[MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068

Thu Dec 6 18:42:08 UTC 2007

Hi Mark et al.,

On 5-dec-2007, at 18:36, Mark Wilkinson wrote:

> Here is the (very rapid!) review from Briefings in Bioinformatics.
>
> LOL!  Well, the reviewers couldn't differ more in their desires for  
> the
> manuscript!!  It's almost as if we should write TWO manuscipts...  
> one for
> each audience.

"The editor leaves it to the author to decide how to deal with these  
different emphases."

Hmmm that sounds like what I sometimes do when I'm making a new tool  
and don't know how to solve a problem: make it a user configurable  
parameter and sell my lack of inspiration as a feature as in "it's  
completely customisable" :).

Anyway, in the end it's the editors who decide what they want in  
their magazine, so in my opinion it's the editor who should tell us  
what he/she wants in BIB. We could adjust according to reviewer one  
or two or split up into two articles and adjust according to both,  
but it would be a shame if we adjust to reviewer 1 and then in the  
end BIB tells us they rejected the manuscript, because they were  
looking for something like suggested by reviewer two. Maybe we should  
just explicitly ask the editor to tell us what they want...

My 0.02 €

Pi

> Actually, I did suggest this on-list a few weeks ago, but
> nobody was brave enough to take me up on the suggestion...  are  
> there any
> takers now?
>
> Comments are welcome.  I'm leaving for Moby meetings/talks in Koln,
> Wageningen, and Amsterdam tomorrow so I am away for the next 10  
> days.  I
> should still have time to do some editing if anyone has suggestions.

> Best wishes!
>
> Mark
>
>
>
>
> ------- Forwarded message -------
> From: briefings at oxfordjournals.org
> To: markw at illuminae.com
> Cc:
> Subject: Briefings in Bioinformatics - Decision on BIB-07-0068
> Date: Tue, 04 Dec 2007 08:04:55 -0800
>
> 04-Dec-2007
>
> Dear Dr Wilkinson,
>
> I am writing to inform you that your manuscript entitled  
> 'Interoperability
> with Moby 1.0 - It’s Better than Sharing Your  
> Toothbrush!' (BIB-07-0068)
> has now been peer-reviewed.  The comments of the reviewers follow  
> at the
> end of this email.
>
> We should like to invite you to respond to the comments of the  
> reviewers
> and revise your manuscript according to their suggestions.
>
> To revise your manuscript, log into http://mc.manuscriptcentral.com/ 
> bib
> and enter your Author Center, where you will find your manuscript  
> listed
> under "Manuscripts with Decisions."  Under "Actions," click on  
> "Create a
> Revision."
>
> When creating your revision, you will be asked to provide a  
> response to
> the reviewers' comments, point-by-point.  Where possible, please  
> provide
> this response in the text box provided, rather than uploading your
> response as a document.  Please ensure that any changes made to your
> manuscript are highlighted in colour, bold or underlining.  By  
> doing this,
> you will help us to minimise the time needed to provide you with a
> decision.
>
> IMPORTANT:  Your original files are available to you when you  
> upload your
> revised manuscript.  Please delete any redundant files before  
> completing
> the submission.
>
> Because we are trying to facilitate timely publication of manuscripts
> submitted to Briefings in Bioinformatics, we request that you  
> submit your
> revised manuscript within the next four weeks.
>
> Once again, thank you for submitting your manuscript to Briefings in
> Bioinformatics and I look forward to receiving your revised paper  
> in due
> course.
>
> Yours sincerely,
>
>
>
> Sophie Gilmour
> On behalf of Dr Martin Bishop,
> Editor-in-Chief, Briefings in Bioinformatics
>
> Reviewers' Comments to Author:
> Reviewer: 1
> Comments to the Author
> This manuscript presents BioMoby, a mature framework for data  
> integration
> and interoperability between web services. BioMoby has been  
> developed over
> the last 5 years by a world wide community. These developments have  
> now
> reached an important point: the stable version 1.0 of BioMoby is being
> presented here. This manuscript gives a description of how the  
> framework
> is organized technically, compares it to peer semantic and schema
> technologies and presents a use case how a “Biologist” can use it to
> execute an analysis workflow.
>
> For a reader with technical background the paper is well written  
> and gives
> a good overview   of the framework. At the same time this issue is  
> also
> our largest concern with this manuscript. Overall it feels rather
> technical and it seems to be addressing primarily bioinformatics
> developers. This manuscript has been submitted to Briefings in
> Bioinformatics which has a more user oriented target group. It  
> would be
> nice to introduce BioMoby particularly to those end users, but we feel
> that the focus of this manuscript needs an adjustment for this.
>
> The example of pages 4 and 5 of the actual workflow of an analysis is
> interesting to read and demonstrates the power of BioMoby well. We  
> suggest
> to support this with screenshots of how the user can actually  
> perform the
> steps of this analysis. The comparison with other semantic web  
> standards
> is fine for a technical audience, but in this case it might be  
> going too
> much into detail.
>
> Reviewer: 2
> Comments to the Author
> I believe it could be improved with additional discussion and  
> assessment
> of the differences between its approach and W3C Semantic Web.
>
> As the author states, BioMoby developed independently from the W3C
> semantic web specifications yet is addressing at least in part,  
> some of
> the same use-cases in bioinformatics. Granted this is more from a  
> service
> perspective than a knowledge-model perspective. Nonetheless, the  
> rather
> "independent" evolution of these two approaches, particularly in  
> light of
> the more productionized current state of BioMoby, suggests a more
> extensive comparison of the two paths of development.
>
> I would like to see such an expanded discussion in the paper - even  
> a few
> more paragraphs.
>
> Editor's Comments to Author:
> Editor: 1
> Comments to the Author:
> The referees differ somewhat in the balance expected.
> It is true that Briefings is orientated to Biological users.
> However, it is also read by Bioinformatics developers.
> The editor leaves it to the author to decide how to deal with these
> different emphases.
>
>
>
> -- 
> --
> Mark Wilkinson
> Assistant Professor, Dept. Medical Genetics
> University of British Columbia
> PI Bioinformatics
> iCAPTURE Centre, St. Paul's Hospital
> Tel:  604 682 2344 x62129
> Fax:  604 806 9274
>
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