[MOBY-l] Presentation on the WWW site?

[Jason E. Stewart]

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

> I'll try to get that on the website this afternoon as well.
> I'm also formatting the MOBY-Central API document so that it is readable
> and making notes of certain aspects of it that might not be clear on
> first reading.  That should be on the website within a day or two.

Excellent, thanks.

> First:  I realized (again) in the shower this morning that there is one
> more CV that we need - for the 'namespace' element of a MOBY-Triple.
> Thus, as I recall, we have three CV/O's:  1) Service Type, 2)
> MOBY-Object Type, 3) Namespace.

Yeah ...

I'd rather not, but I can't think of a better alternative.

> Midori - how do you think we should deal with these ontologies?  Flat
> files?  or a database?  

For now, I think it would be simplest with flat files and CVS. Since
we're likely to make major changes left and right, it seems more
flexible. 

> Second:  There appears to be an object type that we (or at least, I)
> have been taking for granted all this time - an "ID" object.  This
> allows us to send, for example, genbank ID's as a query:
> 
> <ID   namespace="Genbank"   id="A334572.2">
> 
> This may have been obvious to everyone else, but it just crystallized in
> my own mind this morning.  Is the name "ID" okay with everyone?  I
> thought of "Accession", but that might be too specific.

Why not just use the top-level <MOBY> object for this purpose? The
<ID> object would have no new attributes, so it seems redundant.

> Third:  a question to everyone who was involved in the discussion:  am I
> mistaken, or did we flip back from a MOBY-Quadruple to a MOBY-Triple by
> putting the "Authority" tag into the MOBY return envelope, making it
> applicable to all contained objects?

Yes, I believe we did.

> In addition, Ethan Cerami has just submitted an article to appear on the
> O'Reilly website which will mention BioMOBY, and he will be writing a
> follow-up article in a couple of weeks.  He will be using the BioMOBY
> website as his source.  

Good, I'm glad that O'Reilly is taking notice.

> I'd like to get the website "sparkling" by then!  Does anyone do
> good website design?  I'm just crap at it...  I know, I know!
> Content is more important than presentation ;-)

I doubt my design skills are all that much more impressive, although I
do know my way around GIMP nowadays. Let me know if you need help.

jas.