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List Info
Thread: RE: SfN meeting submission
|
|
| RE: SfN meeting submission |
  United States |
2007-05-03 12:06:22 |
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-b
erlin.de/calendar/
>
>
> International Brain Research Organization (IBRO):
> ht
tp://www.ibro.org/Pub_Events_Search.asp?Search=.
>
> The Japan Neuroscience Society
> http://www.j
nss.org/english/index_e.html
> http://www2.conv
ention.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.or
g.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.a
c.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
>>>>
------------------------------------------------------------
----------
>>>> ---
>>>> This SF.net email is sponsored by DB2
Express
>>>> Download DB2 Express C - the FREE version
of DB2 express and take
>>>> control of your XML. No limits. Just data.
Click to get it now.
>>>> http://sourcefor
ge.net/powerbar/db2/
>>>>
_______________________________________________
>>>> Obo-discuss mailing list
>>>> Obo-discuss lists.sourceforge.net
>>>> <mailto:Obo-discuss lists.sourceforge.net>
>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>
>>>
>>>
>>>
>>
>> --
>> "Feel free" - 10 GB Mailbox, 100
FreeSMS/Monat ...
>> Jetzt GMX TopMail testen: http://www.gmx.net/d
e/go/topmail
>>
>>
>>
>>
>
>
>
> 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>
>
>
>
>
|
|
| Re: SfN meeting submission |
  United States |
2007-05-03 12:32:25 |
I would make a couple of suggestions.
1) Allow those who were most deeply involved in the project
(both in raw
energy and in actual contributions) to recommend who the
author (s) should
be. They are (usually in my experience) in the best position
to understand
who understands their work, and can then communicate same.
Further, to
involve the individual who had the original idea,
particularly if it was
deeply considered before sharing with others.
2) Then consider selecting additional members based on the
needs of the
subject and desired outcome. For example, knowledge systems
covers a lot of
territory beyond either discipline of neuroscience or
computer science. I
coined the term mega disciplinary on accident a few years
ago when writing
about this particular challenge within knowledge systems
(forgive me if
someone coined it first). I would include both of these
disciplines and
weighted heavily of course for this particular target, but
depending on the
specific goal of the demo and paper (s), the group might
consider inviting
others with deep experience in areas that can contribute to
the desired
outcome, even if not an author.
3) Then elect a team leader. Online and group collaboration
is fine to a
point, but as most who have experienced same over time have
often enough
confronted one or more of the negatives.
4) Take it semi private for expediency with occasional
public updates.
My brother died of ALS about 7 years ago after three years
of multi family
hell, and my wife was recently diagnosed with seizure
disorders fairly late
in life (fortunately fine), so I wish you God's speed in
your work.
Neuro disease (s) and the complexities of the broad areas of
related
research to my understanding provide an excellent match for
applied
ontological languages, as well as related areas we are all
working on.
.02- MM
----- Original Message -----
From: "Donald Doherty" <donald.doherty brainstage.com>
To: "'Kei Cheung'" <kei.cheung yale.edu>; "'William Bug'"
<William.Bug DrexelMed.edu>
Cc: "'public-semweb-lifesci hcls'"
<public-semweb-lifesci w3.org>
Sent: Thursday, May 03, 2007 10:06 AM
Subject: RE: SfN meeting submission
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-b
erlin.de/calendar/
>
>
> International Brain Research Organization (IBRO):
> ht
tp://www.ibro.org/Pub_Events_Search.asp?Search=.
>
> The Japan Neuroscience Society
> http://www.j
nss.org/english/index_e.html
> http://www2.conv
ention.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.or
g.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.a
c.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
>>>>
------------------------------------------------------------
----------
>>>> ---
>>>> This SF.net email is sponsored by DB2
Express
>>>> Download DB2 Express C - the FREE version
of DB2 express and take
>>>> control of your XML. No limits. Just data.
Click to get it now.
>>>> http://sourcefor
ge.net/powerbar/db2/
>>>>
_______________________________________________
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>
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Informatics
> www.neuroterrain.org
> Department of Neurobiology & Anatomy
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> 2900 Queen Lane
> Philadelphia, PA 19129
> 215 991 8430 (ph)
> 610 457 0443 (mobile)
> 215 843 9367 (fax)
>
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> Please Note: I now have a new email - William.Bug DrexelMed.edu
> <mailto:William.Bug DrexelMed.edu>
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| Re: SfN meeting submission |
  United States |
2007-05-03 16:00:09 |
|
| 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-sem web-lifesci-request w3.org">public-semweb-lifesci-request w3.org[ public-sem web-lifesci-request w3.org">mailto:public-semweb-lifesci-request w3.org] On Behalf Of Kei CheungSent: 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):
International Brain Research Organization (IBRO):
The Japan Neuroscience Society
Federation of Asian and Oceanian Neuroscience Societies (FAONS)
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-sem web-lifesci-request w3.org">public-semweb-lifesci-request w3.org < public-sem web-lifesci-request w3.org">mailto:public-semweb-lifesci-request w3.org>[ public-sem web-lifesci-request w3.org">mailto:public-semweb-lifesci-request w3.org] On Behalf Of samwald  gmx.at < samwald  gmx.at">ma ilto:samwald gmx.at>Sent: Wednesday, May 02, 2007 9:37 AM To: donald.doh erty brainstage.com">donald.doherty brainstage.com < public-sem web-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-sem web-lifesci-request w3.org">public-semweb-lifesci-request w3.org < public-sem web-lifesci-request w3.org">mailto:public-semweb-lifesci-request w3.org>[ public-sem web-lifesci-request w3.org">mailto:public-semweb-lifesci-request w3.org] On Behalf Of Alan Ruttenberg Sent: Tuesday, May 01, 2007 12:57 AM 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:
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 European Bioinformatics Institute email: sansone  ebi.ac.uk < 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 ---------------------------------------------------------------------- --- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. _______________________________________________ Obo-discuss mailing list Obo-discus s lists.sourceforge.net">Obo-discuss lists.sourceforge.net < Obo-discus s lists.sourceforge.net">mailto:Obo-discuss lists.sourceforge.net>
-- "Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ...
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.Bu g DrexelMed.edu">William.Bug DrexelMed.edu < William.Bu g 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.Bu g DrexelMed.edu">William.Bug DrexelMed.edu
|
| Re: SfN meeting submission |
  United States |
2007-05-03 16:22:22 |
|
|
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 -----
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-----
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):
International Brain Research Organization
(IBRO):
The Japan Neuroscience Society
Federation of Asian and Oceanian Neuroscience
Societies (FAONS)
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-----
Sent: Wednesday, May 02, 2007 9:37 AM
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-----
Ruttenberg
Sent: Tuesday, May 01, 2007 12:57 AM
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:
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
European Bioinformatics Institute
- 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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