Hi Lucian
Adding to that, I'll emphasise again that this list forms the bare
minimum and we will be happy to expand on the list in the future.
"validity" and "simulation" could be two areas which we choose to
expand on first - for example simulation in a specific named tool, etc.
Thank you for your feedback.
Best wishes
Catherine
On 3/06/2010, at 8:45 PM, Lucian Smith wrote:
My only comment is that lines 6 and 9 ('is it valid?' and 'is it
simulatable?') are the ones I'd be looking at/for the most, so if
those
bit of the glyphs were emphasized or at least easy to pick out,
that'd be
great.
-Lucian
* Catherine Lloyd <[email protected]> [2010-06-03 13:27] writes:
My apologies - my original email was more exclusive to its recipients
that to the discussion list!
I will be happy to leave this another week to give anyone else a
change to respond if they have comments.
Best wishes
Catherine
Begin forwarded message:
*From: *Catherine Lloyd <[email protected]
<mailto:[email protected] >>
*Date: *13 May 2010 9:22:00 AM
*To: *[email protected]
<mailto:[email protected] >
*Cc: *Poul Nielsen <[email protected]
<mailto:[email protected] >>, Tommy Yu <[email protected]
<mailto:[email protected]>>, David Nickerson
<[email protected] <mailto:[email protected]>>,
Peter
Hunter <[email protected] <mailto:[email protected]>>,
Randall Britten <[email protected]
<mailto:[email protected]>>
*Subject: **Curation flags*
Dear All
During my last visit to the EBI in August last year I circulated a
document describing the issues we have with the current star system
of curation ratings, and the proposal to replace these stars with
more meaningful curation "flags". Once I was back in Auckland James
Lawson and I went through several iterations of testing out
different flag options, and the topic was also extensively
discussed at the weekly team meetings and also on the Physiome
Tracker (https://tracker.physiomeproject.org/show_bug.cgi?id=87).
Further, the topic was raised at the CellML workshop in February
this year.
In the end, as the bare minimum (we are happy to add further flags
if needs be), we decided to go with the MIRIAM guidelines (see
attached spreadsheet). This highlighted 2 issues with all the
CellML models in the current repository - 1) None were associated
with a specific terms of use/distribution and 2) None were
annotated with biological data.
The former has been addressed and we have chosen a creative commons
attribution licence to cover all the data in the repository. Tommy
has been implementing a "terms of use" page and also a "how to cite
this model" page. We'd also like to include the licence term in
the metadata of each model (we have found the correct RDF tag for
this).
The latter issue is still being addressed. I have annotated 2
CellML models (Goldbeter 1991 and Teusink 2000) but we have to
decide if this is the way we want to annotate models, and if so,
confirm it in the metadata specification. Also until we have
better annotation tools, adding these terms using a text editor is
the only method available and it is less than ideal - that said, I
will be meeting Allyson and Morgan next week to see if it is
possible for me to use Saint to annotate the models. This would be
fantastic from my point of view - BUT - there is then the danger of
me annotating several models in a certain way - only to have to re-
do them later when it's decided the method of annotation has to
change.
I'll also attend the annotation meeting at the EBI next week.
I'm circulating this now at the request of the BioModels team, who
are interested in our thoughts on the flags. Ideally the two
efforts would adopt the same set of flags.
Camille and Lukas looked at our spreadsheets a while ago, and the
attached spreadsheet has been modified in response to their
comments. Additional feedback is always welcome.
Once we have confirmed the set of flags, Tommy will be able to
start to implement them in the next version of PMR2.
Best wishes
Catherine
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