[MOBY-dev] Moby API/LSID (Was: dashboard)

[Mark Wilkinson]

Martin Senger wrote:

> Well, as usual, I am confused :-) What discussion? And what website?
>   No, I am not making jokes now, I do not remember any discussion how to
>use LSIDs in Biomoby. At least no recently. Anyway, here are the remarsks
>I have promise to send:
>  
>
I pointed you to this a couple of weeks ago and asked for your comments 
(or at least, I think I did... maybe not to you directly, but to the 
-dev list):

http://biomoby.open-bio.org/index.php/for-developers/moby_extensions


>   2) The contents of the RDF document returned when a provider registered
>a service is part of the API mentioned above, but it is not documented (at
>least I have not seen any documentation). In theory, providers do not
>"need to know" the contents, they just get it from the registry and put it
>somewhere as a token for the RDF agent. But in practice, it was
>recommended to use it to enhance information about your services. In order
>to do that a provider needs to know the predicate names (and what they
>mean) that are there always and that may be there. Such discussion about
>predicate names started (at least I and Eddie discussed it in Malaga, and
>people briefly discussed it already in Vancouver) but it was never
>"officially" approved and made part of the Biomoby well-defined behaviour.
>  
>
The predicates have only recently been defined  for Service Instances 
since we have just finished working with myGrid to merge our data 
models.  They've been defined for longer for the ontologies, but there 
have been no comments one way or the other on whether or not people like 
the RDF structure for the ontologies.

In any case, I've listed all of the predicates on the new website, and 
am starting to document them now... slowly!  Some of them I cannot 
document since they are in the mygrid namespace, and they aren't 
documented there (though I could guess).  They are, however, all defined 
in a machine-readable way within their respective namespaces.  The MOBY 
ones can be resolved to additional explanatory RDF if you resolve the 
predicate's namespace.  I think the mygrid namespace does not currently 
resolve, but you can get it from some other URL (which escapes me at the 
moment).



>   * LSID API has methods getData and getMetadata. Any of them can return
>an empty result. What would be recommended for us: an empty getData() or
>not? For some entities it would be quite good to get something from
>getData()...
>  
>
I note this behaviour as being undefined on the website.  It may or may 
not return something, since we are experimenting with what kinds of 
things are best to return, but it is explicitly stated on the website 
that you should not rely on what is returned until the behaviour is defined


>   * Resolving LSID metadata has more steps than just to make an HTTP
>connection and to get an RDF file. But I guess that we want to
>recommend to use just this step. So we are slightly "abusing" (in a
>possitive way) the LSID spec, but we do not document it.
>  
>
Can you write a sentence that explains this?  I don't really understand 
what you mean either...


>   * LSID metadata must have well defined predicates (at least some) -
>this is the same problem as described in paragraph ad 2).
>  
>
this is done at least in part, but the definitions are not well written yet.

The more comments the better, since it would be nice to get this 
documented in a robust way!

M