On Thu, Apr 2, 2009 at 5:35 PM, Michel_Dumontier
wrote:
>> Actually, I'd say OWL is to blame here... that is, the OWL class was
>> not properly defined.
>
> Just to clarify - it's not OWL that's the problem. It's the
> representation of Chemistry in a formal logic-based language where it
> actuall
lic-semweb-lifesci
> Subject: Re: blog: semantic dissonance in uniprot
>
> On Tue, Mar 31, 2009 at 2:09 PM, Matthias Samwald
> wrote:
> >>> Reaction equations describe stochastic processes, that's why you
> can
> >>> have non-integer molecule numbers
> &g
On Tue, Mar 31, 2009 at 2:09 PM, Matthias Samwald wrote:
>>> Reaction equations describe stochastic processes, that's why you can
>>> have non-integer molecule numbers
>>
>> I think you can't have non-integer molecule numbers because it makes
>> no chemical sense. Half a molecule is a whole molecu
On Tue, Mar 31, 2009 at 2:49 PM, Oliver Ruebenacker wrote:
> On Tue, Mar 31, 2009 at 8:30 AM, Wacek Kusnierczyk
> wrote:
>> i'd agree that having non-integer *molecule numbers* sounds nonsense,
>> but having non-integer *relative molecule numbers* certainly doesn't.
>> in any case, the equation
>
On Apr 2, 2009, at 2:47 AM, Wacek Kusnierczyk wrote:
Pat Hayes wrote:
On Mar 31, 2009, at 7:49 AM, Oliver Ruebenacker wrote:
What about this statement:
"Two grams of hydrogen react with 16 grams of oxygen to 18 grams of
water"
If I were trying to do a professional job of 'ontologizing' t
Pat Hayes wrote:
>
> On Mar 31, 2009, at 7:49 AM, Oliver Ruebenacker wrote:
>
>> What about this statement:
>>
>> "Two grams of hydrogen react with 16 grams of oxygen to 18 grams of
>> water"
>
> If I were trying to do a professional job of 'ontologizing' this, it
> would be a formal rendering of
well.
Quite.
Pat
Cheers,
Matthias Samwald
DERI Galway, Ireland
http://deri.ie/
Konrad Lorenz Institute for Evolution & Cognition Research, Austria
http://kli.ac.at/
--
From: "Oliver Ruebenacker"
Sent: Monday, March 30, 2009 10:53 PM
On Mar 31, 2009, at 7:49 AM, Oliver Ruebenacker wrote:
Hello Wacek, All,
On Tue, Mar 31, 2009 at 8:30 AM, Wacek Kusnierczyk
wrote:
i'd agree that having non-integer *molecule numbers* sounds nonsense,
but having non-integer *relative molecule numbers* certainly doesn't.
in any case, the
On Mar 30, 2009, at 3:53 PM, Oliver Ruebenacker wrote:
Hello Pat, All,
Let me try to take a step back and summarize what I think I learned
so far:
The Ontologists have gained impressive mastery over what I would
call the World of Discrete Particulars. They know how to deal with
parti
2009/3/31 Phillip Lord :
> "Matthias Samwald" writes:
>> To use a (still quite naive) physics example: 'Temperature' is a quality of
>> an
>> object (say, a solution in a petri dish). This quality only inheres in the
>> solution, but not in a single molecule.
>
> I think this is wrong; temperatur
Hello Wacek, All,
On Tue, Mar 31, 2009 at 9:00 AM, Wacek Kusnierczyk
wrote:
> Oliver Ruebenacker wrote:
>> What about this statement:
>>
>> "Two grams of hydrogen react with 16 grams of oxygen to 18 grams of water"
> what about it?
Can we make a correct statement that says what appea
Oliver Ruebenacker wrote:
> Hello Wacek, All,
>
> On Tue, Mar 31, 2009 at 8:30 AM, Wacek Kusnierczyk
> wrote:
>
>> i'd agree that having non-integer *molecule numbers* sounds nonsense,
>> but having non-integer *relative molecule numbers* certainly doesn't.
>> in any case, the equation
>>
Hello Wacek, All,
On Tue, Mar 31, 2009 at 8:30 AM, Wacek Kusnierczyk
wrote:
> i'd agree that having non-integer *molecule numbers* sounds nonsense,
> but having non-integer *relative molecule numbers* certainly doesn't.
> in any case, the equation
>
> N2O2 -> 2 NO2 + 1/2 O2
>
> is equival
Matthias Samwald wrote:
>
>>> Reaction equations describe stochastic processes, that's why you can
>>> have non-integer molecule numbers
>>
>> I think you can't have non-integer molecule numbers because it makes
>> no chemical sense. Half a molecule is a whole molecule of a different
>> kind.
>
> Y
Reaction equations describe stochastic processes, that's why you can
have non-integer molecule numbers
I think you can't have non-integer molecule numbers because it makes
no chemical sense. Half a molecule is a whole molecule of a different
kind.
You can have reaction equations that look li
"Matthias Samwald" writes:
> To use a (still quite naive) physics example: 'Temperature' is a quality of an
> object (say, a solution in a petri dish). This quality only inheres in the
> solution, but not in a single molecule.
I think this is wrong; temperature can be applied to a single molecul
ri.ie/
Konrad Lorenz Institute for Evolution & Cognition Research, Austria
http://kli.ac.at/
--
From: "Oliver Ruebenacker"
Sent: Monday, March 30, 2009 10:53 PM
To: "Pat Hayes"
Cc: "Matthias Samwald" ; "public-semwe
Hello Pat, All,
Let me try to take a step back and summarize what I think I learned so far:
The Ontologists have gained impressive mastery over what I would
call the World of Discrete Particulars. They know how to deal with
particulars, classes of particulars and cardinality restrictions
On Mar 30, 2009, at 11:13 AM, Oliver Ruebenacker wrote:
A class may not be instantiated in every single use, but it is
intended to be instantiated in some cases.
Why?
Pat
IHMC (850)434 8903 or
On Mar 30, 2009, at 9:59 AM, Oliver Ruebenacker wrote:
Hello Pat, All,
On Sun, Mar 29, 2009 at 11:35 PM, Pat Hayes wrote:
On Mar 29, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
I am assuming that these classes all make a commitment about what
their instances mean, so users could decla
Hello Bijan, All,
On Mon, Mar 30, 2009 at 12:20 PM, Bijan Parsia wrote:
> On 30 Mar 2009, at 17:13, Oliver Ruebenacker wrote:
>> A class may not be instantiated in every single use, but it is
>> intended to be instantiated in some cases. To dispute that, you would
>> have to give me an exam
On Mon, 30 Mar 2009 09:11:48 -0700, Michel_Dumontier
wrote:
(although it's unclear from
your website whether services are *actually* described in an OWL
document or they just refer to OWL types).
Both/either (assuming that I understood your question)
The service interfaces are defined as
Argh, I said I wouldn't, but this came after.
On 30 Mar 2009, at 17:13, Oliver Ruebenacker wrote:
Hello Bijan, All,
On Mon, Mar 30, 2009 at 12:07 PM, Bijan Parsia
wrote:
On 30 Mar 2009, at 16:38, Oliver Ruebenacker wrote:
Then it is not clear to me what you are claiming.
I'm claim
On 30 Mar 2009, at 17:04, Oliver Ruebenacker wrote:
Hello Bijan, All,
On Mon, Mar 30, 2009 at 11:39 AM, Bijan Parsia
wrote:
On 30 Mar 2009, at 16:23, Oliver Ruebenacker wrote:
That is probably the most used phrase in the Semantic Web
community.
And least adhered to?
Most used
Hello Bijan, All,
On Mon, Mar 30, 2009 at 12:07 PM, Bijan Parsia wrote:
> On 30 Mar 2009, at 16:38, Oliver Ruebenacker wrote:
>> Then it is not clear to me what you are claiming.
>
> I'm claiming that classes in OWL are not typically intended to be
> "instantiated" by users (in OWL).
A c
onday, March 30, 2009 11:49 AM
> To: Bijan Parsia; public-semweb-lifesci
> Subject: Re: blog: semantic dissonance in uniprot
>
> On Mon, 30 Mar 2009 04:35:08 -0700, Bijan Parsia
> wrote:
>
> >>> that many ontologies (including the OBO ontologies and parts of
the
>
On 30 Mar 2009, at 16:49, Mark wrote:
On Mon, 30 Mar 2009 04:35:08 -0700, Bijan Parsia
wrote:
that many ontologies (including the OBO ontologies and parts of the
Neurocommons Knowledge Base / Banff HCLS demo) encode a lot of
useful
information just by using classes and property restrictio
Hello Bijan, All,
On Mon, Mar 30, 2009 at 11:39 AM, Bijan Parsia wrote:
> On 30 Mar 2009, at 16:23, Oliver Ruebenacker wrote:
>> That is probably the most used phrase in the Semantic Web community.
>
> And least adhered to?
Most used as an empty cliche.
> What's your problem with provid
On 30 Mar 2009, at 16:38, Oliver Ruebenacker wrote:
Hello Bijan, All,
On Mon, Mar 30, 2009 at 11:31 AM, Bijan Parsia
wrote:
On 30 Mar 2009, at 16:12, Oliver Ruebenacker wrote:
Can you name any popular ontology that does not primarily declare
classes and properties?
I don't have to,
Hello Bijan, All,
On Mon, Mar 30, 2009 at 11:31 AM, Bijan Parsia wrote:
> On 30 Mar 2009, at 16:12, Oliver Ruebenacker wrote:
>> Can you name any popular ontology that does not primarily declare
>> classes and properties?
>
> I don't have to, since I'm not claiming that.
Then it is not c
On 30 Mar 2009, at 16:23, Oliver Ruebenacker wrote:
Hello Bijan, All,
On Mon, Mar 30, 2009 at 7:40 AM, Bijan Parsia
wrote:
On 29 Mar 2009, at 16:48, Oliver Ruebenacker wrote:
My first advice would be to develop a clear set of requirements,
That is probably the most used phrase in the
On Mon, 30 Mar 2009 04:35:08 -0700, Bijan Parsia
wrote:
that many ontologies (including the OBO ontologies and parts of the
Neurocommons Knowledge Base / Banff HCLS demo) encode a lot of useful
information just by using classes and property restrictions, without
instances.
It's a bit of a
On Mar 30, 2009, at 8:15 AM, Oliver Ruebenacker wrote:
Hello Pat, All,
On Sun, Mar 29, 2009 at 11:23 PM, Pat Hayes wrote:
On Mar 29, 2009, at 10:48 AM, Oliver Ruebenacker wrote:
Perhaps the question should read: What would you advice to some one
who wants to build an ontology to descri
On 30 Mar 2009, at 16:12, Oliver Ruebenacker wrote:
Hello Bijan, All,
On Mon, Mar 30, 2009 at 7:35 AM, Bijan Parsia
wrote:
Isn't that the typical way, that ontologies define classes and
properties and users of these ontologies instantiate these classes?
Nope. It's "a" way, but it's ha
Hello Bijan, All,
On Mon, Mar 30, 2009 at 7:40 AM, Bijan Parsia
wrote:
> On 29 Mar 2009, at 16:48, Oliver Ruebenacker wrote:
> My first advice would be to develop a clear set of requirements,
That is probably the most used phrase in the Semantic Web community.
We should invent a catchy ac
Hello Bijan, All,
On Mon, Mar 30, 2009 at 7:35 AM, Bijan Parsia
wrote:
>> Isn't that the typical way, that ontologies define classes and
>> properties and users of these ontologies instantiate these classes?
>
> Nope. It's "a" way, but it's hardly typical and the way you talk about it is
>
Hello Pat, All,
On Sun, Mar 29, 2009 at 11:35 PM, Pat Hayes wrote:
> On Mar 29, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
>> I am assuming that these classes all make a commitment about what
>> their instances mean, so users could declares instances and rely on
>> that commitment to be u
Hello Pat, All,
On Sun, Mar 29, 2009 at 11:23 PM, Pat Hayes wrote:
> On Mar 29, 2009, at 10:48 AM, Oliver Ruebenacker wrote:
>> Perhaps the question should read: What would you advice to some one
>> who wants to build an ontology to describe pathways for Systems
>> Biology purposes?
>
> I r
On 29 Mar 2009, at 16:48, Oliver Ruebenacker wrote:
Hello Pat, All,
[snip]
Perhaps the question should read: What would you advice to some one
who wants to build an ontology to describe pathways for Systems
Biology purposes?
My first advice would be to develop a clear set of requiremen
Sad to be drawn in.
On 29 Mar 2009, at 17:15, Oliver Ruebenacker wrote:
Hello Matthias, All,
On Sun, Mar 29, 2009 at 11:13 AM, Matthias Samwald
wrote:
Oliver wrote:
As I understand it, an owl:Class is simply something intended to be
instantiated. I declare something a class if and on
On Mar 29, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
Hello Matthias, All,
On Sun, Mar 29, 2009 at 11:13 AM, Matthias Samwald
wrote:
Oliver wrote:
As I understand it, an owl:Class is simply something intended to be
instantiated. I declare something a class if and only if I intend
t
On Mar 29, 2009, at 10:48 AM, Oliver Ruebenacker wrote:
Hello Pat, All,
On Sun, Mar 29, 2009 at 12:10 AM, Pat Hayes wrote:
On Mar 28, 2009, at 3:52 PM, Oliver Ruebenacker wrote:
Arithmetic can be described by ontologies.
Not full arithmetic, because of Goedel's incompleteness theorem
Hello Matthias, All,
On Sun, Mar 29, 2009 at 11:13 AM, Matthias Samwald wrote:
> Oliver wrote:
>> As I understand it, an owl:Class is simply something intended to be
>> instantiated. I declare something a class if and only if I intend
>> there to be instances.
>
> This is how you might choo
Hello Pat, All,
On Sun, Mar 29, 2009 at 12:10 AM, Pat Hayes wrote:
> On Mar 28, 2009, at 3:52 PM, Oliver Ruebenacker wrote:
>> Arithmetic can be described by ontologies.
>
> Not full arithmetic, because of Goedel's incompleteness theorem. You might
> manage with Peano arithmetic, but I doub
Oliver wrote:
As I understand it, an owl:Class is simply something intended to be
instantiated. I declare something a class if and only if I intend
there to be instances.
This is how you might choose to use OWL, but it is important to emphasize
that many ontologies (including the OBO ontolog
On Mar 28, 2009, at 3:52 PM, Oliver Ruebenacker wrote:
Hello Pat, All,
On Sat, Mar 28, 2009 at 4:32 PM, Pat Hayes wrote:
On Mar 28, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
Why not? I don't see any fundamental problem.
Well, the very idea of a statistical ensemble is way more
Hello Pat, All,
On Sat, Mar 28, 2009 at 4:32 PM, Pat Hayes wrote:
> On Mar 28, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
>> Why not? I don't see any fundamental problem.
>
> Well, the very idea of a statistical ensemble is way more complicated than
> anything any ontology language seman
On Mar 28, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
Hello Pat, All,
On Sat, Mar 28, 2009 at 10:54 AM, Pat Hayes wrote:
Actually, I doubt a protein is a set. It seems to me, in Systems
Biology, a protein is an operator working on statistical ensembles,
from which we can derive expect
Hello Pat, All,
On Sat, Mar 28, 2009 at 10:54 AM, Pat Hayes wrote:
>> Actually, I doubt a protein is a set. It seems to me, in Systems
>> Biology, a protein is an operator working on statistical ensembles,
>> from which we can derive expectation values and variances.
>
> Um. OK, you obvious
On Mar 27, 2009, at 4:23 AM, John Madden wrote:
So, here's how I'd do this. Introduce a property linking a protein
to something (which might be anything from a piece of text to a
protein) called sameProteinAs. Its reflexive and transitive but
might not be symmetric (though it probably i
On Mar 26, 2009, at 3:52 PM, Oliver Ruebenacker wrote:
Hello Pat, All,
On Thu, Mar 26, 2009 at 3:28 AM, Pat Hayes wrote:
Just because it refers to a set of things does not mean I need to
model it by an owl:Class.
No, but if it really is a set, that would be a very good idea.
Actual
So, here's how I'd do this. Introduce a property linking a protein
to something (which might be anything from a piece of text to a
protein) called sameProteinAs. Its reflexive and transitive but
might not be symmetric (though it probably is when the value is
itself a protein). It is NOT
On 26 Mar 2009, at 22:02, John Madden wrote:
Hi Peter,
It would be infinitely better than seeAlso where you have no idea
what
the intent is, other than it isn't owl:sameAs or anything else in
between.
Of course, you could create a property ex:similarTo in your own
namespace, and then dec
2009/3/27 John Madden :
> Hi Peter,
>
>
>>
>> It would be infinitely better than seeAlso where you have no idea what
>> the intent is, other than it isn't owl:sameAs or anything else in
>> between.
>
> Of course, you could create a property ex:similarTo in your own namespace,
> and then declare tha
2009/3/27 Oliver Ruebenacker :
> On Thu, Mar 26, 2009 at 5:54 PM, Peter Ansell wrote:
>> It would be infinitely better than seeAlso where you have no idea what
>> the intent is, other than it isn't owl:sameAs or anything else in
>> between.
>
> owl:usersWhoLookedAtThisRecordAlsoLookedAt :)
:)
A
Hi Peter,
It would be infinitely better than seeAlso where you have no idea what
the intent is, other than it isn't owl:sameAs or anything else in
between.
Of course, you could create a property ex:similarTo in your own
namespace, and then declare that
ex:similarTo rdfs:subProper
On Thu, Mar 26, 2009 at 5:54 PM, Peter Ansell wrote:
> It would be infinitely better than seeAlso where you have no idea what
> the intent is, other than it isn't owl:sameAs or anything else in
> between.
owl:usersWhoLookedAtThisRecordAlsoLookedAt :)
--
Oliver Ruebenacker, Computational Cell
2009/3/27 John F. Madden :
> Pat et al.,
>
> It sounds like people sometimes have an irresistible itch to say that "A is
> similar to B", but this statement as such has very little semantic content.
>
> Perhaps it's not really intended as a statement that has a truth value, but
> rather as a record
Hello Matthias, All,
On Thu, Mar 26, 2009 at 4:30 PM, Matthias Samwald wrote:
>> I think more useful for Systems Biology is that they participate in
>> the same reactions with the same kinetics.
>
> But that is a very personal opinion, right? Without doubt, when two classes
> of proteins ha
is Mungall
Sent: Thursday, March 26, 2009 4:35 PM
To: Michel_Dumontier
Cc: Kei Cheung; W3C HCLSIG hcls; Matthias Samwald
Subject: Re: blog: semantic dissonance in uniprot
On Mar 26, 2009, at 8:33 AM, Michel_Dumontier wrote:
The Gene Ontology says a Protein (GO:0003675) is a Thing (the entity
was re
Oliver wrote:
Some people involved in BioPAX think they are the same if and only
if they have the same sequence.
I think more useful for Systems Biology is that they participate in
the same reactions with the same kinetics.
But that is a very personal opinion, right? Without doubt, when two
Hello Philip, All,
On Thu, Mar 26, 2009 at 8:20 AM, Phillip Lord
wrote:
> Besides which, the issue being discussed here is one of equality. When
> are two proteins the same protein?
Some people involved in BioPAX think they are the same if and only
if they have the same sequence.
I thi
Hello Pat, All,
On Thu, Mar 26, 2009 at 3:28 AM, Pat Hayes wrote:
>> Just because it refers to a set of things does not mean I need to
>> model it by an owl:Class.
>
> No, but if it really is a set, that would be a very good idea.
Actually, I doubt a protein is a set. It seems to me, in
] On Behalf Of Chris Mungall
> Sent: Thursday, March 26, 2009 4:35 PM
> To: Michel_Dumontier
> Cc: Kei Cheung; W3C HCLSIG hcls; Matthias Samwald
> Subject: Re: blog: semantic dissonance in uniprot
>
>
> On Mar 26, 2009, at 8:33 AM, Michel_Dumontier wrote:
>
> > The
On Mar 26, 2009, at 8:33 AM, Michel_Dumontier wrote:
The Gene Ontology says a Protein (GO:0003675) is a Thing (the entity
was removed, but then later added so the identifier wouldn't be
reused)
More accurately: very early versions of the GO had a term named
"protein", but this was obsolet
Pat,
So what would you say about an rdf:property called, say, "http://www.example.com/intuit#similarTo
" that could be used simply to post a record that somebody intuited
a "similarity" between two things?
Well, what's wrong with seeAlso? Thats pretty much what we intended
it for.
Go
On Mar 26, 2009, at 11:31 AM, John F. Madden wrote:
Pat et al.,
It sounds like people sometimes have an irresistible itch to say
that "A is similar to B", but this statement as such has very little
semantic content.
Perhaps it's not really intended as a statement that has a truth
value
On Mar 26, 2009, at 11:28 AM, eric neumann wrote:
Pat,
Basically I'm in agreement with all of your points, but need to
correct some mis-interpretations you made of my comments...
Sure, thanks for clarifying.
On Thu, Mar 26, 2009 at 3:13 AM, Pat Hayes wrote:
On Mar 25, 2009, at 5:27 PM
Wacek Kusnierczyk writes:
So insulin is not a protein, wheras a dipeptide is?
>>> indeed; insulin is a protein complex, and a dipeptide, following this
>>> and other similar definitions, is a protein.
>>>
>>>
>>
>> Insulin is two polypeptide changes so following this
+1
On Thu, Mar 26, 2009 at 12:31 PM, John F. Madden wrote:
> Pat et al.,
>
> It sounds like people sometimes have an irresistible itch to say that "A is
> similar to B", but this statement as such has very little semantic content.
>
> Perhaps it's not really intended as a statement that has a tru
Pat et al.,
It sounds like people sometimes have an irresistible itch to say that
"A is similar to B", but this statement as such has very little
semantic content.
Perhaps it's not really intended as a statement that has a truth
value, but rather as a record of somebody's feelings.
The
Pat,
Basically I'm in agreement with all of your points, but need to correct some
mis-interpretations you made of my comments...
On Thu, Mar 26, 2009 at 3:13 AM, Pat Hayes wrote:
>
> On Mar 25, 2009, at 5:27 PM, eric neumann wrote:
>
> Several different issues here.
>
>
>
> On Wed, Mar 25, 2009
On Mar 26, 2009, at 10:45 AM, Phillip Lord wrote:
Pat Hayes writes:
Besides which, the issue being discussed here is one of equality.
When
are two proteins the same protein?
TWO proteins are never the same protein. Two mangelwurzels are
never the same
mangelwurzel, either. What 'same'
Michel's point resonate with my experiences also, though I hesitate trying
to push the definition of 'ProteinAggregate' to the rest of the bio world...
but it's in the right spirit. : )
-Eric
On Thu, Mar 26, 2009 at 9:28 AM, Michel_Dumontier <
michel_dumont...@carleton.ca> wrote:
> Pursuant to my
Phillip Lord wrote:
> Wacek Kusnierczyk writes:
>
I don't know whether the BioPAX Level 2 definition of protein is the
most useful one, but at least it sounds clear to me:
protein = anything containing exactly one polypeptide chain
Clear enough?
>>>
> Distinctions like object/substance/piece/mixture were worked out by
> ontologists over 20 years ago, by the way. None of this is rocket
> science.
Hhhh! How I am gonna get any consulting work when you
say things like that!
-=Michel=-
>
> Pat
>
>
Pat Hayes writes:
>> Besides which, the issue being discussed here is one of equality. When
>> are two proteins the same protein?
>
> TWO proteins are never the same protein. Two mangelwurzels are never the same
> mangelwurzel, either. What 'same' means, is that there is ONE thing with two
> nam
On Mar 26, 2009, at 8:28 AM, Michel_Dumontier wrote:
Pursuant to my email, and in light of several other comments, if our
goal is to now rectify what Uniprot:Protein _actually_ means in our
domain, and how it can be semantically mapped to other bio-ontologies,
then I might also suggest that ins
Wacek Kusnierczyk writes:
>>> I don't know whether the BioPAX Level 2 definition of protein is the
>>> most useful one, but at least it sounds clear to me:
>>>
>>> protein = anything containing exactly one polypeptide chain
>>>
>>> Clear enough?
>>>
>>
>>
>> So insulin is not a protein,
heung [mailto:kei.che...@yale.edu]
> Sent: Thursday, March 26, 2009 10:07 AM
> To: Michel_Dumontier
> Cc: W3C HCLSIG hcls; Matthias Samwald
> Subject: Re: blog: semantic dissonance in uniprot
>
> In addition to Uniprot, in light of Matthias' earlier email, what
about
> ht
On Mar 26, 2009, at 7:20 AM, Phillip Lord wrote:
Oliver Ruebenacker writes:
Hello Philip, All,
On Wed, Mar 25, 2009 at 1:05 PM, Phillip Lord
wrote:
My own feeling is that it's biology which wove the web; we're just
caught in the middle. What role for the web and semantics? Well, I
th
On Mar 26, 2009, at 6:53 AM, Phillip Lord wrote:
Oliver Ruebenacker writes:
Besides, how do we know it's wrong? Two species can have the same
protein for different functions, right?
Depends how you define "same". This is the crux of the problem.
No, really, its not. Defining 'same' is
In addition to Uniprot, in light of Matthias' earlier email, what about
http://en.wikipedia.org/wiki/Protein, http://dbpedia.org/page/Protein,
and the protein related ontologies listed in OBO
(http://www.obofoundry.org/)?
-Kei
Michel_Dumontier wrote:
Pursuant to my email, and in light of sev
Pursuant to my email, and in light of several other comments, if our
goal is to now rectify what Uniprot:Protein _actually_ means in our
domain, and how it can be semantically mapped to other bio-ontologies,
then I might also suggest that instances of Uniprot:Protein are
aggregates of proteins (err
Phillip Lord wrote:
> Oliver Ruebenacker writes:
>
>> Hello Philip, All,
>>
>> On Wed, Mar 25, 2009 at 1:05 PM, Phillip Lord
>> wrote:
>>
>>> My own feeling is that it's biology which wove the web; we're just
>>> caught in the middle. What role for the web and semantics? Well, I thin
Oliver Ruebenacker writes:
> Hello Philip, All,
>
> On Wed, Mar 25, 2009 at 1:05 PM, Phillip Lord
> wrote:
>> My own feeling is that it's biology which wove the web; we're just
>> caught in the middle. What role for the web and semantics? Well, I think
>> we need a coordinated, controlled an
Oliver Ruebenacker writes:
> Besides, how do we know it's wrong? Two species can have the same
> protein for different functions, right?
>
Depends how you define "same". This is the crux of the problem.
Phil
On 26 Mar 2009, at 11:01, David Booth wrote:
On Wed, 2009-03-25 at 21:34 -0400, David Booth wrote:
[ . . . ] the important criterion for using owl:sameAs are: (a)
in *your* RDF graph the two terms are intended to denote the *same*
individual; and (b) your RDF graph is consisistent with their
de
On Wed, 2009-03-25 at 21:34 -0400, David Booth wrote:
> [ . . . ] the important criterion for using owl:sameAs are: (a)
> in *your* RDF graph the two terms are intended to denote the *same*
> individual; and (b) your RDF graph is consisistent with their
> definitions. [ . . . . ]
After writing th
Pat Hayes wrote:
> [...] or use rdf: seeAlso, which was put in
> the language pretty much for this reason, to be a blank carry-all for
> a loose association with no formal properties.
I think that rdfs:seeAlso is the way to go, as I recently suggested in a
similar discussion on the Linked Dat
On 25 Mar 2009, at 23:59, David Booth wrote:
On Wed, 2009-03-25 at 14:13 +, Bijan Parsia wrote:
On 25 Mar 2009, at 10:41, Phillip Lord wrote:
"Michel_Dumontier" writes:
And I'm trying to explain that there is no pragmatic reason to make
explicit the distinction between a biomolecule (an
On Mar 25, 2009, at 12:30 PM, Oliver Ruebenacker wrote:
Hello Mark, All,
On Wed, Mar 25, 2009 at 1:13 PM, Mark Wilkinson
wrote:
Well, the statement would *imply* that it is... so given that the
individual
"embryo" that was referred to as a uniprot tissue is the same
individual
"emb
On Mar 25, 2009, at 5:27 PM, eric neumann wrote:
Several different issues here.
On Wed, Mar 25, 2009 at 5:47 PM, Bijan Parsia > wrote:
Eric,
Thanks for the use case!
On 25 Mar 2009, at 21:31, eric neumann wrote:
This is the kind of "similar" used in most internal genomic/compound
sy
On Mar 25, 2009, at 4:31 PM, eric neumann wrote:
Bijan,
From your descriptions, I can't tell which one would best handle the
following situation:
"Object 1 refers to exactly the same molecule (exemplar) as object 2
refers to"
That sure sounds like sameAs, applied to molecules. Why isn'
On Mar 26, 2009, at 12:28 AM, Peter Ansell wrote:
2009/3/26 Pat Hayes :
Well, if you can tell us how to do some weaving, we maybe can make
progress.
The properties of sameAs are fairly easy to list. It is transitive,
reflexive, symmetric and substitutive: if A sameAs B and something
is tru
2009/3/26 Pat Hayes :
> Well, if you can tell us how to do some weaving, we maybe can make progress.
> The properties of sameAs are fairly easy to list. It is transitive,
> reflexive, symmetric and substitutive: if A sameAs B and something is true
> of A, then its also true of B. So, which of thes
On Mar 25, 2009, at 11:25 AM, Mark Wilkinson wrote:
On Wed, 25 Mar 2009 03:41:37 -0700, Phillip Lord > wrote:
If I remember correctly the original post that started this of Ben
has
it about right. We need some tags which say "these two database
records
are about the same protein, well,
On Mar 25, 2009, at 12:13 PM, Mark Wilkinson wrote:
On Wed, 25 Mar 2009 10:03:43 -0700, Oliver Ruebenacker > wrote:
http://www.uniprot.org/tissues/229 (subject)
http://www.w3.org/2002/07/owl#sameAs (predicate)
http://purl.uniprot.org/po/0009009 (object)
my concern is whether http://purl.un
On Wed, 2009-03-25 at 09:25 -0700, Mark Wilkinson wrote:
> [ . . . ]
> Another predicate is needed that is less "rigourous" - owl:kindOfLike :-)
I disagree. I think it is more a matter of getting used to the fact
that terms (URIs in the case of RDF) are almost always ambiguous -- they
admit mult
David,
I agree that different URIs should be used when trying to denote
different things. Like for instance, we might have different URIs for
different representations (eg html, xhtml, rdf, etc). I know the
NeuroCommons people like to formulate URIs with the representation and
others, like UniProt
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