- From: Mark Montgomery <markm@kyield.com>
- Date: Thu, 3 May 2007 14:22:22 -0700
- To: "William Bug" <William.Bug@DrexelMed.edu>, "public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>
- Message-ID: <001401c78dc9$25c5a040$a100a8c0@Inspiron>
PS- it just occurred to me that the workgroup already has a leader, or co-leaders, which doesn't necessarily also mean they desire to lead each paper/project coming out of the WG, but I would defer to them. - Mark
----- Original Message -----
From: William Bug
To: public-semweb-lifesci hcls
Sent: Thursday, May 03, 2007 2:00 PM
Subject: Re: SfN meeting submission
Hi Don,
This works for me.
In regards to the suggestion Mark made, I think some of his suggestions sound very practical. I'd be glad to participate - or not - depending on the need and intended outcome.
With this in mind, if you'd like someone to vet what you work up - or work with you on it, Don - I'd be glad to do that.
Cheers,
Bill
On May 3, 2007, at 1:06 PM, Donald Doherty wrote:
Here's my proposal:
I write a quick rough draft and send a copy to all interested parties.
People actually contributing to the writing should mostly be neuroscientists
but of course include input from the rest.
Then I'll take all of the input and work up a revised abstract and send it
back out to all interested parties for further feedback.
Repeat until everyone is happy and/or we run out of time. Then we decide to
submit or not.
About authors, here is the Neuroscience community standard. First author is
usually the graduate student and last author is usually the principal
investigator.
Submitter must be first author...so if I take this on everyone must be
comfortable with me being the grad student :^). We should probably put the
person who put the most sweat into the demo as last author.
Hopefully the author issue won't be too divisive since this is simply an
abstract. The important thing is that everyone is acknowledged.
Of highest importance is that the demo gets in front of the neuroscience
community at their biggest meeting.
What do you think?
Don
-----Original Message-----
From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Kei Cheung
Sent: Thursday, May 03, 2007 12:19 PM
To: William Bug
Cc: public-semweb-lifesci hcls
Subject: Re: SfN meeting submission
Hi Bill et al.,
I agree that it's important to make our SW/Neuro demo visible to the
neuroscience community. For example, I have asked Gordon Shepherd (PI of
SenseLab) to look at the AD use case written by June, Gwen, et al to see
if any comments/suggestions can be made. It would be great if we can get
more neuroscientists involved to help make our work more scientifically
relevant. I believe this would also help make SW technologically credible.
Regarding the SfN abstract, my concern is that we might not be able to
meet the deadline given that people are currently busy preparing for the
upcoming demo at WWW2007 next week. In addition to what to write and how
to write it (it probably won't take long for an abstract), we need to
discuss how the author list should appear. All these may take some time
to resolve as part of the community process, but we'd better start
thinking/discussing about it soon ...
Cheers,
-Kei
William Bug wrote:
Hi Don, Matthias, John, Kei, et al.,
I too would like to contribute to an SfN abstract in this context.
I believe given the domain HCLS IG is covering - neurodegenerative
disease - despite the lack of a full, refereed article, this is a very
important venue in which to present, in order to help bolster the
relevance and credibility of this effort to the general neuroscience
community. With a working demo, it would be a shame NOT to have it
represented at the SfN meeting.
We could also look to use such an abstract as starting material for a
full submission to journals that cover neuroinformatics such as
Neuroinformatics, PLoS Computational Biology, or Journal of
Computational Neuroscience.
In regards to relevant neuroscience meetings, there are also the
meetings hosted by:
Federation of European Neuroscience Societies (FENS):
http://fens.mdc-berlin.de/calendar/
International Brain Research Organization (IBRO):
http://www.ibro.org/Pub_Events_Search.asp?Search=.
The Japan Neuroscience Society
http://www.jnss.org/english/index_e.html
http://www2.convention.jp/neuro2007/
Federation of Asian and Oceanian Neuroscience Societies (FAONS)
http://www.faons.org/
I'm not certain what the deadlines are for the associated meetings.
Cheers,
Bill
On May 2, 2007, at 11:51 AM, Donald Doherty wrote:
Hi Matthias,
That'd be great! SfN abstracts are brief (max. 2300 characters including
punctuation!) so focusing on the value to neuroscientists sounds like the
right course.
Abstract may be presented or posters. Slide presentations are kept very
brief and there is so much going on most people won't see a
particular slide
presentation. Even if we indicate our preference for a slide presentation
it's likely we wouldn't get it.
If we do a poster it will be up half a day. We can bring our demo machine
and set it up next to the poster. (I've seen BIRN and others do this.
Wireless is generally available.) I think this is the preferred mode
for us.
There is also a $75 submission fee.
I'm willing to take responsibility for paying the submission fee, getting
the poster up, staying there while it's up, and working the demo as
long as
everyone is interested in doing this and a demo machine will be
available.
We won't get a paper out of it but I think it's worthwhile to expose the
end-user community (neuroscientists) to the value the Semantic Web
technologies may provide to them.
Best wishes,
Don
-----Original Message-----
From: public-semweb-lifesci-request@w3.org
<mailto:public-semweb-lifesci-request@w3.org>
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of
samwald@gmx.at <mailto:samwald@gmx.at>
Sent: Wednesday, May 02, 2007 9:37 AM
To: donald.doherty@brainstage.com
<mailto:donald.doherty@brainstage.com>; public-semweb-lifesci@w3.org
<mailto:public-semweb-lifesci@w3.org>
Subject: SfN meeting submission
Hi Don,
I would help with the abstract for SfN where I can, of course. I guess it
should be even more focussed on the requirements and use cases in
Neuroscience than the BMC Bioinformatics paper. Mainly a description
of the
collaborating neuroscience groups, their motivation and the types of
information that we are integrating, and less about the technical
details.
I guess it is much too late to start writing a group paper for the ISMB
workshop now. A poster abstract would be possible, but I think we
don't want
to present a poster.
cheers,
Matthias
This year's Society for Neuroscience meeting abstracts are due May 15th.
I'd
like to take the lead on submitting an abstract if the team is
interested.
Don
P.S. This year's meeting is November 3-7 in San Diego, California.
-----Original Message-----
From: public-semweb-lifesci-request@w3.org
<mailto:public-semweb-lifesci-request@w3.org>
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Alan
Ruttenberg
Sent: Tuesday, May 01, 2007 12:57 AM
To: public-semweb-lifesci@w3.org <mailto:public-semweb-lifesci@w3.org>
Subject: ISMB Bio-Ontologies Meeting
I forget, was someone submitting an abstract about our work to this
workshop?
-Alan
On Apr 26, 2007, at 1:18 PM, Susanna wrote:
** Apologies for cross posting **CALL FOR PAPERS and POSTER
ABSTRACTS (Deadline May 1st)
Proceedings in BMC Bioinformatics
*^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^**
Bio-Ontologies SIG Workshop
Vienna, Austria: July 20 2007
"Bio-Ontologies: ten years past and looking to the future"
*^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^**
15th ISMB & 6th ECCB Vienna, Austria: July 18-25, 2007
CALL FOR PAPERS and POSTER ABSTRACTS (Deadline May 1st)
Proceedings in BMC Bioinformatics
The long-standing ISMB Bio-Ontologies SIG is in its tenth
consecutive year. This year the workshop will have a celebratory
and reflective discussion on "Bio-Ontologies: ten years past and
looking to the future".
PROGRAM CHAIRS:
Robert Stevens (1), Phillip Lord (2), Robin McEntire (3), Susanna-
A. Sansone (4)
1. School of Computer Science, University of Manchester, UK
2. School of Computing Science, University of Newcastle, UK
3. GlaxoSmithKline, USA
4. EMBL-EBI The European Bioinformatics Institute, Cambridge, UK
WEBSITES:
Bio-Ontologies SIG workshop: http://bio-ontologies.org.uk
ISMB & ECCB main conference website http://www.iscb.org/ismbeccb2007
ABOUT THE BIO-ONTOLOGIES SIG WORKSHOP
The workshop will continue offer an informal environment for
presentation and discussion of ontologies and their role in
providing a mechanism for organising, sharing and reconciling data.
This year, to celebrate its tenth anniversary, we have invited four
presenters from the first bio-ontologies tutorial and meeting
organisers to sit on a panel, namely: Mark Musen, Peter Karp, Russ
Altman and Steffen Schulze-Kremer
They will be asked to present positions on the following questions:
1. What has been the best thing to have happened in bio-ontologies
in the past ten years?
2. What has been the worst thing to have happened in bio-ontologies
in the past ten years?
3. How must bio-ontologies progress in the next ten years?
4. How must bio-ontologies not progress in the next ten years
CALL FOR PAPERS AND POSTER ABSTRACT:
We are inviting two types of submissions SHORT PAPER papers (up to
4 pages) and POSTER ABSTRACT (up to 1/2 page) from any aspect doing
bio-ontology research or using bio-ontologies to do bioinformatics
research. Topics include, but are not restricted to:
- Biological Applications of Ontologies
- Reports on Newly Developed or Existing Bio-Ontologies
- Tools for Developing Ontologies
- Use of Ontologies in Data Communication Standards
- Use of Semantic Web technologies in Bioinformatics
- The implications of Bio-Ontologies or the Semantic Web for the
drug discovery process
- Current Research In Ontology Languages and its implication for
Bio-Ontologies
PROGRAM COMMITTEE
Abstracts will be reviewed by the Program Committee, including the
Program Chairs and additionally: David Benton, Suzanna Lewis, Chris
Mungall and Alan Ruttenberg.
PUBLICATION OF THE PROCEEDINGS
The Programme Committee will also select those papers, which are
suitable for further publication in a BMC Bioinformatics
Supplement. Authors will be invited to resubmit full papers.
DEADLINES
Submissions due: May 1st 2007
Notification of acceptance: May 21st 2007
Final versions due: May 31st 2007
Workshop: July 20th 2007
-- Susanna-Assunta Sansone, PhD NET Project - Coordinator
www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project> The
European Bioinformatics Institute
email: sansone@ebi.ac.uk <mailto:sansone@ebi.ac.uk> EMBL Outstation
- Hinxton direct: +44 (0)
1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK room: A229
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Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
Please Note: I now have a new email - William.Bug@DrexelMed.edu
<mailto:William.Bug@DrexelMed.edu>
Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
Please Note: I now have a new email - William.Bug@DrexelMed.edu
Received on Thursday, 3 May 2007 21:22:54 UTC