[MOBY-l] Presentation on the WWW site?

[Mark Wilkinson]

Hi Jason (and all!)

I've finally plowed through the majority of "critical" (ha!) paperwork
that piled up on my desk while I was away over the past month, so I can
now switch my focus back to the merely "important" stuff.  I will put
the MOBY part of my talk up on the website, but I want to edit it first
to reflect the changes that we made during this meeting.  I got most of
the way through the minutes from the meeting, and have the HTML page on
my laptop.  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.

Some things have been running around in my head, so I want to throw them
out to the group for comment:

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.

Midori - how do you think we should deal with these ontologies?  Flat
files?  or a database?  I'm not sure if open-bio will host a database,
but we can certainly set one up here at PBI for the time being until we
find a more stable home if that is the direction we chose to go.  What
works best, in your experience, when multiple people are working on
(ack! ) or browsing the ontologies at the same time?   Should we use a
trimmed-down version of the GO database schema, or will that prevent us
from using the tools that have been developed for GO?

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.

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?


In other news - I've been invited to present MOBY at the E-BioSci/ORIEL
meetings in Heidelberg on the 21st of June, and at another meeting (name
escapes me for the moment) in Cologne the preceeding week.  If any of
you can think of something that came up at the last meeting that you
think I should stress in these talks please let me know.  It would be
nice if we get EMBO looking and thinking in our direction right from the
start!  We've also been asked to submit a manuscript to Briefings in
Bioinformatics - the deadline is the end of the month.  I'll write up a
draft by the end of next week but I'd like to have a couple of other
MOBY'ers proof it for me... so if any of you has an hour or so free...

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.  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 ;-)

That's all the news from my end.  Things are really alive at the moment,
and I think we moved forward enough at this meeting that we wont lose
momentum as quickly this time...  and having some funding certainly
helps :-)

Sorry if this sounds rushed - it was!

Best wishes all!

Mark


"Jason E. Stewart" wrote:

> Hey Mark,
>
> Can you make your powerpoint presentation of MOBY available from the
> biomoby.org WWW site? That would help me remember some of the things
> we talked about.
>
> Thanks,
> jas.
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l

--
--------------------------------
"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada