[MOBY-dev] PLoS ONE Decision

[Mark Wilkinson]

There was a single reviewer, who decided that the manuscript required  
major revisions.  It's probably worthwhile discussing as a group what our  
response to the review will be.

Here is the review:

====================
The manuscript “Interoperability with Moby 1.0” deals in standardizing
methodologies to facilitate information exchange and access to analytical
resources. The manuscript provides the detailed development that has
occurred in BioMoby. The authors present and discuss why BioMoby is a
distinct from other semantic web services.

Major Compulsory Revisions (that author must respond to before decision
on publication is reached)

To Authors:

To begin with the paper is well written in terms of technical and
implementation aspects.

What I see is that author’s do not clearly present difference between the
earlier versions with the current version of BioMoby. It would be really
helpful if the authors could explain this using a concrete example to
understand the functioning of the BioMoby framework.

The paper looks more like a user manual with technical specification rather
than any scientific implication to the readers. The authors could improve  
the
paper by providing a strong biological input as motivation for developing
such a framework.

As I read through the paper I see the author’s speak about semantic web
services. It would be interesting for the readers to know what the other
semantic web services and how BioMoby is better. Is it possible for u to
demonstrate it with an example?

In the results section the author’s speak about Namespaces Ontology
wherein there are 300 different Namespaces that includes prominent public
data resources. It would be interesting to know weather BioMoby also
supports PSI MI, MAGE standards that are also coming in from prominent
databases.

In the Object Ontology the author’s specify BioMoby framework can
receive any data-type and it does not re-define the legacy of the data  
type.
Please provide a more concrete example for this point.
In BioMoby web services Second Paragraph the author’s say:
“The providers do not need to be concerned about the exact structure of
incoming data and do not need to query the ever- changing BioMoby
ontology”.

1. Justify this statement.

2. Summaries what are the BioMoby’s ontology’s that was present in the
earlier and in the current version.

3. How can you compare it with the other semantic web services ontology’s?

Justify how SOAP concept implemented in BioMoby is better than the
others service providers that could improve the interoperability of the
framework.

Through out the paper the author’s have introduced various terms as
ontology. It is quite misleading for me to associate these different  
ontology
under one roof of BioMoby.   [[does anyone understand what this comment  
means??]]

Finally, I feel that BioMoby is one of the most prominent approaches in the
bioinformatics community. The paper contains less scientific inputs and
more technical inputs. The paper does not contain strong examples to
validate various arguments.

Hence the paper cannot be accepted in the current form. If the author’s  
could
answer some of the question raised, that could make the paper more
interesting and more relevant to the PLoS ONE readers.

============================



-- 
--
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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