[MOBY-dev] The winds of change are a-blowin'!

[Mark Wilkinson]

Hi everyone, 

I want to give you a heads-up that there are going to be some *enormous*
changes to BioMOBY over the next 60-120 days.  I can't forsee them all,
but I can certainly see some of the most obvious ones:

1)  As we leave the early-prototype "proof of concept" stage of the
project, MOBY is going to stop using infantile XML and start using
properly namespaced and formatted XML.  I will update and re-register
all objects that are in the database when I make this change, but you
might need to modify your services if you have been hard-coding your XML
parsers to find particular tags, as the tags will now have the prefix
"moby:" or something to that effect.

1a)  Query/Response structure is going to change - as I have thought
about it over the past week or two, I realize that the correct (??)
solution is quite similar to what Lukas proposed last week, but with a
few extra tags to hold metadata (provision metadata should be associated
with each individual response object, rather than the response itself,
since a service provider might be using different methodologies to
achieve the transformation of one input object versus another...). 
Unfortunately, your services *will* have to be modified to deal with
these new structures, as we have not build enough code wrappers yet to
insulate you from these kinds of changes.  Hopefully that code will be
built soon so that future changes don't throw you into despair.

2) MOBY is going to adopt the I3C's LSID as a ~replacement of the MOBY
Triple.  The 'Triple' will likely become the "Duple"; LSID's contain
both namespace and ID, so they replace two of the attributes of the
Triple.  We will, however, maintain our Instantiation tag, so the
"Duple" will still act like the "Triple".  There may be other changes as
we determine the value of (and methodology for) working with the I3C's
LSID resolver.  Stay tuned boys and girls!

3)  Brian Gilman and I are going to put our minds toward building a more
reliable object/WSDL construction engine in MOBY-Central.  Given the
modular/heritable nature of MOBY Objects, it should be possible for MOBY
Central to use the Object ontology to figure out the structure of
complex objects from their component parts and build them on the fly. 
At the moment, when you register a complex object, you must register the
full XSD for that object.  Thus, if we change the object structure, the
structure of your subcomponents may go out of sync with the valid
structure of that subcomponent 'standalone'  (any questions in the
back?).  In the future you will simply register complex objects by
reference to their component parts.  This will simplify registration of
complex objects, and ensure that the structure of complex objects
evolves in hand with the simple objects.  Brian is also hoping to make
the BioMOBY registry the primary data discovery system for OmniGene and
a new gene expression array software package called GenePattern, so the
breadth of object types that MOBY handles will be expanding rapidly in
this direction! 

4)  I am meeting with the myGrid group sometime late March/early April
to talk about their ontology registry engine (among other things).  This
may lead to a significant change in the way the ontology component of
MOBY Central works.  What that will look like, I can't say at the moment
- I hope to be able to make changes on this level without significantly
affecting the way services/clients interact with MOBY Central today... I
hope...


Anyway, that's a birds-eye view of the most concrete upcoming changes. 
Hopefully much of this can be done "behind the scenes" so that your
services are not disastrously affected, but certainly it can't *all* be
done transparently, so... Sorry for the dust!

I hope you are all enjoying the ride ;-)

Mark


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