[MOBY-dev] getting RDF from BioMoby

[Martin Senger]

Mark,
   Thanks for a fast reply.

> This part of the system (I wouldn't call it part of the API yet :-) ) is 
> not at all stable, but once people start using it I will be forced to 
> make some hard decisions and make it stable, so... let's keep working 
> through these issues :-)
>
   Well, I can start using it if I know that it will not disappear anytime 
:-) Catch-22. Anyway, I am willing to play with it (a ka 'use it') and 
later we will see...

> The code is pretty tightly connected to the main public registry, though 
> it could be made more generic if necessary.
>
   It's okay for now. Thanks for the clarification.

   But I have (two) more questions (with sub-questions): The main reason
for using these calls is that I can get "everything" in one go. So this is
useful for people creating things like 'moby browsers' because they
usually need the whole contents of the registry. Because of that I am
willing to dive into RDF if:

   a) it is the best way how to get "everything" (is it? are there better 
ways? DUMP probably is not the best way)

   b) is there really everything?
   I am new to RDF so I am probably wrong. But, for example, when I have
looked into returned RDF of Objects and found CommentedDNASequence object,
I found all its parents (not in one place, but I found them, even though I
do know why all parents are listed directly under CommentedDNASequence,
except Object that is listed separately under VirtualSequence) referred as
'subClassOf' but I could not find (it may be my mistake by reading the
RDF) that it HASA two strings (sequencestring and description) and an
integer (length). Are these HAS[A] relationship there?

   And the second question: Even though it seem quite obvious from reading 
RDF, it would be nice if you provide (even still unofficial) list how are 
the various attributes mapped into RDF predicates. For example, that 
'<contactMail>' becomes 'cd:creator', or that '<Input>' becomes 
'mobyPred:consumes'.

   Cheers,
   Martin

-- 
Martin Senger

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