Hi all,
Just a friendly reminder of today's teleconference call:
''' Conference Details'''
* Date of Call: Thursday June 30 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.0479 (Londo
All I meant is that you can index the labels to do your URI substitution in
writing code (axioms/queries) in some program (exact matching here). Perfectly
reasonable for a selected set of orthogonal ontologies. Search/partial matches
would obviously need to match other requirements.
m.
From: p
Hi Sivaram,
Identifiers, whether opaque or not, hold meaning when they identify some
thing (or things) - otherwise they do not serve their intended purpose.
Where there is disagreement is in terms of the syntax of the identifier. Some
want to incorporate language mnemonic and others use an alp
Hi,
Just a reminder for Thursday's TM teleconference cal:
''' Conference Details'''
* Date of Call: Thursday June 23 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.0479 (London, UK
Reposting to the list:
> >>> Honestly, I read this stuff and I'm thinking that you aren't listening
> >>> to what you are saying and applying even a minimal amount of critical
> >>> analysis to relate working with RDF to any other kind of skilled
> >>> labor.
> >>
> >> Most skilled workers want t
I ran across this @lamebook, and I couldn't help but draw a parallel to our
conversation :
http://www.lamebook.com/meet-shameful/
in good fun ;)
m.
> I think one of the main point is the role of the 'web'.
The role of the 'web' in Semantic Web is that we can publish and share our
formalized data/knowledge using HTTP URIs - with minimal coordination (e.g.
once you find something you like, you can reference it using its URI;
regardless of wh
From: Sivaram Arabandi, MD [mailto:sivaram.araba...@gmail.com]
Sent: Monday, June 20, 2011 8:42 PM
To: Andrea Splendiani
Cc: Michel_Dumontier; Chime Ogbuji; andrea splendiani (RRes-Roth);
Vagnoni,Matthew M; James Malone; HCLS
Subject: Re: My task from last week: Semantic free identifiers
On
> Perhaps I'm getting the feeling that the different points of view reflects
> a
> different perception of OWL vs RDF ?
> Just a thought. I'm much more likely to move triples via scripts than using
> a tool.
>
> ciao,
> Andrea
You're partly right. I don't look at RDF/XML or turtle when I repres
eb-lifesci-requ...@w3.org
[mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of Andrea Splendiani
Sent: Monday, June 20, 2011 7:48 PM
To: Michel_Dumontier
Cc: Sivaram Arabandi, MD; Chime Ogbuji; andrea splendiani (RRes-Roth);
Vagnoni,Matthew M; James Malone; HCLS
Subject: Re: My task from last
IMHO, if you're still coding the content of an information system by hand, then
you're going to introduce errors. A database curator should never assign their
own identifier - this is internal to the technology and the information system.
If you're a programmer, you should query the resource (on
It's exactly the same reason why we have tables with incremental primary keys
or have social security numbers for people and ISBN's for books. The
identifier is meant to identify one thing, and should not clash with other
things having similar or exact names. What that thing is, is up to you. B
We've faced the problem of formulating SPARQL queries using alphanumeric
identifiers, and have developed software to make queries using the labels :
http://www.slideshare.net/elmccarthy/sparql-assist-language-neutral-query-composer
http://sadiframework.org/content/2010/11/29/sparql-assist-langu
Quick reminder of today's teleconference call:
''' Conference Details'''
* Date of Call: Thursday June 16 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.0479 (London, UK)
* Particip
Hi All,
Here is the reminder for Thursday's TM conference call:
''' Conference Details'''
* Date of Call: Thursday June 2 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.0479 (Londo
jhu.edu]
> Sent: Thursday, May 26, 2011 11:45 AM
> To: Michel_Dumontier
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: HCLS chartering/next steps Thur 26 May
>
> Michel,
>
> I concur. As the overwhelming emphasis of the HCLS is in the lifesciences
> (biology, basic res
In addition to having the "problem" based task forces, I would suggest that we
establish sub-groups based on interest/technical capability with
responsibilities to develop and maintain our efforts.
· Terminology (to coordinate and maintain a shared vocabulary)
· Knowledge Bases
+1
By charting a course towards solving outstanding problems or an application
area, we are well motivated to develop and evaluate the (SW) solutions. The
resulting work can find a nice home in both technical and non-technical forums,
which increases our outreach potential.
M
From: public-se
Hi TM'ers
Just a friendly reminder of today's teleconference call :
''' Conference Details'''
* Date of Call: Thursday May 26 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.0479 (Lon
Hi TMers,
In today's teleconference call we'll welcome two new members: Dr. Fred
Whipple and Dr. Iker Huerga. Fred is a genomics educator who provides with
physicians with the knowledge to understand and use SNP-based disease risk
tests (more about Fred at [1]). Iker is the co-founder of LINKa
Dear TM'ers,
Today's Translational Medicine conference call picks up from our call nearly
3 weeks ago [http://www.w3.org/2011/04/14-hcls2-minutes.html] and will be
focused on developing the ideas in the pharmacogenomics paper. Talk to you soon!
''' Conference Details'''
* Date of Call: Thursd
Hi James,
In Bio2RDF, and linked data in general, it's common to have a predicate for
nearly every relation in the dataset - this at least solves the syntactic
interoperability problem, by at least having the data in RDF and available to
query using SPARQL. However, it makes dataset integration
Dear colleagues,
There will be no TM call today. Let's rejoin next week.
Best,
m.
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com
Hi all,
Tomorrow's teleconference (April 21 @ 12pm EST / 9AM PDT) will feature Dr. Jeff
Shrager (Co-Founder and Chief Technology Officer of CollabRx and Consulting
Associate Professor at Stanford University) who will talk to us about the work
being done at CollabRx. You might be interesting in r
Hi!
Just a reminder for today's Translational Medicine conference call.
''' Conference Details'''
* Date of Call: Thursday April 14 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.047
Hi!
Just a reminder of today's conference call for Translational Medicine.
''' Conference Details'''
* Date of Call: Thursday April 7 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.
Hi!
Here's the details for today's Translational Medicine teleconference call:
''' Conference Details'''
* Date of Call: Thursday March 24 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.20
Hi TM'ers,
At tomorrow's call (noon EST), we'll hear about OSCAR/MyOSCAR
(http://oscarmcmaster.org/) from Dr. David H Chan @ McMaster University.
Please dial in to the W3C conferencing system
''' Conference Details'''
* Date of Call: Thursday March 17 2011
* Time of Call: 12:00pm - 1:00pm ET
Hi everybody,
Just a reminder for today's teleconference call on translational medicine:
''' Conference Details'''
* Date of Call: Thursday March 10 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In
Hi,
Just a reminder for this week's Translational Medicine call:
''' Conference Details'''
* Date of Call: Thursday March 3 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.0479 (Lon
Hello TM'ers,
There will be no call on Thursday Feb 24 due to several conflicts, including
the CSHALS conference
http://www.iscb.org/cshals2011
Talk with you next week,
m.
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com
Hi TM'ers,
In preparation for this meeting, I started a wiki page for pharmacogenomics
http://www.w3.org/wiki/HCLSIG/TranslationalMedicine/pharmacogenomics
feel free to add to it :)
also, I may be late for this meeting, but feel free to start without me.
Cheers!
m.
From: Michel_Dumo
Hi!
Just a reminder for today's Translational Medicine conference call:
''' Conference Details'''
* Date of Call: Thursday February 17 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.31
Given that IBM's AI system called Watson is competing in Jeopardy against grand
champions, you might find the following overview of interest :
http://www.youtube.com/watch?v=3G2H3DZ8rNc
m.
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com
Hi all,
Just a reminder for today's Translational Medicine call. I imagine we'll spend
a brief bit of time discussing the not-quite-yet submitted paper, and move on
to other topics.
Cheers,
m.
''' Conference Details'''
* Date of Call: Thursday February 10 2011
* Time of Call: 12:00pm - 1:00
Hello,
Just a friendly reminder of the TM call at noon EST today - we'll be focusing
our discussion on the reviews for the JBMS special issue.
''' Conference Details'''
* Date of Call: Thursday January 20 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
Hello,
Just a reminder for today's Translational Medicine teleconference call:
''' Conference Details'''
* Date of Call: Thursday January 13 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.
> In Health Care and Life Science domains, image data is a common form
> of data under discussion so a best practice for referring to an image
> or to an (extractable) feature *within* an image would cover a
> fundamental need in biomedicine to point to 'raw' data as evidence (as
> well as giving
> > 1 - sPCHR (semantic Personally Controlled Health Care Records) -> to
> capture
> > patient data using Semantic Web technologies, thereby making use of
> existing
> > Linked Open Data (drug, clinical, etc) and becoming a valuable source of
> > structured information for epidemiological research,
nd certainly to new participants :) What do you think?
m.
> -Original Message-
> From: Melanie Courtot [mailto:mcour...@gmail.com]
> Sent: Friday, January 07, 2011 3:41 PM
> To: Michel_Dumontier
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: TM teleconference call
&
Happy New Year!
Here's the reminder for the TM teleconference call - note that we hope to
start up new subgroups, new participants welcome!
''' Conference Details'''
* Date of Call: Thursday January 6 2011
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Di
Hello,
This is a reminder for today's teleconference call:
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-12-16_Conference_Call
''' Conference Details'''
* Date of Call: Thursday December 16 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-
[Apologies for cross posting]
=
CALL FOR PAPERS
OWLED 2011
OWL: Experiences and Directions
The Eighth International Workshop
June 5-6, San Francisco, California, USA
http://www.webont.org/owled/2011/
Co-located with
2011 Semantic Technology Conference (SemTech
Hello TMOers,
The meeting for today is cancelled as many of us are unable to attend due to
overlapping obligations. Let's try to have our last meeting of the year next
week. In the meantime, let's accumulate a set of datasets/resources related to
pharmacogenomics and discuss which ones we might
Just a reminder of today's TMO call
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-12-02_Conference_Call
''' Conference Details'''
* Date of Call: Thursday December 2 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (P
Due to anticipated turkey-based feasting, the TMO call is cancelled for this
week.
m.
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com
Just a reminder for today's teleconference call
''' Conference Details'''
* Date of Call: Thursday November 18 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France)
* Dial-In #: +44.203.318.0479 (London, UK)
* Par
A friendly reminder of today's TMO teleconference call will focus on the JBMS
paper in preparation.
Minutes from last week's call are available (thanks to Bob for scribing!):
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-11-04_Conference_Call_minutes
''' Conference Details'''
* Date of
The minutes from yesterday's conference call are now available:
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-11-04_Conference_Call_minutes
m.
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com
Here's a reminder of today's teleconference call
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-11-04_Conference_Call
''' Conference Details'''
* Date of Call: Thursday November 4 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.2
Just a reminder for tomorrow's TMO teleconference call
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-10-28_Conference_Call
''' Conference Details'''
* Date of Call: Thursday October 28 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +
Here's a reminder for today's TMO call:
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-10-21_Conference_Call
''' Conference Details'''
* Date of Call: Thursday October 21 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.0
Here's a reminder for today's teleconference call:
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-10-14_Conference_Call
''' Conference Details'''
* Date of Call: Thursday October 14 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4
lic-semweb-lifesci-requ...@w3.org
[mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of Michel_Dumontier
Sent: Wednesday, October 13, 2010 11:37 AM
To: public-semweb-lifesci@w3.org
Subject: CANARIE C-BRASS Project - 1 Position at Carleton University, Ottawa,
Ontario, Canada
1 open positio
1 open position with the CANARIE funded C-BRASS Project
http://dumontierlab.com/postings/c-brass-programmer-nov2010.pdf
OVERVIEW: The programmer will be primarily responsible for the design and
deployment of SADI-compatible bioinformatic services. SADI is an open-source
Semantic Web Service f
Here's the notice for today's telecom:
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-10-07_Conference_Call
''' Conference Details'''
* Date of Call: Thursday October 7 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03
Here's a reminder for today's TMO call:
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-09-30_Conference_Call
''' Conference Details'''
* Date of Call: Thursday September 30 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79
Minutes for today's call are now available
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-09-23_Conference_Call
Thanks to Bob Powers for scribing :)
m.
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com
Here's a reminder for Thursday's TMO call
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-09-23_Conference_Call
''' Conference Details'''
* Date of Call: Thursday September 23 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.
Here's a reminder for Thursday's TMO call
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-09-16_Conference_Call
''' Conference Details'''
* Date of Call: Thursday September 16 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.
> -Original Message-
> From: Eric Prud'hommeaux [mailto:eric...@gmail.com] On Behalf Of Eric
> Prud'hommeaux
> Sent: Saturday, September 11, 2010 5:13 PM
> To: Michel_Dumontier
> Cc: Lee Feigenbaum; Chimezie Ogbuji; public-semweb-lifesci@w3.org
> Su
Hi Lee!
> -Original Message-
> From: Lee Feigenbaum [mailto:figt...@gmail.com] On Behalf Of Lee
> Feigenbaum
> Sent: Saturday, September 11, 2010 2:54 AM
> To: Michel_Dumontier
> Cc: Eric Prud'hommeaux; Chimezie Ogbuji; public-semweb-lifesci@w3.org
> Subject
> > It's not a restriction on the predicates - it's a restriction on
> instances of a certain class - like that of blood pressure
> measurements. Checking consistency would tell you whether your data
> conforms to the specification described by the ontology document.
>
> Right, but tells whom, and
> -Original Message-
> From: Eric Prud'hommeaux [mailto:eric...@gmail.com] On Behalf Of Eric
> Prud'hommeaux
> Sent: Friday, September 10, 2010 6:41 PM
> To: Michel_Dumontier
> Cc: Chimezie Ogbuji; public-semweb-lifesci@w3.org
> Subject: RE: [TM
> But then anyone merging two TMO documents with different units has the
> normalization burden. If we pick a unit and annotate the predicates,
> then the folks who would have to do the work of merging with non-TMO
> documents (who would have to introduce some rules/canonicalization
> pipeline any
Hi,
I think the model where we separate the unit from the value is preferred (as
per CPR) because it is highly flexible. You are right however that people could
then refer to any unit, although an ontology could specify the unit involved
(universal restriction). The alternative, which Bijan wo
Here's a reminder for Thursday's TMO conference call
http://esw.w3.org/HCLSIG/PharmaOntology/Meetings/2010-09-09_Conference_Call
m.
''' Conference Details'''
* Date of Call: Thursday September 9 2010
* Time of Call: 12:00pm - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #
There are two issues I'd like to raise to our communities:
1 - What metrics should we use to assess ontology quality and determine whether
an ontology is "good".
2 - Can we re-factor existing, and well used terminologies (SNOMED-CT, NCI-T,
ICD) into "good" ontologies for health care and the lif
Hi François,
You can imagine that Linking Open Data (LOD) is the first generation of making
*open data* available with semantic web technologies. It takes significant
amounts of time and effort to determine whether "drug" is the same or different
concept in DrugBank, PharmGKB, Dailymed, ChEBI,
oblem which we don't attempt to
solve.
m.
-Original Message-
From: Eric Miller [mailto:subscription...@squishymedia.com]
Sent: Thursday, March 11, 2010 1:19 PM
To: Michel_Dumontier
Cc: Oliver Ruebenacker; public-semweb-lifesci@w3.org
Subject: Re: Thickness of lines in this figure
Hi
Hello,
It comes from the number of relations between the datasets.
m.
-Original Message-
From: public-semweb-lifesci-requ...@w3.org
[mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of Oliver Ruebenacker
Sent: Thursday, March 11, 2010 8:35 AM
To: public-semweb-lifesci@w3.org
Subj
===
1st Int. Workshop on Semantics of Visual Objects (SEMVO 2010)
Raleigh, NC, USA, April 27 (morning), 2010
held in conjunction with WWW 2010
--- Final Call for Papers ---
Submission deadlin
===
1st Int. Workshop on Semantics of Visual Objects (SEMVO 2010)
Raleigh, NC, USA, April 27 (morning), 2010
held in conjunction with WWW 2010
--- 2nd Call for Papers ---
Submission deadline:
Hello,
There are many elements of warehousing semantic data that have yet to
be solved, both in terms of efficient algorithms for storage, indexing,
retrieval and visualization as well as in the core representation of
knowledge. In developing tools and applications, I'm quite sure that
both Mark
Hello,
I've added a pharmacogenomics use case
http://esw.w3.org/topic/HCLSIG/PharmaOntology/UseCases
and have reviewed the suggested terminology, in part by organizing them
into discovery/development sub-categories.
http://esw.w3.org/topic/TMO_Review_MD
Cheers,
-=Michel=-
> -Original Message-
> From: public-semweb-lifesci-requ...@w3.org [mailto:public-semweb-
> lifesci-requ...@w3.org] On Behalf Of Egon Willighagen
> Sent: Thursday, April 02, 2009 10:57 AM
> To: Matthias Samwald
> Cc: Phillip Lord; Oliver Ruebenacker; Pat Hayes; public-semweb-lifesci
> Subj
Mark,
It's clear that the declaration and accurate description of domain
terminology is essential. In the hands of curators or other KA
approaches, this creates structural knowledge. Linked data efforts need
ontologies for typing. The SADI framework requires its associated
services to do this *exp
] 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
But Kei - if you are aware that differences exist between these
entities, that they are unequivocally _not_ the same - then you should
not use owl:sameAs. A better relation is rdfs:seeAlso ... that they are
related in some way, but there is uncertainty as to what the relation
is, until the communit
> -Original Message-
> From: public-semweb-lifesci-requ...@w3.org [mailto:public-semweb-
> lifesci-requ...@w3.org] On Behalf Of Kei Cheung
> Sent: Thursday, March 26, 2009 1:52 PM
> To: Matthias Samwald
> Cc: public-semweb-lifesci
> Subject: Re: DBpedia to OBO mapping: did someone already w
> 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
>
>
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
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
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
> I just want to focus on the essence of my comments to Michel and Peter
> who have issues with the use of 303 redirection to achieve separation
> of
> datum identity from descriptive representation, when using a
particular
> URI scheme.
>
> I am simply interested in explaining to them what this
We track provenance with namespace and/or graphs. What could be simpler?
-=Michel=-
-Original Message-
From: David Booth [mailto:da...@dbooth.org]
Sent: Monday, March 23, 2009 10:27 PM
To: Michel_Dumontier
Cc: W3C HCLSIG hcls
Subject: RE: blog: semantic dissonance in uniprot
Eric,
On Sat,
Eric and friends,
I'm very sympathetic to the simplifying assumption of not distinguishing
between a record and the molecular entity it represents, but there are some
important considerations. First, we need to be cautious in the transformation
of recorded facts (as they appear in these dat
Eric,
I'll be attending DILS, which does indeed look to be very interesting from our
perspective. Holger will also be attending. Together, we will certainly raise
the issue of HCLS participation with relevant or potential semweb groups.
The work that we will be presenting describes our transfo
While Xiaoshu brings up an important point of constructive criticism,
it's not clear from the text that is being done. In the first case, bugs
happen, and these will get fixed, I don't think it's worth mentioning.
In the second, I think the topic is much more relevant. However, how
_exactly_ can t
Regrets, I won't be able to participate.
-=Michel=-
-Original Message-
From: [EMAIL PROTECTED] on behalf of Susie M Stephens
Sent: Sat 2008/04/26 11:18
To: public-semweb-lifesci@w3.org
Subject: BioRDF Telcon
Here's the reminder for Monday's BioRDF call.
Susie
== Conference Details
Jonathan,
I regret not mentioning this in the first place, but thanks for the
time and effort to put the note together. It makes debating it so much
easier ;-)
In general, I think my objections are related to philosophical
recommendations that are difficult or impossible to follow. I would
expec
Hi all,
I read the latest URI note [1], and here are some comments:
[1] http://sw.neurocommons.org/2007/uri-note/
"A usage spec for a name is simply a graph that is designated as one
that specifies when the name should and shouldn't be used"
Given that RDF semantics are open world, and RDF
Regrets. I won't be able to make this call.
-=Michel=-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Eric Neumann
Sent: Wednesday, September 26, 2007 3:35 PM
To: Public-semweb-lifesci@w3.org
Subject: HCLSIG TC Sept 27th
Thurs, September
> Can't speak for BioPAX, but I can say that for me one problem with DC
> is that it's RDF(S), so I can't use the properties in my OWL
> restrictions etc!
>
> There are some OWL versions (Protege even allows you to import one),
> but I don't know if that is a good idea, as far as I can see thi
ED] [mailto:[EMAIL PROTECTED] On Behalf Of Marc-
> Alexandre Nolin
> Sent: Monday, August 20, 2007 3:11 PM
> To: Michel_Dumontier
> Cc: [EMAIL PROTECTED]; public-semweb-lifesci hcls
> Subject: Re: making statements on the semantic web
>
> Hi,
>
> Sorry, I miss a conversation
> > > and making URIs
> > > dereferenceable to useful metadata is certainly one
> > > convenient way to help do so.
> >
> > Really? The point of these examples is that there are a variety of
> > cases which for a variety of reasons it's not so convenient
> > (actually, either for the minter or th
Fantastic material Nigam (and co)! I hope you don't mind if I use some
for my 4th year bioinformatics class :-)
Couple of points:
Problem: Asserting disjointness between classes that are definable.
Example (slide 100): Rural Area and Urban Area are disjoint; Woomera is
initially asserted to be
Center
Mailing: 209 Nesbitt, 1125 Colonel By Drive, Ottawa, ON K1S5B6
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> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf
Of
> Greg Tyrelle
&g
> > Sure, HTTP URIs can be used as identifiers, but why would I
> > mint arbitrary HTTP URIs when I can use a scheme that has no
> > resolution protocol implicitly or explicitly associated with
> > it?
>
> Indeed, in this case there would be no benefit to using HTTP URIs.
But
> the situation you
> In any case, the most practical non-HTTP URIs that are in use at the
> moment
> seem to be LSIDs and DOIs; both have an associated resolution
protocol...
Whereas the bm or info scheme does not.
-=Michel=-
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