: [EMAIL PROTECTED] [mailto:public-semweb-lifesci-
[EMAIL PROTECTED] On Behalf Of Miller, Michael D (Rosetta)
Sent: Tuesday, August 08, 2006 1:50 PM
To: kei cheung; [EMAIL PROTECTED]
Cc: w3c semweb hcls
Subject: RE: [HCLS] RE: scientific publishing task force update
Hi Kei,
It means that
c: w3c semweb hcls
> Subject: RE: [HCLS] RE: scientific publishing task force update
>
>
> Hi Kei,
>
> > It means that things might not overlap at
> > the same level, but may overlap at different levels between different
> > ontologies (entity modeled at a h
Good point, Michael.I think there maybe ways to use some combination of NamedGraphs, SKOS, and Topic Maps to address different aspects of this general issue. We're working on this in the BIRN project and expect it will help us - and others - make use of the OBO Foundry ontologies - and data/litera
to
> >finish a prototype that is now in debug hell...but that's
> another story.]
> >
> >Don
> >
> >-
> >Donald Doherty, Ph.D.
> >Brainstage Research, Inc.
> >www.brainstage.com
> >[EMAIL PROTECTED]
> >412-478-4552
> >
tory.]
Don
-
Donald Doherty, Ph.D.
Brainstage Research, Inc.
www.brainstage.com
[EMAIL PROTECTED]
412-478-4552
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of kei cheung
Sent: Thursday, June 15, 2006 1:04 PM
To: Eric Neumann
Cc: Phillip Lord; w3c semw
ay, June 15, 2006 1:04 PM
To: Eric Neumann
Cc: Phillip Lord; w3c semweb hcls
Subject: Re: scientific publishing task force update
Hi Eric et al,
The more I think of, would your OntologyCovering task relate to Don
Doherty's Bridging Ontology task
(http://esw.w3.org/topic/H
Hi Eric et al,
The more I think of, would your OntologyCovering task relate to Don
Doherty's Bridging Ontology task
(http://esw.w3.org/topic/HCLS/OntologyTaskForce/Create_Bridging_Ontology_between_NeuronDB_and_CoCoDat_databases_and_UMLS_Common_Vocabulary#preview)?
In other words, can your On
experimental
data.
Yong
-Original Message-
From: [EMAIL PROTECTED] on behalf of Mark Musen
Sent: Fri 6/9/2006 1:29 PM
To: AJ Chen
Cc: public-semweb-lifesci@w3.org
Subject: Re: scientific publishing task force update
On Jun 8, 2006, at 10:09 PM, AJ Chen wrote:
The first task is to devel
To: AJ Chen
Cc: public-semweb-lifesci@w3.org
Subject: Re: scientific publishing task force update
On Jun 8, 2006, at 10:09 PM, AJ Chen wrote:
> The first task is to develop an ontology for self-publishing of
> experiment. I have proposed a list of objects and properties
> related to sel
Dear John, I do hope your kidney stones "pass" with as little pain as possible. Ouch! :-(The general nature of your comment - echoed by others on this thread - that our description of biological reality is an evolving target is of course true. There'd be little point - or attraction - for most o
By all means - versioning is crucial - and all knowledge maps/
association files/annotations referencing nodes in an ontology MUST
include the version number.
For an example of how biomed. ontology curators deal with the issue
of versioning, see the Gene Ontology Consortium web site pages
Forgot to say that I hope your kidney stone issues get resolved much
sooner than these ontological issues. :-)
-Kei
John Rumble wrote:
An unwritten rule about higher level ontologies is that they reflect
our knowledge today, not tomorrow. As knowledge evolves, the upper
level ontologies, e
This brings up an interesting issue -- how ontological evolution would
impact mapping or integration of overlapping ontologies. I believe it's
quite a research challenge. We might need to incorporate the notion of
versioning into the ontological structure. For example, what versions of
the pr
An unwritten rule about higher level ontologies is
that they reflect our knowledge today, not tomorrow. As knowledge evolves, the
upper level ontologies, especially, must also evolve. The example of the concept
"protein" is very apropos here. We can view it from functional,
structural, inte
Following up to Phil's point, an alternative to building upper ontologies (UO) first, is to consider constructing a "Covering Map" between apparent overlapping sets of "related" ontologies. These are light weight, RDF associations that can help "pin-down" potentially related items/classes from dif
William Bug wrote:
BTW - I'd really appreciate hearing from folks what tool they prefer
for viewing, editing, and creating graphical representations of OWL
instances. I've tried several tools from oXygen through Protégé, and
several other Open Source tools in between and am not complete
Here, here!
I think Matthias is making a very important point here - one equally
important to efforts to define biological reality empirically from
the ground up (semantic web and/or computational linguistic/NLP
approaches to distilling KR from the literature-base), as it is to
top-down,
> That is very true, and I think that the importance of having
> huge top-level ontologies like SUMO or maybe Cyc is largely
> overrated.
I can't agree anymore.
Having top level ontology is important as a guideline for the design of a
lower level ontology. But that does not imply that all lo
I think this is good. Using upper levels to guide towards good
choices of properties is very useful.
robert.
At 13:29 13/06/2006, Matthias Samwald wrote:
> One small, but significant, dislike of the bio-ontology community
> for SUMO (as used by Solditova and King) is that it isn't really
>
> One small, but significant, dislike of the bio-ontology community
> for SUMO (as used by Solditova and King) is that it isn't really
> only an upper level. It strays into, for instance, stating a
> protein is a foodstuff. this, as you might suppose, causes
> biologists to laugh.
That is very t
The range of upper ontology reflects the different philosophical
viewpoints on the nature of what exists in the world. Different upper
ontologies make different distinctions. Most of the upper ontologies
have a great deal in common, but different philosophies make
different distinction and ev
> "SC" == Steve Chervitz <[EMAIL PROTECTED]> writes:
>> They also wrote an interesting paper on the state of
>> bio-ontologies.
>>
>> Nature Biotechnology 23, 1095 - 1098 (2005)
>> doi:10.1038/nbt0905-1095 Are the current ontologies in biology
>> good ontologies?
>>
>> Lari
Phillip Lord <[EMAIL PROTECTED]> on Mon, 12 Jun 2006:
>
>> "MM" == Mark Musen <[EMAIL PROTECTED]> writes:
>
> MM> A colleague just pointed me to this (rather vacuous) article.
> MM> Does anyone know more about this work?
> MM> http://www.newscientisttech.com/article/dn9288-translator
Ditto to Kei's note at the bottom - with a few qualifiers added in
the interstices.
BTW - I'd really appreciate hearing from folks what tool they prefer
for viewing, editing, and creating graphical representations of OWL
instances. I've tried several tools from oXygen through Protégé, an
Jim Hendler wrote:
At 9:36 -0700 6/12/06, Miller, Michael D (Rosetta) wrote:
Hi Kei,
Once an OWL ontology is published there are no typos! If one wants to
use the ontology, one must conform to the definitions.
cheers,
Michael
or produce a new, backward compatible version which makes the
At 9:36 -0700 6/12/06, Miller, Michael D (Rosetta) wrote:
Hi Kei,
Once an OWL ontology is published there are no typos! If one wants to
use the ontology, one must conform to the definitions.
cheers,
Michael
or produce a new, backward compatible version which makes the change...
(or inform
r, Michael D (Rosetta)
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: scientific publishing task force update
>
>
> "Eperimental" looks to me like a typo, it should be "Experimental"?
>
> Cheers,
>
> -Kei
>
> Miller, Michael D (Rosetta) wrote:
&
ne 12, 2006 8:07 AM
To: William Bug
Cc: Mark Musen; public-semweb-lifesci@w3.org
Subject: Re: scientific publishing task force update
Hi Bill and Mark et al.,
I also went the EXPO site (http://sourceforge.net/projects/expo/) and
found the EXPO ontology in OWL format (I agree that it's
quit
means!
cheers,
Michael
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of kei cheung
> Sent: Monday, June 12, 2006 8:07 AM
> To: William Bug
> Cc: Mark Musen; public-semweb-lifesci@w3.org
> Subject: Re: scientific publishing tas
Hi Bill and Mark et al.,
I also went the EXPO site (http://sourceforge.net/projects/expo/) and
found the EXPO ontology in OWL format (I agree that it's quite hidden).
I have unzipped it and make it available at:
http://twiki.med.yale.edu/kei_web/sw_group/EXPO04-19-06.owl
It might be interes
> "MM" == Mark Musen <[EMAIL PROTECTED]> writes:
MM> On Jun 8, 2006, at 10:09 PM, AJ Chen wrote:
>> The first task is to develop an ontology for self-publishing of
>> experiment. I have proposed a list of objects and properties
>> related to self-publishing experiment. Please download
There's an OWL ontology on the download page.
http://sourceforge.net/project/showfiles.php?group_id=148379
-Alan
On Jun 9, 2006, at 2:34 PM, Bob Futrelle wrote:
You'd have to download EXPO to see what it contains.
Those references would be really wonderful to have in hand. Many
thanks, Bob.
Given the direction we are trying to go in on the BIRN project - very
extensive use of FuGO (http://fugo.sourceforge.net/) & PATO (http://
obo.sourceforge.net/cgi-bin/detail.cgi?attribute_and_value) - both of
Yes - please do post your references, John. They are very relevant to this discussion, and I would certainly profit from getting the chance to peruse them.Being in Oak Ridge, have you overlapped at all with the various bioinformatics groups at ORNL? One in particular who would be very much intere
You'd have to download EXPO to see what it contains. My guess is that
it's a continuation of the work that King has been doing for some time
now. He works on robot experimental configurations for bio expts. and
wants to represent a structured version of the output (or drivers?).
He has a studen
This was a new one on me too, Mark. It was posted to Slashdot the
other day, and the Sorceforge site the article points to is
essentially empty.
http://sourceforge.net/projects/expo/
As you might gather, EXPO is not a very good term to search in all
the usual suspect search engines - IN
On Jun 8, 2006, at 10:09 PM, AJ Chen wrote:
The first task is to develop an ontology for self-publishing of
experiment. I have proposed a list of objects and properties
related to self-publishing experiment. Please download the attached
file under Task Status and review the proposal. Your f
There has been some important work done on this
subject over the last 20 years. A. Shoshoni, F. Olken and others wrote some very
insightful papers about differentiating between different types of independent
variables in an experiment. I have given several talks in recent years about the
pro
Title: The content of biomedical research and its representation in papers
This note was stimulated by a note from A J Chen posted today, 9 June
2006, on public-semweb-lifesci@w3.org, with a link to:
http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce
I realize that I am going beyond wh
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