[moby] [MOBY-dev] Reserved word... perhaps unnecessary...

[Martin Senger]

Hi,
   Nice to hear from you.
   Yout email helps to clarify the issues. They are (at least for now) two
issues: rootedness (not mentioned in my neither Mark's emails) and
flatteness. Rootedness (or not rootnedness) can be addressed by choosing
pure XML message or RDF-based message. Flatteness is an issue only for
pure XML messages (RDF is not flatten by default).
   So we have (beter: would have) three ways how to pass Biomoby messages:

   1) Flatten traditional XML. This is the current situation in
Moby-S. Because of this flatteness, Mark finds problems with not knowning
the "primary contents" without traversing/contacting Biomoby registry.

   2) Hierarchical traditional XML. This creates more complex messages but
it is fully in the XML concepts. It carries all parental, ISA
relationships. This is what Moby-S does not use. And there is no strong
movement to this (except me advocating at least discussion about it).

   3) RDF-based message. This would, additionally to not being flat, so
keeping ISA hierarchy, add also non-rootedness. There is no discussion
whether to move Moby-S this direction. My guess is that if we move Moby-S
to any big changes regarding the message structure, it would probably be
better to jump here and skip the "hierarchical traditional XML" structure.

   One last comment regarding rootedness: If you interpres a message, you
always need to know when to start, so anyway you define a root node. This
is the same for RDBS: you need to know which table to start with. So the
rootedness is not about "not having a root" but about "having more roots
than just one". But that is very probably what you meant anyway.

> I might benefit from some clarification of your example. I can easily imagine
> a sensible case of a sequence with an annotation with a sequence 
>
   I can clarify further, but it seems to me that you got it already
right. Yes, your example is a better way to say what I was expressing. But
please let me know if I can clarify better.

> Have some more tea, I'm relieved that you haven't completely shut out those
> of us who can't help using the RDF-word...
>
   I am not against RDF. I am just against jumping to it without saying
why.

   Cheers,
   Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)