Christine Golbreich was I thought involved in developing an OWl based
version of this
the annotations of the objects in the MAGE-ML.
cheers,
Michael
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> Marco Brandizi
> Sent: Sunday, June 11, 2006 1:26 PM
> To: public-semweb-lifesci@w3.org
> Cc: public-semweb-li
Miller, Michael D (Rosetta) wrote:
One other issue is that the actual objects in a microarray experiment
are for the most part one offs--i.e. a chip is a chip, it is only
hybridized once, the current investigation is only performed once
with a set of chips and so on. Even the genes that are
William Bug wrote:
If the goal of the semantic web were to serve end users only, I would
agree Marco. Since the data we express via SW technologies will also
be used for "large-scale, data integration and meta-analysis on data
derived from disparate studies," and since to perform such st
I think Marco makes several very important points - some of which
relate to the follow-up comments Michael has posted in reponse.
I though it might be worth highlighting them again - and bringing
them up for discussion in the call Michael will be giving next week
On Jun 9, 2006, at 11:39 A
.com
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> Marco Brandizi
> Sent: Friday, June 09, 2006 8:39 AM
> To: public-semweb-lifesci@w3.org
> Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
>
>
>
>
Hi all,
some notes on the discussion of MAGE/FUGE/FUGO and RDF.
- I think that converting the whole MAGE or FUGE into RDF is hard in
practice and maybe not so useful. The problems are:
- FUGE and MAGE are object models and should be reviewd in order to
provide an OWL modelling. For instan
(to be clear, when i say hotel, i mean the rental of a meeting room in a
hotel, not the costs of hotel rooms!)
John Wilbanks wrote:
OK. I will be traveling most of the rest of the month for
non-Neurocommons related work. But I'll return to this end of June and
start gathering some forces
OK. I will be traveling most of the rest of the month for
non-Neurocommons related work. But I'll return to this end of June and
start gathering some forces. I'll also get in touch with Karen Skinner.
I'd been thinking about early December as a time frame and Boston as a
location. I'll
Ditto, John!
I'd also suggest including NCBO folks on this (specifically Daniel
Rubin and Barry Smith), as I see an obvious convergence of needs and
focus here - despite the fact some see the top-down ontological
approach and the bottom-up SW approach as being difficult to reconcile.
Che
Hi John et al.,
I think it's a great idea. Do you have some more information (e.g.,
meeting location and draft meeting agenda) about the Neurocommons
meeting you mentioned which Bill and I (and possibly others) can share
with the neurosceintists we're working (have worked) with to see what
t
Hi Kei,
I agree on all points.
As far as getting all of these busy folks together at one time, you
are certainly correct - that is tough. Having said that, they each
represent a category of neuroinformatics researcher, and there are
others, so we could fall back to other folks. To my mi
All,
I've been following the discussion here with interest the last two weeks
- with the Neurocommons project, Science Commons is taking on both
issues of intellectual property (on ontologies and databases) and the
semantic web in neuroscience. We're text mining the open content and
indexin
Hi Bill,
Thanks for your passionate response. When I said "outreach", I did imply
to establish a mutually beneficial relationship between the semantic web
and neuroscience communities. I agree with you that such a relationship
would help bring scientific/techological advances to both communit
Many thanks, Daniel, for forwarding this to Onard - and can certain
clear up any ambiguous or incorrect statements I have made regarding
the FMA.
He should definitely be involved in this discussion.
Cheers,
Bill
On Jun 7, 2006, at 9:53 PM, Daniel Rubin wrote:
At 11:30 AM 6/7/2006, Willi
I do run on, sometimes, don't I, Kei?
I emphatically agree with the general tenor of your suggestion.
I would word it a bit differently.
I wouldn't call this outreach so much as going to the "customer" and
asking them to help us - the technology experts - to define their
user requirements.
Daniel,
if I remember correctly, you have a Protege version of the
Foundational Model of Anatomy.
Was this in Frames or OWL format?
Did it include the NeuroNames integration with FMA (NeuroFMA)?
It's still unclear to me whether NeuroFMA is still active as a
project, and how this would al
--
eric miller http://www.w3.org/people/em/
w3c world wide web consortiumhttp://www.w3.org/
On Jun 6, 2006, at 7:42 PM, kc28 wrote:
Hi Bill,
You really can write faster than I can read :-). Actually, we have
discussed in a previous telconf about
Hi Bill,
You really can write faster than I can read :-). Actually, we have
discussed in a previous telconf about how to outreach to the
neuroscience community. I think this represents a good opportunity to
try to get people like Doug Bowden involved, as we are interested in
converting Neu
Dear Matthias,
I would strongly recommend you contact Doug Bowden and colleagues at
NeuroNames before you undertake this task - or at least take a look
at the NeuroNames specifics I list in my previous email. I'd be glad
to answer any questions you may have about statements I made. Doug
Hi Kei,
I am under the impression that the neuronames ontology available on their
website (as an Excel file...) is different from the version that is licensed as
part of the UMLS. I guess the version that is online is a newer version of the
one incorporated in UMLS. However, this might be seen
I'm interested in a scenario of how a research group in a new area could
use use these kinds of termilogies in finding possibly relevant terms
and then more related information.
For instance, I have collected and organized some neuroscience links
into an Annotea bookmark file such as
http:/
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of kei cheung
Sent: Tuesday, June 06, 2006 9:52 AM
To: Alan Ruttenberg
Cc: [EMAIL PROTECTED];
[EMAIL PROTECTED]; 'Daniel Rubin';
public-semweb-lifesci@w3.org; 'Matthew Cockerill'
Subject: Re: MGED/FuGO. was: Re: Bio
> From: kei cheung [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, June 06, 2006 10:34 AM
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; Daniel Rubin;
> public-semweb-lifesci@w3.org; Matthew Cockerill
> Subject: Re: MGED/Fu
M
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; public-semweb-lifesci@w3.org
> Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for
> the UMLS presentation
>
>
> Hi Michael and Larry,
>
> As I understand it, Gavin Sherlock who is a member of MGED is
&g
Hi Matthias,
Thanks for doing that, but do we still have the licensing issue as
stated by Olivier?
Cheers,
-Kei
Matthias Samwald wrote:
I will convert the neuronames - ontology to SKOS (an OWL ontology used for the
representation of taxonomies / theasauri). It will be added to the extens
public-semweb-lifesci@w3.org
Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for
the UMLS presentation
Hi Michael,
Thanks for sharing your thoughts. MGED still has rooms for
ontological
improvement. As Larry suggested, we would have a better luck
if we can
work with the MGED consor
ED]; 'Daniel Rubin';
> public-semweb-lifesci@w3.org; 'Matthew Cockerill'
> Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for
> the UMLS presentation
>
>
>
> Hi Alan,
>
> Thanks for pointing us to FuGO. To me, it seems like that the F
day, June 06, 2006 9:41 AM
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; public-semweb-lifesci@w3.org
> Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for
> the UMLS presentation
>
>
> Hi Michael,
>
> Thanks for sharing your thoughts. MGED still h
Hi Alan,
Thanks for pointing us to FuGO. To me, it seems like that the FuGO
community is currently defining an upper ontology that can be
universally used to describe different types of genomic/proteomic
experiments including microarray experiments. There is a draft OWL
version of FuGO (http
ng [mailto:[EMAIL PROTECTED]
Sent: Tuesday, June 06, 2006 7:54 AM
To: Miller, Michael D (Rosetta)
Cc: Alan Ruttenberg; public-semweb-lifesci@w3.org
Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for
the UMLS presentation
Hi Michael et al,
Is there a converter available which can tak
Larry,
Thanks for the clarification. I agree that it would be great to have an
OWL version of MGED-ML (at least for experimental descriptions)
Best,
-Kei
Larry Hunter wrote:
On Tue, 2006-06-06 at 10:54 -0400, kei cheung wrote:
Hi Michael et al,
Is there a converter available which ca
On Tue, 2006-06-06 at 12:18 -0400, kei cheung wrote:
> Larry,
>
> I totally agree with you. The NIH Neuroscience Microarray Consortium
> (http://arrayconsortium.tgen.org/np2/home.do) might be a good use case
> since it's MIAME-compliant and it's neuroscience-specific. Do you and/or
> others ha
Larry,
I totally agree with you. The NIH Neuroscience Microarray Consortium
(http://arrayconsortium.tgen.org/np2/home.do) might be a good use case
since it's MIAME-compliant and it's neuroscience-specific. Do you and/or
others have any suggestion on how we can possibly approach the MGED
cons
cheers,
Michael
> -Original Message-
> From: kei cheung [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, June 06, 2006 7:54 AM
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; public-semweb-lifesci@w3.org
> Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for
> the UM
I will convert the neuronames - ontology to SKOS (an OWL ontology used for the
representation of taxonomies / theasauri). It will be added to the extension of
the bio-zen ontologies framework [1]. I will keep you updated.
kind regards,
Matthias Samwald
[1] http://neuroscientific.net/index.php?
On Mon, 2006-06-05 at 19:18 -0400, Donald Doherty wrote:
> it’s an embarrassment that the anatomy ontologies that are out there
> are locked up behind licensing.
Amen to that!
Imagine the state we'd be in if, starting in 1991, all web pages had
password protection on them, or you had to do
On Tue, 2006-06-06 at 10:54 -0400, kei cheung wrote:
> Hi Michael et al,
>
> Is there a converter available which can take existing datasets in
> mage-ml format and convert them into mged-owl format?
These are two different things. An MAGE-ML dataset describes gene
chips, hybridizations to the
On Mon, 2006-06-05 at 21:15 -0400, kc28 wrote:
> It might be time to think about how to
> convert mged ontology or mage-ml into RDF/OWL.
Kei,
This has the added advantage of enabling a large number of other life
science applications as well. It's possible that the MGED consortium
(http://www.
l Message-
> From: Benjamin Good [mailto:[EMAIL PROTECTED]
> Sent: Monday, June 05, 2006 10:45 PM
> To: Miller, Michael D (Rosetta)
> Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]; public-semweb-lifesci
> Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
>
>
&g
]
[mailto:[EMAIL PROTECTED] On Behalf Of
Alan Ruttenberg
Sent: Tuesday, June 06, 2006 6:40 AM
To: kc28
Cc: [EMAIL PROTECTED];
[EMAIL PROTECTED]; 'Daniel Rubin';
public-semweb-lifesci@w3.org; 'Matthew Cockerill'
Subject: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for the
UMLS
in';
> public-semweb-lifesci@w3.org; 'Matthew Cockerill'
> Subject: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for the
> UMLS presentation
>
>
>
> On Jun 5, 2006, at 9:15 PM, kc28 wrote:
>
> > It might be time to think about how to convert mged ont
On Jun 5, 2006, at 9:15 PM, kc28 wrote:
It might be time to think about how to convert mged ontology or
mage-ml into RDF/OWL. The following are two related articles:
http://www.nature.com/msb/journal/v2/n1/full/msb4100052.html
http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html
C
With minor tweaks this can be used in OWL - Matthias Samwald has done
this and used it in his BioPAX work. I am working on a proposal to
formally include it in BioPAX, for an upcoming workshop we are having.
That said, merely being syntactically OWL adds little semantic benefit.
Semantics, i
On Jun 5, 2006, at 1:00 PM, Olivier Bodenreider wrote:
Benjamin Good wrote:
Are there any plans to release the UMLS or parts thereof as RDF /
OWL ?
Not to my knowledge, Ben. And I certainly would be very cautious of
any attempt to doing it. The main reason is that many relations
used fo
On Jun 5, 2006, at 1:04 PM, Miller, Michael D (Rosetta) wrote:
Hi Ben and Matt,
An RDF version of the
UMLS knowledge sources would be seem to be very useful - at
least for
bioinformatics research purposes ...
What I was trying to discover was, from a purely RDF/ontology
standpoint, what is
5 June 2006 22:54:01 BDT
*To: *kei cheung <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
*Cc: *'public-semweb-lifesci' <mailto:public-semweb-lifesci@w3.org>>
*Subject: **Re: BioRDF [Telcon]: slides for the UMLS presentation*
*Reply-To: [EMAIL PROTECTED] <mailto
Don
-Original Message-
From: kc28 [mailto:[EMAIL PROTECTED]
Sent: Monday, June 05, 2006 9:16 PM
To: [EMAIL PROTECTED]
Cc: 'Matthew Cockerill'; public-semweb-lifesci@w3.org;
[EMAIL PROTECTED]; 'Daniel Rubin'
Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
For mo
;mailto:public-semweb-lifesci@w3.org>>
*Subject: **Re: BioRDF [Telcon]: slides for the UMLS presentation*
*Reply-To: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
kei cheung wrote:
Hi Olivier,
Sorry, I missed part of your talk (the beginning part and the ending
part) as I needed t
;mailto:public-semweb-lifesci@w3.org>>
*Subject: **Re: BioRDF [Telcon]: slides for the UMLS presentation*
*Reply-To: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
kei cheung wrote:
Hi Olivier,
Sorry, I missed part of your talk (the beginning part and the ending
part) as I needed t
To: kei cheung <[EMAIL PROTECTED]>
Cc: 'public-semweb-lifesci' <public-semweb-lifesci@w3.org>
Subject: Re: BioRDF
[Telcon]: slides for the UMLS presentation
Reply-To: [EMAIL PROTECTED]
kei cheung wrote:
Hi Olivier,
Sorry
kei cheung wrote:
Hi Olivier,
Sorry, I missed part of your talk (the beginning part and the ending
part) as I needed to be at other meetings. Is Neuronames
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9410576&dopt=Abstract)
part of UMLS now? If so, does it
BioRDF [Telcon]: slides for the UMLS presentation
But presumably the relations which characterize the structure
of UMLS could be given their own URIs, no?
Along with the concepts themselves.
And then UMLS could then be expressed in RDF, using UMLS
specific relations, rather than standard OWL
Hi Olivier,
Sorry, I missed part of your talk (the beginning part and the ending
part) as I needed to be at other meetings. Is Neuronames
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9410576&dopt=Abstract)
part of UMLS now? If so, does it make sense to conve
: Benjamin Good [mailto:[EMAIL PROTECTED]
> Sent: Monday, June 05, 2006 12:52 PM
> To: Miller, Michael D (Rosetta)
> Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED];
> public-semweb-lifesci@w3.org
> Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
>
>
> Hi,
>
>
elations can be reasonably mapped to is_a and
part_of relations.
Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Olivier
Bodenreider
Sent: 05 June 2006 18:00
To: Benjamin Good
Cc: 'public-semweb-lifesci'
Subject: Re: BioRDF [Telcon]: slides
Sent: Monday, June 05, 2006 10:06 AM
> To: [EMAIL PROTECTED]; [EMAIL PROTECTED]
> Cc: public-semweb-lifesci@w3.org
> Subject: RE: BioRDF [Telcon]: slides for the UMLS presentation
>
>
>
> But presumably the relations which characterize the structure
> of UMLS could be given th
reasonably mapped to is_a and part_of relations.
Matt
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] Behalf Of Olivier
> Bodenreider
> Sent: 05 June 2006 18:00
> To: Benjamin Good
> Cc: 'public-semweb-lifesci'
> Subject: Re: Bi
Benjamin Good wrote:
Are there any plans to release the UMLS or parts thereof as RDF / OWL ?
Not to my knowledge, Ben. And I certainly would be very cautious of any
attempt to doing it. The main reason is that many relations used for
creating hierarchies in biomedical vocabularies are not true
Are there any plans to release the UMLS or parts thereof as RDF / OWL ?
thanks
-Ben
On Jun 5, 2006, at 7:44 AM, Olivier Bodenreider wrote:
A PDF file with the slides of my UMLS presentation this morning is
available at:
http://mor.nlm.nih.gov/pubs/pres/060605-BioRDF.pdf
-- Olivier
Sus
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