Re: SfN meeting submission

Hi Don, Kei, John, Matthias, et al.,

Kudos to us all.  I realize what a crunch folks preparing for next  
week's demo are under, but this is an important aspect of amortizing  
the FANTASTIC EFFORT so many have invested in this.

I'd suggest a Google Doc, Don.  It's really the easiest way to go by  
far.  Anything else - passing around a Word file or culling/ 
integrating copy from a Wiki are much more labor intensive.  I've  
been using Google Docs more and more since we did the work last Nov/ 
Dec. on the earlier HCLS manuscript, and it's definitely been  
greasing the wheels on these sorts of far reaching, collaborative  
manuscripts.  I'd be glad to set it up - or help you set it up - if  
you like.  I've done this for several recent manuscripts, so I've got  
the "gotchas" pretty well worked out.

Re: the content - remember - for the abstract - it's just text and  
very little of that.  I'd recommend the goal should be to take  
whatever we already have describing the demo and re-tool that for a  
neuroscientist/neuroinformaticist audience.

Matthias had an excellent suggestion for a figure - which will be  
just what we want for the result poster, but that won't be needed  
until late October.  By then, if there's sufficient data, we'll be  
able to use the FANTASTIC tool Alan R. had recommended - Vizster  
(http://jheer.org/vizster/) - to create a very impressive  
visualization for the poster!
Just my unsolicited $0.02 - as always.

Cheers,
Bill

On May 4, 2007, at 10:23 AM, Kei Cheung wrote:

> Hi John, Don, Matthias, Bill, Mark , et al.,
>
> It sounds like the group has an increasing interest, enthusiasm,  
> commitment, and support to submit an abstract to SfN. If there is  
> no objection, let's go for it.
>
> Don, thanks for taking the lead on this. Is the deadline May 15?  
> Some people will be away next week for WWW2007. You might want to  
> consider creating a wiki page so that people who have been involved  
> in the demo (use case, data conversion, coordination ...) can  
> participate (just my personal suggestion). Please let me know what  
> I can do to help. I'll try to see if I can go to SfN this year as  
> the SenseLab group was invited to give a demo at the INCF booth  
> (International Neuroinformatics Coordinating Facility). I'll try to  
> talk to Gordon to see if we can include a semantic web related demo  
> there ...
>
> Best,
>
> -Kei
>
> jbarkley@nist.gov wrote:
>> hi don,
>>
>> Works for me as well, and I'll be glad to help anyway I can.
>>
>> thanks,
>>
>> jb
>>
>>
>> Date:  Thu, 3 May 2007 17:00:09 -0400 From:  William Bug  
>> <William.Bug@DrexelMed.edu> To:  public-semweb-lifesci hcls  
>> <public-semweb-lifesci@w3.org> Subject:  Re: SfN meeting  
>> submission Quoting William Bug <William.Bug@DrexelMed.edu>:
>>
>>
>>> Hi Don,
>>>
>>> This works for me.
>>>
>>> In regards to the suggestion Mark made, I think some of his   
>>> suggestions sound very practical.  I'd be glad to participate -  
>>> or  not - depending on the need and intended outcome.
>>>
>>> With this in mind, if you'd like someone to vet what you work up  
>>> - or  work with you on it, Don - I'd be glad to do that.
>>>
>>> Cheers,
>>> Bill
>>>
>>> On May 3, 2007, at 1:06 PM, Donald Doherty wrote:
>>>
>>>
>>>> Here's my proposal:
>>>>
>>>> I write a quick rough draft and send a copy to all interested  
>>>> parties.
>>>> People actually contributing to the writing should mostly be   
>>>> neuroscientists
>>>> but of course include input from the rest.
>>>>
>>>> Then I'll take all of the input and work up a revised abstract  
>>>> and  send it
>>>> back out to all interested parties for further feedback.
>>>>
>>>> Repeat until everyone is happy and/or we run out of time. Then  
>>>> we  decide to
>>>> submit or not.
>>>>
>>>> About authors, here is the Neuroscience community standard.  
>>>> First  author is
>>>> usually the graduate student and last author is usually the  
>>>> principal
>>>> investigator.
>>>>
>>>> Submitter must be first author...so if I take this on everyone  
>>>> must be
>>>> comfortable with me being the grad student :^). We should  
>>>> probably  put the
>>>> person who put the most sweat into the demo as last author.
>>>>
>>>> Hopefully the author issue won't be too divisive since this is   
>>>> simply an
>>>> abstract. The important thing is that everyone is acknowledged.
>>>>
>>>> Of highest importance is that the demo gets in front of the   
>>>> neuroscience
>>>> community at their biggest meeting.
>>>>
>>>> What do you think?
>>>>
>>>> Don
>>>>
>>>> -----Original Message-----
>>>> From: public-semweb-lifesci-request@w3.org
>>>> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Kei  
>>>> Cheung
>>>> Sent: Thursday, May 03, 2007 12:19 PM
>>>> To: William Bug
>>>> Cc: public-semweb-lifesci hcls
>>>> Subject: Re: SfN meeting submission
>>>>
>>>>
>>>> Hi Bill et al.,
>>>>
>>>> I agree that it's important to make our SW/Neuro demo visible to  
>>>> the
>>>> neuroscience community. For example, I have asked Gordon  
>>>> Shepherd  (PI of
>>>> SenseLab) to look at the AD use case written by June, Gwen, et  
>>>> al  to see
>>>> if any comments/suggestions can be made. It would be great if  
>>>> we  can get
>>>> more neuroscientists involved to help make our work more   
>>>> scientifically
>>>> relevant. I believe this would also help make SW  
>>>> technologically  credible.
>>>>
>>>> Regarding the SfN abstract, my concern is that we might not be  
>>>> able to
>>>> meet the deadline given that people are currently busy  
>>>> preparing  for the
>>>> upcoming demo at WWW2007 next week. In addition to what to  
>>>> write  and how
>>>> to write it (it probably won't take long for an abstract),  we  
>>>> need to
>>>> discuss how the author list should appear. All these may take  
>>>> some  time
>>>> to resolve as part of the community process, but we'd better start
>>>> thinking/discussing about it soon ...
>>>>
>>>> Cheers,
>>>>
>>>> -Kei
>>>>
>>>> William Bug wrote:
>>>>
>>>>> Hi Don, Matthias, John, Kei, et al.,
>>>>>
>>>>> I too would like to contribute to an SfN abstract in this context.
>>>>>
>>>>> I believe given the domain HCLS IG is covering - neurodegenerative
>>>>> disease - despite the lack of a full, refereed article, this is  
>>>>> a  very
>>>>> important venue in which to present, in order to help bolster the
>>>>> relevance and credibility of this effort to the general  
>>>>> neuroscience
>>>>> community.  With a working demo, it would be a shame NOT to  
>>>>> have it
>>>>> represented at the SfN meeting.
>>>>>
>>>>> We could also look to use such an abstract as starting material  
>>>>> for a
>>>>> full submission to journals that cover neuroinformatics such as
>>>>> Neuroinformatics, PLoS Computational Biology, or Journal of
>>>>> Computational Neuroscience.
>>>>>
>>>>> In regards to relevant neuroscience meetings, there are also the
>>>>> meetings hosted by:
>>>>> Federation of European Neuroscience Societies (FENS):
>>>>> http://fens.mdc-berlin.de/calendar/
>>>>>
>>>>>
>>>>> International Brain Research Organization (IBRO):
>>>>> http://www.ibro.org/Pub_Events_Search.asp?Search=.
>>>>>
>>>>> The Japan Neuroscience Society
>>>>> http://www.jnss.org/english/index_e.html
>>>>> http://www2.convention.jp/neuro2007/
>>>>>
>>>>> Federation of Asian and Oceanian Neuroscience Societies (FAONS)
>>>>> http://www.faons.org/
>>>>>
>>>>> I'm not certain what the deadlines are for the associated  
>>>>> meetings.
>>>>>
>>>>> Cheers,
>>>>> Bill
>>>>>
>>>>> On May 2, 2007, at 11:51 AM, Donald Doherty wrote:
>>>>>
>>>>>
>>>>>> Hi Matthias,
>>>>>>
>>>>>> That'd be great! SfN abstracts are brief (max. 2300  
>>>>>> characters  including
>>>>>> punctuation!) so focusing on the value to neuroscientists  
>>>>>> sounds  like the
>>>>>> right course.
>>>>>>
>>>>>> Abstract may be presented or posters. Slide presentations are   
>>>>>> kept very
>>>>>> brief and there is so much going on most people won't see a
>>>>>> particular slide
>>>>>> presentation. Even if we indicate our preference for a slide   
>>>>>> presentation
>>>>>> it's likely we wouldn't get it.
>>>>>>
>>>>>> If we do a poster it will be up half a day. We can bring our  
>>>>>> demo  machine
>>>>>> and set it up next to the poster. (I've seen BIRN and others  
>>>>>> do  this.
>>>>>> Wireless is generally available.) I think this is the  
>>>>>> preferred mode
>>>>>> for us.
>>>>>>
>>>>>> There is also a $75 submission fee.
>>>>>>
>>>>>> I'm willing to take responsibility for paying the submission  
>>>>>> fee,  getting
>>>>>> the poster up, staying there while it's up, and working the  
>>>>>> demo as
>>>>>> long as
>>>>>> everyone is interested in doing this and a demo machine will be
>>>>>> available.
>>>>>>
>>>>>> We won't get a paper out of it but I think it's worthwhile to   
>>>>>> expose the
>>>>>> end-user community (neuroscientists) to the value the Semantic  
>>>>>> Web
>>>>>> technologies may provide to them.
>>>>>>
>>>>>> Best wishes,
>>>>>> Don
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: public-semweb-lifesci-request@w3.org
>>>>>> <mailto:public-semweb-lifesci-request@w3.org>
>>>>>> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of
>>>>>> samwald@gmx.at <mailto:samwald@gmx.at>
>>>>>> Sent: Wednesday, May 02, 2007 9:37 AM
>>>>>> To: donald.doherty@brainstage.com
>>>>>> <mailto:donald.doherty@brainstage.com>; public-semweb- 
>>>>>> lifesci@w3.org
>>>>>> <mailto:public-semweb-lifesci@w3.org>
>>>>>> Subject: SfN meeting submission
>>>>>>
>>>>>>
>>>>>> Hi Don,
>>>>>>
>>>>>> I would help with the abstract for SfN where I can, of course.  
>>>>>> I  guess it
>>>>>> should be even more focussed on the requirements and use cases in
>>>>>> Neuroscience than the BMC Bioinformatics paper. Mainly a  
>>>>>> description
>>>>>> of the
>>>>>> collaborating neuroscience groups, their motivation and the  
>>>>>> types of
>>>>>> information that we are integrating, and less about the technical
>>>>>> details.
>>>>>>
>>>>>> I guess it is much too late to start writing a group paper  
>>>>>> for  the ISMB
>>>>>> workshop now. A poster abstract would be possible, but I think we
>>>>>> don't want
>>>>>> to present a poster.
>>>>>>
>>>>>> cheers,
>>>>>> Matthias
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> This year's Society for Neuroscience meeting abstracts are  
>>>>>>> due  May 15th.
>>>>>>> I'd
>>>>>>> like to take the lead on submitting an abstract if the team is
>>>>>>> interested.
>>>>>>>
>>>>>>> Don
>>>>>>>
>>>>>>> P.S. This year's meeting is November 3-7 in San Diego,  
>>>>>>> California.
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: public-semweb-lifesci-request@w3.org
>>>>>>> <mailto:public-semweb-lifesci-request@w3.org>
>>>>>>> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Alan
>>>>>>> Ruttenberg
>>>>>>> Sent: Tuesday, May 01, 2007 12:57 AM
>>>>>>> To: public-semweb-lifesci@w3.org <mailto:public-semweb-  
>>>>>>> lifesci@w3.org>
>>>>>>> Subject: ISMB Bio-Ontologies Meeting
>>>>>>>
>>>>>>>
>>>>>>> I forget, was someone submitting an abstract about our work  
>>>>>>> to this
>>>>>>> workshop?
>>>>>>> -Alan
>>>>>>>
>>>>>>>
>>>>>>> On Apr 26, 2007, at 1:18 PM, Susanna wrote:
>>>>>>>
>>>>>>>
>>>>>>>> ** Apologies for cross posting **CALL FOR PAPERS and POSTER
>>>>>>>> ABSTRACTS (Deadline May 1st)
>>>>>>>> Proceedings in BMC Bioinformatics
>>>>>>>>
>>>>>>>> *^**^***^****^****^****^****^****^****^****^****^****^*****^**^ 
>>>>>>>> *** ^**
>>>>>>>> Bio-Ontologies SIG Workshop
>>>>>>>> Vienna, Austria: July 20 2007
>>>>>>>>
>>>>>>>> "Bio-Ontologies: ten years past and looking to the future"
>>>>>>>>
>>>>>>>> *^**^***^****^****^****^****^****^****^****^****^****^*****^**^ 
>>>>>>>> *** ^**
>>>>>>>> 15th ISMB & 6th ECCB Vienna, Austria: July 18-25, 2007
>>>>>>>>
>>>>>>>>
>>>>>>>> CALL FOR PAPERS and POSTER ABSTRACTS (Deadline May 1st)
>>>>>>>> Proceedings in BMC Bioinformatics
>>>>>>>>
>>>>>>>> The long-standing ISMB Bio-Ontologies SIG is in its tenth
>>>>>>>> consecutive year. This year the workshop will have a  
>>>>>>>> celebratory
>>>>>>>> and reflective discussion on "Bio-Ontologies: ten years past  
>>>>>>>> and
>>>>>>>> looking to the future".
>>>>>>>>
>>>>>>>> PROGRAM CHAIRS:
>>>>>>>> Robert Stevens (1), Phillip Lord (2), Robin McEntire (3),  
>>>>>>>> Susanna-
>>>>>>>> A. Sansone (4)
>>>>>>>> 1.    School of Computer Science, University of Manchester, UK
>>>>>>>> 2.    School of Computing Science, University of Newcastle, UK
>>>>>>>> 3.    GlaxoSmithKline, USA
>>>>>>>> 4.    EMBL-EBI The European Bioinformatics Institute,   
>>>>>>>> Cambridge, UK
>>>>>>>>
>>>>>>>> WEBSITES:
>>>>>>>> Bio-Ontologies SIG workshop: http://bio-ontologies.org.uk
>>>>>>>> ISMB & ECCB main conference website http://www.iscb.org/  
>>>>>>>> ismbeccb2007
>>>>>>>>
>>>>>>>> ABOUT THE BIO-ONTOLOGIES SIG WORKSHOP
>>>>>>>> The workshop will continue offer an informal environment for
>>>>>>>> presentation and discussion of ontologies and their role in
>>>>>>>> providing a mechanism for organising, sharing and  
>>>>>>>> reconciling  data.
>>>>>>>> This year, to celebrate its tenth anniversary, we have  
>>>>>>>> invited  four
>>>>>>>> presenters from the first bio-ontologies tutorial and meeting
>>>>>>>> organisers to sit on a panel, namely: Mark Musen, Peter  
>>>>>>>> Karp, Russ
>>>>>>>> Altman and Steffen Schulze-Kremer
>>>>>>>>
>>>>>>>> They will be asked to present positions on the following   
>>>>>>>> questions:
>>>>>>>> 1. What has been the best thing to have happened in bio- 
>>>>>>>> ontologies
>>>>>>>> in the past ten years?
>>>>>>>> 2. What has been the worst thing to have happened in bio-  
>>>>>>>> ontologies
>>>>>>>> in the past ten years?
>>>>>>>> 3. How must bio-ontologies progress in the next ten years?
>>>>>>>> 4. How must bio-ontologies not progress in the next ten years
>>>>>>>>
>>>>>>>> CALL FOR PAPERS AND POSTER ABSTRACT:
>>>>>>>> We are inviting two types of submissions SHORT PAPER papers  
>>>>>>>> (up to
>>>>>>>> 4 pages) and POSTER ABSTRACT (up to 1/2 page) from any  
>>>>>>>> aspect  doing
>>>>>>>> bio-ontology research or using bio-ontologies to do  
>>>>>>>> bioinformatics
>>>>>>>> research. Topics include, but are not restricted to:
>>>>>>>> - Biological Applications of Ontologies
>>>>>>>> - Reports on Newly Developed or Existing Bio-Ontologies
>>>>>>>> - Tools for Developing Ontologies
>>>>>>>> - Use of Ontologies in Data Communication Standards
>>>>>>>> - Use of Semantic Web technologies in Bioinformatics
>>>>>>>> - The implications of Bio-Ontologies or the Semantic Web for  
>>>>>>>> the
>>>>>>>> drug discovery process
>>>>>>>> - Current Research In Ontology Languages and its implication  
>>>>>>>> for
>>>>>>>> Bio-Ontologies
>>>>>>>>
>>>>>>>> PROGRAM COMMITTEE
>>>>>>>> Abstracts will be reviewed by the Program Committee,  
>>>>>>>> including the
>>>>>>>> Program Chairs and additionally: David Benton, Suzanna  
>>>>>>>> Lewis,  Chris
>>>>>>>> Mungall and Alan Ruttenberg.
>>>>>>>>
>>>>>>>> PUBLICATION OF THE PROCEEDINGS
>>>>>>>> The Programme Committee will also select those papers, which  
>>>>>>>> are
>>>>>>>> suitable for further publication in a BMC Bioinformatics
>>>>>>>> Supplement. Authors will be invited to resubmit full papers.
>>>>>>>>
>>>>>>>> DEADLINES
>>>>>>>> Submissions due: May 1st 2007
>>>>>>>> Notification of acceptance: May 21st 2007
>>>>>>>> Final versions due: May 31st 2007
>>>>>>>> Workshop: July 20th 2007
>>>>>>>>
>>>>>>>> -- Susanna-Assunta Sansone, PhD NET Project - Coordinator  
>>>>>>>> www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project>  
>>>>>>>> The
>>>>>>>> European Bioinformatics Institute
>>>>>>>> email: sansone@ebi.ac.uk <mailto:sansone@ebi.ac.uk> EMBL   
>>>>>>>> Outstation
>>>>>>>> - Hinxton direct: +44 (0)
>>>>>>>> 1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223  
>>>>>>>> 494 468
>>>>>>>> Cambridge CB10 1SD, UK room: A229
>>>>>>>> --------------------------------------------------------------- 
>>>>>>>> --- ----
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> -- 
>>>>>> "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.Bug@DrexelMed.edu
>>>>> <mailto:William.Bug@DrexelMed.edu>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>> Bill Bug
>>> Senior Research Analyst/Ontological Engineer
>>>
>>> Laboratory for Bioimaging  & Anatomical Informatics
>>> www.neuroterrain.org
>>> Department of Neurobiology & Anatomy
>>> Drexel University College of Medicine
>>> 2900 Queen Lane
>>> Philadelphia, PA    19129
>>> 215 991 8430 (ph)
>>> 610 457 0443 (mobile)
>>> 215 843 9367 (fax)
>>>
>>>
>>> Please Note: I now have a new email - William.Bug@DrexelMed.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>
>

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