[MOBY-dev] PLoS ONE Decision

Wed Jul 4 19:16:08 UTC 2007

Hi,

On  03 Jul 2007, at 20:00, Mark Wilkinson wrote:

> There was a single reviewer,

Huh, a single reviewer? That doesn't sound very professional :(. I  
thought they called it PLoS *One* for different reasons :)

> 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's my € 0.02...

> 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.

Well this is officially the first version as in 1.0 isn't it?. This  
is a first "milestone" release, so there is not much to compare it  
with. Of course BioMOBY has been slowly evolving as a beta in several  
labs, but which CVS date should we compare against? Compared to  
version 0.0 every feature in BioMOBY is a new feature: so it's a  
major improvement :). Doesn't make much sense to me... If they insist  
on a comparison we might compare the current state of art with what  
was described in "BioMOBY: an open-source biological web services  
proposal" by Wilkinson, MD, Links, M. (2002). That's the oldest  
publication on BioMOBY a.f.a.i.k.

> 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?

If I understand the items above correctly, what the reviewer wants to  
see is basically a good example case, that clearly shows the  
advantages of BioMOBY and the differences between BioMOBY and other  
web service technology. When I read this I'm thinking of the graph on  
the front page: the one that says "Tired of this? ... Try This!".  
Maybe we can make such a comparison between the way too many  
Biologist in the lab have their work slowly flowing and the kind of  
workflow you can make with BioMOBY.

> 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.

Correct me if I'm wrong, but as far as I know we support any  
namespace: just register thing if it wasn't already. Maybe it is not  
clear enough though that BioMOBY allows you to support *any*  
namespace or kind of data format you like. Whether or not datatypes  
and/or namespaces for a certain standard have already been registered  
or not is not crucially important in my opinion, but if PLoS insists  
certain standards must be there to make BioMOBY interesting enough  
for their readers, I can easily create a small script that registers  
them... (Just hope they do not insist there are also services that  
actually use those objects and namespaces, because that will be a lot  
more work.)

> 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??]]

For me BioMOBY is a collection of several tools, frameworks/ 
libraries, concepts, a community and several ontologies. We have a  
namespace ontology, an object ontology and a service ontology.  
Although these are strongly related they do not share the same root.  
Maybe it's not clear to the reviewer what BioMOBY exactly is. To be  
honest it's not a bad question... According to "What is BioMOBY from  
the website BioMOBY:

"The MOBY-S system defines an ontology-based messaging standard  
through which a client will be able to automatically discover and  
interact with task-appropriate biological data and analytical service  
providers, without requiring manual manipulation of data formats as  
data flows from one provider to the next."

Hence it's a messaging standard. That does not include the  
ontologies, the libraries, etc. It's only the standard, so the part  
labelled on the website as "Latest MOBY Services API".

Maybe we should be more clear on what is all included when we talk  
about BioMOBY...  Not sure if this is what the reviewer was  
complaining about, but it's the best I can make from the comment...

> 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.

Cheers,

Pi

> ============================
>
>
>
> -- 
> --
> 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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