[MOBY-dev] MOBY II (Was: fixes in Moses)

[Andrew D. Farmer]

Hey all-

> > I am *so* looking forward to 'Moby II' where we model things in RDF rather  
> > than XML
> >
>    To be honest I am rather affraid of that. We all invested time and
> efforts into making biomoby working. If we are going to change all API and
> the way how it works we will need to invest gain. Change is not bad, but
> must be discussed and must have a merit, not just that RDF is more
> fancy. I hope that we are still on the same board...
> 

I am glad to hear Mark's enthusiasm for the future use of RDF in MOBY, as well
as sympathetic to Martin's concerns (which perhaps Mark's subsequent message
has helped to allay). 

Along those lines, as some of you already know, a few of us at NCGR and a
collaborating group (CCGB) from the University of Minnesota recently released 
the first prototype of a RDF-based service discovery/invocation system, using
the basic semantic MOBY approach. You can check it out at:

http://lin.ncgr.org

Do be aware that it is definitely a prototype and it is far too easy at the
moment to invoke services with unreasonable amounts of data; also, it is a bit 
underdocumented at the moment, though we have put a few sets of
slides off the Help link that may help explain; anyway it is pretty intuitive 
and should not be a quantum leap for the MOBY crowd ;)
<even more self-serving plug>
It also makes some rough inroads in realizing my old dream of getting 
ISYS back into the picture...
</even more self-serving plug>

We'll be evolving it (we've only scratched the surface!) as funding and 
involvement in the VPIN project permit, but we have a few lessons learned
at this point some of which are a bit relevant to this discussion (which I 
hope is an omen of blessed days when the two MOBYs are as one ;) ) One of
these brings me back from "publicity mode" to Martin's concerns:

>From what I understand of MOBY services, it seems 
that it ought to be entirely possible to use RDF as the data 
modelling and ontology development substrate without much impacting the
messaging aspect of MOBY services and hence presumably allowing the S-MOBY 
"API" to remain relatively intact (at least, those parts that don't have
to do with the interpretation of the "payload" data, although I am sure 
those are the most important parts!);
this step would seem to be a logical one to allow the two branches of MOBY
to converge on ideas for shared representation of data even if we cannot come to
agreement about the right formalisms for messaging. I am personally
not at all convinced that RDF is the right approach for the messaging layer,
but certainly trying to be open-minded about it and other ideas.

In any case, I am a bit ignorant as to whether any real discussions have
been taking place as to the path to "MOBY II", but remain hopeful that they
will take place "real soon now".

Regards to all, 
(and apologies for long-windedness and for the somewhat duplicative post
you'll receive off the semantic web life sciences mailing list thread
that has just mentioned BioMOBY- get your 2c in now!)

-- 

Andrew Farmer
adf at ncgr.org
(505) 995-4464
Database Administrator/Software Developer
National Center for Genome Resources

---
"To live in the presence of great truths and eternal laws,
to be led by permanent ideals-
that is what keeps a man patient when the world ignores him,
and calm and unspoiled when the world praises him."
-Balzac
---