Re: Observations about facts in genomics

2013-03-21 Thread Peter Ansell
On 22 March 2013 14:38, Alan Ruttenberg wrote: > On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell > wrote: >> On 22 March 2013 12:05, Alan Ruttenberg wrote: >> > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll >> > wrote: >> >> >> >> To me, that seems to lead us back to the earlier discussion (r

Re: Observations about facts in genomics

2013-03-21 Thread Alan Ruttenberg
On Thu, Mar 21, 2013 at 10:19 PM, Alan Ruttenberg wrote: > > > On Thu, Mar 21, 2013 at 10:15 PM, Pat Hayes wrote: > >> >> On Mar 21, 2013, at 11:38 PM, Alan Ruttenberg wrote: >> >> > >> > >> > On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell >> wrote: >> > On 22 March 2013 12:05, Alan Ruttenberg >

Re: Observations about facts in genomics

2013-03-21 Thread Alan Ruttenberg
On Thu, Mar 21, 2013 at 10:15 PM, Pat Hayes wrote: > > On Mar 21, 2013, at 11:38 PM, Alan Ruttenberg wrote: > > > > > > > On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell > wrote: > > On 22 March 2013 12:05, Alan Ruttenberg > wrote: > > > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll > wrote:

Re: Observations about facts in genomics

2013-03-21 Thread Peter Ansell
On 22 March 2013 15:15, Pat Hayes wrote: > On Mar 21, 2013, at 11:38 PM, Alan Ruttenberg wrote: >> On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell wrote: >> On 22 March 2013 12:05, Alan Ruttenberg wrote: >> > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll wrote: >> >> >> >> I am not sayin

Re: Observations about facts in genomics

2013-03-21 Thread Pat Hayes
On Mar 21, 2013, at 11:38 PM, Alan Ruttenberg wrote: > > > On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell wrote: > On 22 March 2013 12:05, Alan Ruttenberg wrote: > > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll wrote: > >> > > I am not saying that science presented as fact is infall

Re: Observations about facts in genomics

2013-03-21 Thread Alan Ruttenberg
On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell wrote: > On 22 March 2013 12:05, Alan Ruttenberg wrote: > > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll > wrote: > >> > >> To me, that seems to lead us back to the earlier discussion (rathole?) > >> about owl:sameAs > >> I tend to a view that t

Re: Observations about facts in genomics

2013-03-21 Thread Jeremy J Carroll
Alan, that is a superb message, very well-articulated I will ponder it. And as I said I don't really want to keep doing this theoretical dance and look forward to more substantive conversations. Jeremy On Mar 21, 2013, at 9:38 PM, Alan Ruttenberg wrote: > > > On Thu, Mar 21, 2013 at 7:

Re: Observations about facts in genomics

2013-03-21 Thread Peter Ansell
On 22 March 2013 12:05, Alan Ruttenberg wrote: > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll wrote: >> >> To me, that seems to lead us back to the earlier discussion (rathole?) >> about owl:sameAs >> I tend to a view that there are diminishing returns in terms of levels of >> indirection he

Re: Observations about facts in genomics

2013-03-21 Thread Alan Ruttenberg
On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll wrote: > To me, that seems to lead us back to the earlier discussion (rathole?) > about owl:sameAs > Don't think so. It is a simple application of the pattern of having information about something. The statements don't have to be true. > > Yes,

Re: 'Variants' and Chromosome Modelling

2013-03-21 Thread Michel Dumontier
On Thu, Mar 21, 2013 at 6:00 PM, Jeremy J Carroll wrote: > > Jerven suggests: > > "instead of saying chrM it would have been solved by > using > http://my.lab.org/confidential/patientXXYYZZ/genome/sampleXX/ChrM/assemblyTTv43/VariantCalls5 > " > > rather than continuing the philosophical/theologic

Re: 'Variants' and Chromosome Modelling

2013-03-21 Thread Joachim Baran
On 2013-03-21, at 6:00 PM, Jeremy J Carroll wrote: > "instead of saying chrM it would have been solved by > using > http://my.lab.org/confidential/patientXXYYZZ/genome/sampleXX/ChrM/assemblyTTv43/VariantCalls5"; > In this way of thinking, I am not really interested in an assembly of ChrM > for

'Variants' and Chromosome Modelling

2013-03-21 Thread Jeremy J Carroll
Jerven suggests: "instead of saying chrM it would have been solved by using http://my.lab.org/confidential/patientXXYYZZ/genome/sampleXX/ChrM/assemblyTTv43/VariantCalls5"; rather than continuing the philosophical/theological threads …. I am interested in this practical question. chrM as an ad

ESWC 2013: Call for Participation

2013-03-21 Thread Philipp Cimiano
ESWC 2013 Call for Participation http://2013.eswc-conferences.org/ ESWC 2013 is the major Europe-based conference on Semantic Technologies and the Semantic Web. It is the ideal venue for discussing the latest scientific results and technology innovations and is equally relevant to researchers,

Re: Observations about facts in genomics

2013-03-21 Thread Pat Hayes
Well, I don't quite know what to say. I feel a bit like a designer of cheap, workable, everyday town cars, and I have a customer who wants a Ferrari. I agree, Jeremy, you have a hard problem here. It sounds like you need statistical or probabilistic methods to keep track of these small likeliho

Re: owl:sameAs - Is it used in a right way?

2013-03-21 Thread Pat Hayes
On Mar 20, 2013, at 9:58 PM, David Booth wrote: > On 03/20/2013 12:04 AM, Pat Hayes wrote: >> >> On Mar 18, 2013, at 4:04 PM, David Booth wrote: >>> On 03/17/2013 10:02 PM, Pat Hayes wrote: On Mar 16, 2013, at 11:26 PM, David Booth wrote: > [ . . . ] > Read the spec: http://www.w3.org/T

Re: owl:sameAs - Is it used in a right way?

2013-03-21 Thread Kingsley Idehen
On 3/21/13 12:26 PM, Michel Dumontier wrote: my problem largely lies in the "identifies" relation between a URI and a document Yes, but in the context of RDF based Linked Data, a single HTTP URI can in fact denote one thing in a manner to uses indirection (implicit or explicit) to identify a

Re: owl:sameAs - Is it used in a right way?

2013-03-21 Thread Michel Dumontier
my problem largely lies in the "identifies" relation between a URI and a document. and generally, that it wouldn't represent as a triad, but a bilateral relation between an entity (identified by uri) and a document (which refers or describes it). m. On Thu, Mar 21, 2013 at 11:05 AM, Kingsley Ideh

Re: owl:sameAs - Is it used in a right way?

2013-03-21 Thread Kingsley Idehen
On 3/21/13 10:57 AM, Michel Dumontier wrote: Kingsley, I think you raise good points. I also nominally speak of entities, their attributes and the relations that hold between them. But I think your diagram is somewhat misleading. URIs do denote (can stand in the place of) entities of interest

Re: owl:sameAs - Is it used in a right way?

2013-03-21 Thread Michel Dumontier
Kingsley, I think you raise good points. I also nominally speak of entities, their attributes and the relations that hold between them. But I think your diagram is somewhat misleading. URIs do denote (can stand in the place of) entities of interest in order to refer to and/or describe them. If you

Re: Observations about facts in genomics

2013-03-21 Thread Jerven Bolleman
On Thu, Mar 21, 2013 at 2:55 PM, Phillip Lord wrote: > This is a broken definition of "good" to my mind. It suggests that we > should make all the distinctions that we can make, all the time. > Unfortunately, this means that everyone bears the cost of the complexity > all the time also. True but t

RE: owl:sameAs - Is it used in a right way?

2013-03-21 Thread Erich Gombocz
Agree with Kingsley. The challenges have been really reflected throughout the entire trail of these conversations, and lots of valid points have been made from diverse *perspectives* presented as the only way of thinking about it. We need to have a clear strategy based on rules and definiti

Re: owl:sameAs - Is it used in a right way?

2013-03-21 Thread Kingsley Idehen
On 3/20/13 10:58 PM, David Booth wrote: Thus, to be very clear, under the existing RDF Semantics specification, a given URI does *not* necessarily map to only one resource. True, but I don't think the statement above always provides the clarity intended. "Resource" is a synonym of "Entit

Re: Observations about facts in genomics

2013-03-21 Thread Phillip Lord
This is a broken definition of "good" to my mind. It suggests that we should make all the distinctions that we can make, all the time. Unfortunately, this means that everyone bears the cost of the complexity all the time also. A good data model should be an accurate reflection of biology. But