[MOBY-l] MOBY Duple? :-)

[Jason E. Stewart]

"Mark Wilkinson" <mwilkinson at gene.pbi.nrc.ca> writes:

> "Jason E. Stewart" wrote:
> 
> > I would
> > advise using what I3C is proposing for the LSID: Life Science
> > Identifier, a sub-category of LOID: Location Independent Object
> > Identifier being promoted by the grid-computing folks.
> 
> > Now this already looks a lot like what we're talking about:
> 
> I agree, the LSID is completely compatible with the namespace/id parts of the
> Triple.
> 
> 
> > * authority - we were using this as where the data came from, but in
> >   the identifier case, it means who controls the namespace. Examples:
> >   i3c.org, ncbi.nih.nlm.gov, ebi.ac.uk.
> 
> Then we probably need both senses of "authority" in the MOBY system,
> in light of the 'user'-requests to know who is providing them with
> the data.  This is no problem - "Distributor" can go in the envelope
> and "Authority" can go in the Identifier.

I agree.

> So... has the MOBY Triple now evolved into:
> 
>   <Object lsid="urn:loid:lsid:bioinfo.pbi.nrc.ca:ArabidopsisGID:At2332487:">
> 
> ??  a "duple"...

Since we know it's an 'lsid' we can make it shorter:

  <Object lsid="bioinfo.pbi.nrc.ca:ArabidopsisGID:At2332487:">

But even so, don't you think that it's worth calling out these bits
explicitly:

  <Object auth="bioinfo.pbi.nrc.ca" ns="ArabidopsisGID" id="At2332487"
          sec="">

and since 'seq' is optional it would be:

  <Object auth="bioinfo.pbi.nrc.ca" ns="ArabidopsisGID" id="At2332487">

I still think this is completely compatible with the LSID proposal,
it's just that we pre-parse the information into its components.

So this would take us back to the MOBY quad.

Also, I would advise making the namespaces hierarchical, so instead of

  <Object auth="bioinfo.pbi.nrc.ca" ns="ArabidopsisGID" id="At2332487">

I would have:

  <Object auth="bioinfo.pbi.nrc.ca" ns="Arabidopsis/GID" id="At2332487">

so that you could later have:

  <Object auth="bioinfo.pbi.nrc.ca" ns="Arabidopsis/FooID" id="At2332487">

It's not a big deal, but we might get some power out of this in the
future. One example was for versioning:

  <Object auth="bioinfo.pbi.nrc.ca" ns="Arabidopsis/2.0/FooID" id="At2332487">
  <Object auth="bioinfo.pbi.nrc.ca" ns="Arabidopsis/2.1/FooID" id="At2332487">

etc.

Cheers,
jas.