
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Alan Ruttenberg
Sent: Friday, September 08, 2006 3:07 PM
To: Marco Brandizi
Cc: [EMAIL PROTECTED]; public-semweb-lifesci@w3.org
Subject: Re: Playing
f
> Alan Ruttenberg
> Sent: Friday, September 08, 2006 3:07 PM
> To: Marco Brandizi
> Cc: [EMAIL PROTECTED]; 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'
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 r
Kashyap, Vipul wrote:
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
[VK] Actually, I missed this
> 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 m
> Another problem is that the set could have properties on its own, for
> instance:
>
> Set1 hasAuthor Jhon
[VK] One way of doing this could be to use "has Author" as an annotation of the
class Set1. I believe, some DL reasoners do not reason on Annotations, but at
the same time you can query
17 matches
Mail list logo
