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Re: SfN meeting submission

From: Mark Montgomery <markm@kyield.com>
Date: Thu, 3 May 2007 10:32:25 -0700
Message-ID: <001d01c78da9$04332a80$a100a8c0@Inspiron>
To: <donald.doherty@brainstage.com>, "'Kei Cheung'" <kei.cheung@yale.edu>, "'William Bug'" <William.Bug@DrexelMed.edu>
Cc: "'public-semweb-lifesci hcls'" <public-semweb-lifesci@w3.org>

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-berlin.de/calendar/
>
>
> International Brain Research Organization (IBRO):
> http://www.ibro.org/Pub_Events_Search.asp?Search=.
>
> The Japan Neuroscience Society
> http://www.jnss.org/english/index_e.html
> http://www2.convention.jp/neuro2007/
>
> Federation of Asian and Oceanian Neuroscience Societies (FAONS)
> http://www.faons.org/
>
> I'm not certain what the deadlines are for the associated meetings.
>
> Cheers,
> Bill
>
> On May 2, 2007, at 11:51 AM, Donald Doherty wrote:
>
>>
>> Hi Matthias,
>>
>> That'd be great! SfN abstracts are brief (max. 2300 characters including
>> punctuation!) so focusing on the value to neuroscientists sounds like the
>> right course.
>>
>> Abstract may be presented or posters. Slide presentations are kept very
>> brief and there is so much going on most people won't see a
>> particular slide
>> presentation. Even if we indicate our preference for a slide presentation
>> it's likely we wouldn't get it.
>>
>> If we do a poster it will be up half a day. We can bring our demo machine
>> and set it up next to the poster. (I've seen BIRN and others do this.
>> Wireless is generally available.) I think this is the preferred mode
>> for us.
>>
>> There is also a $75 submission fee.
>>
>> I'm willing to take responsibility for paying the submission fee, getting
>> the poster up, staying there while it's up, and working the demo as
>> long as
>> everyone is interested in doing this and a demo machine will be
>> available.
>>
>> We won't get a paper out of it but I think it's worthwhile to expose the
>> end-user community (neuroscientists) to the value the Semantic Web
>> technologies may provide to them.
>>
>> Best wishes,
>> Don
>>
>> -----Original Message-----
>> From: public-semweb-lifesci-request@w3.org
>> <mailto:public-semweb-lifesci-request@w3.org>
>> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of
>> samwald@gmx.at <mailto:samwald@gmx.at>
>> Sent: Wednesday, May 02, 2007 9:37 AM
>> To: donald.doherty@brainstage.com
>> <mailto:donald.doherty@brainstage.com>; public-semweb-lifesci@w3.org
>> <mailto:public-semweb-lifesci@w3.org>
>> Subject: SfN meeting submission
>>
>>
>> Hi Don,
>>
>> I would help with the abstract for SfN where I can, of course. I guess it
>> should be even more focussed on the requirements and use cases in
>> Neuroscience than the BMC Bioinformatics paper. Mainly a description
>> of the
>> collaborating neuroscience groups, their motivation and the types of
>> information that we are integrating, and less about the technical
>> details.
>>
>> I guess it is much too late to start writing a group paper for the ISMB
>> workshop now. A poster abstract would be possible, but I think we
>> don't want
>> to present a poster.
>>
>> cheers,
>> Matthias
>>
>>
>>
>>> This year's Society for Neuroscience meeting abstracts are due May 15th.
>>> I'd
>>> like to take the lead on submitting an abstract if the team is
>>> interested.
>>>
>>> Don
>>>
>>> P.S. This year's meeting is November 3-7 in San Diego, California.
>>>
>>> -----Original Message-----
>>> From: public-semweb-lifesci-request@w3.org
>>> <mailto:public-semweb-lifesci-request@w3.org>
>>> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Alan
>>> Ruttenberg
>>> Sent: Tuesday, May 01, 2007 12:57 AM
>>> To: public-semweb-lifesci@w3.org <mailto:public-semweb-lifesci@w3.org>
>>> Subject: ISMB Bio-Ontologies Meeting
>>>
>>>
>>> I forget, was someone submitting an abstract about our work to this
>>> workshop?
>>> -Alan
>>>
>>>
>>> On Apr 26, 2007, at 1:18 PM, Susanna wrote:
>>>
>>>> ** Apologies for cross posting **CALL FOR PAPERS and POSTER
>>>> ABSTRACTS (Deadline May 1st)
>>>> Proceedings in BMC Bioinformatics
>>>>
>>>> *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^**
>>>> Bio-Ontologies SIG Workshop
>>>> Vienna, Austria: July 20 2007
>>>>
>>>> "Bio-Ontologies: ten years past and looking to the future"
>>>>
>>>> *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^**
>>>> 15th ISMB & 6th ECCB Vienna, Austria: July 18-25, 2007
>>>>
>>>>
>>>> CALL FOR PAPERS and POSTER ABSTRACTS (Deadline May 1st)
>>>> Proceedings in BMC Bioinformatics
>>>>
>>>> The long-standing ISMB Bio-Ontologies SIG is in its tenth
>>>> consecutive year. This year the workshop will have a celebratory
>>>> and reflective discussion on "Bio-Ontologies: ten years past and
>>>> looking to the future".
>>>>
>>>> PROGRAM CHAIRS:
>>>> Robert Stevens (1), Phillip Lord (2), Robin McEntire (3), Susanna-
>>>> A. Sansone (4)
>>>> 1.    School of Computer Science, University of Manchester, UK
>>>> 2.    School of Computing Science, University of Newcastle, UK
>>>> 3.    GlaxoSmithKline, USA
>>>> 4.    EMBL-EBI The European Bioinformatics Institute, Cambridge, UK
>>>>
>>>> WEBSITES:
>>>> Bio-Ontologies SIG workshop: http://bio-ontologies.org.uk
>>>> ISMB & ECCB main conference website http://www.iscb.org/ismbeccb2007
>>>>
>>>> ABOUT THE BIO-ONTOLOGIES SIG WORKSHOP
>>>> The workshop will continue offer an informal environment for
>>>> presentation and discussion of ontologies and their role in
>>>> providing a mechanism for organising, sharing and reconciling data.
>>>> This year, to celebrate its tenth anniversary, we have invited four
>>>> presenters from the first bio-ontologies tutorial and meeting
>>>> organisers to sit on a panel, namely: Mark Musen, Peter Karp, Russ
>>>> Altman and Steffen Schulze-Kremer
>>>>
>>>> They will be asked to present positions on the following questions:
>>>> 1. What has been the best thing to have happened in bio-ontologies
>>>> in the past ten years?
>>>> 2. What has been the worst thing to have happened in bio-ontologies
>>>> in the past ten years?
>>>> 3. How must bio-ontologies progress in the next ten years?
>>>> 4. How must bio-ontologies not progress in the next ten years
>>>>
>>>> CALL FOR PAPERS AND POSTER ABSTRACT:
>>>> We are inviting two types of submissions SHORT PAPER papers (up to
>>>> 4 pages) and POSTER ABSTRACT (up to 1/2 page) from any aspect doing
>>>> bio-ontology research or using bio-ontologies to do bioinformatics
>>>> research. Topics include, but are not restricted to:
>>>> - Biological Applications of Ontologies
>>>> - Reports on Newly Developed or Existing Bio-Ontologies
>>>> - Tools for Developing Ontologies
>>>> - Use of Ontologies in Data Communication Standards
>>>> - Use of Semantic Web technologies in Bioinformatics
>>>> - The implications of Bio-Ontologies or the Semantic Web for the
>>>> drug discovery process
>>>> - Current Research In Ontology Languages and its implication for
>>>> Bio-Ontologies
>>>>
>>>> PROGRAM COMMITTEE
>>>> Abstracts will be reviewed by the Program Committee, including the
>>>> Program Chairs and additionally: David Benton, Suzanna Lewis, Chris
>>>> Mungall and Alan Ruttenberg.
>>>>
>>>> PUBLICATION OF THE PROCEEDINGS
>>>> The Programme Committee will also select those papers, which are
>>>> suitable for further publication in a BMC Bioinformatics
>>>> Supplement. Authors will be invited to resubmit full papers.
>>>>
>>>> DEADLINES
>>>> Submissions due: May 1st 2007
>>>> Notification of acceptance: May 21st 2007
>>>> Final versions due: May 31st 2007
>>>> Workshop: July 20th 2007
>>>>
>>>> -- Susanna-Assunta Sansone, PhD NET Project - Coordinator
>>>> www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project> The
>>>> European Bioinformatics Institute
>>>> email: sansone@ebi.ac.uk <mailto:sansone@ebi.ac.uk> EMBL Outstation
>>>> - Hinxton direct: +44 (0)
>>>> 1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
>>>> Cambridge CB10 1SD, UK room: A229
>>>> ----------------------------------------------------------------------
>>>> ---
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>>>
>>>
>>>
>>>
>>
>> -- 
>> "Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ...
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>>
>>
>>
>
>
>
> Bill Bug
> Senior Research Analyst/Ontological Engineer
>
> Laboratory for Bioimaging  & Anatomical Informatics
> www.neuroterrain.org
> Department of Neurobiology & Anatomy
> Drexel University College of Medicine
> 2900 Queen Lane
> Philadelphia, PA    19129
> 215 991 8430 (ph)
> 610 457 0443 (mobile)
> 215 843 9367 (fax)
>
>
> Please Note: I now have a new email - William.Bug@DrexelMed.edu
> <mailto:William.Bug@DrexelMed.edu>
>
>
>
>
Received on Thursday, 3 May 2007 17:32:44 UTC

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