List Info

Thread: RE: SfN meeting submission




RE: SfN meeting submission
country flaguser name
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-requestw3.org
[mailto:public-semweb-lifesci-requestw3.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-requestw3.org 
>> <mailto:public-semweb-lifesci-requestw3.org>
>> [mailto:public-semweb-lifesci-requestw3.org]
On Behalf Of 
>> samwaldgmx.at <mailto:samwaldgmx.at>
>> Sent: Wednesday, May 02, 2007 9:37 AM
>> To: donald.dohertybrainstage.com 
>> <mailto:donald.dohertybrainstage.com>;
public-semweb-lifesciw3.org 
>> <mailto:public-semweb-lifesciw3.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-requestw3.org 
>>> <mailto:public-semweb-lifesci-requestw3.org>
>>> [mailto:public-semweb-lifesci-requestw3.org]
On Behalf Of Alan 
>>> Ruttenberg
>>> Sent: Tuesday, May 01, 2007 12:57 AM
>>> To: public-semweb-lifesciw3.org
<mailto:public-semweb-lifesciw3.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: sansoneebi.ac.uk
<mailto:sansoneebi.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-discusslists.sourceforge.net 
>>>> <mailto:Obo-discusslists.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.BugDrexelMed.edu 
> <mailto:William.BugDrexelMed.edu>
>
>
>
>







Re: SfN meeting submission
country flaguser name
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.dohertybrainstage.com>
To: "'Kei Cheung'" <kei.cheungyale.edu>; "'William Bug'" 
<William.BugDrexelMed.edu>
Cc: "'public-semweb-lifesci hcls'"
<public-semweb-lifesciw3.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-requestw3.org
[mailto:public-semweb-lifesci-requestw3.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-requestw3.org
>> <mailto:public-semweb-lifesci-requestw3.org>
>> [mailto:public-semweb-lifesci-requestw3.org]
On Behalf Of
>> samwaldgmx.at <mailto:samwaldgmx.at>
>> Sent: Wednesday, May 02, 2007 9:37 AM
>> To: donald.dohertybrainstage.com
>> <mailto:donald.dohertybrainstage.com>;
public-semweb-lifesciw3.org
>> <mailto:public-semweb-lifesciw3.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-requestw3.org
>>> <mailto:public-semweb-lifesci-requestw3.org>
>>> [mailto:public-semweb-lifesci-requestw3.org]
On Behalf Of Alan
>>> Ruttenberg
>>> Sent: Tuesday, May 01, 2007 12:57 AM
>>> To: public-semweb-lifesciw3.org
<mailto:public-semweb-lifesciw3.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: sansoneebi.ac.uk
<mailto:sansoneebi.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-discusslists.sourceforge.net
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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.BugDrexelMed.edu
> <mailto:William.BugDrexelMed.edu>
>
>
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Re: SfN meeting submission
country flaguser name
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-semweb-lifesci-requestw3.org">public-semweb-lifesci-requestw3.org
[ public-semweb-lifesci-requestw3.org">mailto:public-semweb-lifesci-requestw3.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):


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-semweb-lifesci-requestw3.org">public-semweb-lifesci-requestw3.org 
< public-semweb-lifesci-requestw3.org">mailto:public-semweb-lifesci-requestw3.org>;
[ public-semweb-lifesci-requestw3.org">mailto:public-semweb-lifesci-requestw3.org] On Behalf Of 
samwaldgmx.at < samwaldgmx.at">mailto:samwaldgmx.at>;
Sent: Wednesday, May 02, 2007 9:37 AM
To: donald.dohertybrainstage.com">donald.dohertybrainstage.com 
< donald.dohertybrainstage.com">mailto:donald.dohertybrainstage.com>; public-semweb-lifesciw3.org">public-semweb-lifesciw3.org 
< public-semweb-lifesciw3.org">mailto:public-semweb-lifesciw3.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-requestw3.org">public-semweb-lifesci-requestw3.org 
< public-semweb-lifesci-requestw3.org">mailto:public-semweb-lifesci-requestw3.org>;
[ public-semweb-lifesci-requestw3.org">mailto:public-semweb-lifesci-requestw3.org] On Behalf Of Alan 
Ruttenberg
Sent: Tuesday, May 01, 2007 12:57 AM
To: public-semweb-lifesciw3.org < public-semweb-lifesciw3.org">mailto:public-semweb-lifesciw3.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: sansoneebi.ac.uk < sansoneebi.ac.uk">mailto:sansoneebi.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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_______________________________________________
Obo-discuss mailing list
Obo-discusslists.sourceforge.net">Obo-discusslists.sourceforge.net 
< Obo-discusslists.sourceforge.net">mailto:Obo-discusslists.sourceforge.net>





-- 
"Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ...
Jetzt GMX TopMail testen: http://www.gmx.net/de/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.BugDrexelMed.edu">William.BugDrexelMed.edu 
< William.BugDrexelMed.edu">mailto:William.BugDrexelMed.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.BugDrexelMed.edu">William.BugDrexelMed.edu




Re: SfN meeting submission
country flaguser name
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
To: public-semweb-lifesciw3.org <w3.org">mailto:public-semweb-lifesciw3.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: sansoneebi.ac.uk <ebi.ac.uk">mailto:sansoneebi.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.