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

[Mark Wilkinson]

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.  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.

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and enter your Author Center, where you will find your manuscript listed  
under "Manuscripts with Decisions."  Under "Actions," click on "Create a  
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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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