[MOBY-l] Re: GO & I3C namespace listings - two alternatives

[Brian Gilman]

Hello All,

	Sorry for my lack of response on the list...I'm just now catching
up with mail. The specification is in draft format! Please don't take this
doc as gospel. And, Mark, I hope that *I* didn't make that comment you
quoted?? 

	I think it would be best if we all met in one place to discuss the
LSID specification and naming conventions. To this end, I'd like to
invite everyone on the MOBY development team and other interested parties
to come to the next I3C meeting. I will circulate the date and location to
the list in a follow up e-mail. 

	If we have one naming convention properly specified and put in a
public forum with an API for multiple languages I think we've all won in
the end. 

	In preparation for this meeting I will read the specification at
the link below and also ping this list as I have more questions about use
and intent of the triple as defined in previous e-mails. 

	My comments to you questions will take some more reading of the
thread. I'll get back to you...

					-B

-----------------------
Brian Gilman <gilmanb at genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902


On 31 May 2002, Jason E. Stewart wrote:

> "Mark Wilkinson" <mwilkinson at gene.pbi.nrc.ca> writes:
> 
> > "Jason E. Stewart" wrote:
> > 
> > > * namespace - exactly what we have been discussing. Examples:
> > >   GenBank/GI, GenBank/Accession, EMBL/ID, EMBL/AC, EBI/ArrayDesign
> > 
> > Alan Robinson wrote:
> > 
> > > If MOBY needs a vocabulary for databases names & identifiers, I suggest
> > > that it adopts the same scheme as GO:
> > >
> > >  http://www.geneontology.org/doc/GO.xrf_abbs
> > 
> > Is the I3C following another group's standard in this respect or are they
> > making their own?  Do they have a (publically accessible) list of their
> > namespaces?  Does GO follow the same standard as I3C (apparently not)?
> > 
> > If we go with I3C we get hierarchy, if we go with GO we are more easily
> > compatible with GO.  It makes no sense to build our own namespace CV if there
> > is already one available...  If the I3C list is available I'd like to take a
> > look at it before deciding on this.
> 
> I know of no such list from the I3C. They state explicitly that the
> namespaces will be left up to each Authority, which seems to beg the
> issue of what the hell do we do with the common ones like GenBank GI's
> and SwissProt accession numbers?
> 
> I say use the GO convention for now and begin a discussion with them
> to support a more hierarchical definition in the future.
> 
> Cheers,
> jas.
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