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[cellml-discussion] Fwd: [Fwd: Fwd: Curation flags]


Chronological Thread 
  • From: c.lloyd at auckland.ac.nz (Catherine Lloyd)
  • Subject: [cellml-discussion] Fwd: [Fwd: Fwd: Curation flags]
  • Date: Thu, 3 Jun 2010 20:54:43 +0100
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 <c.lloyd at auckland.ac.nz> [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 <c.lloyd at auckland.ac.nz
>>>> <mailto:c.lloyd at auckland.ac.nz >>
>>>> *Date: *13 May 2010 9:22:00 AM
>>>> *To: *biomodels-net-discuss at lists.sourceforce.net
>>>> <mailto:biomodels-net-discuss at lists.sourceforce.net >
>>>> *Cc: *Poul Nielsen <p.nielsen at auckland.ac.nz
>>>> <mailto:p.nielsen at auckland.ac.nz >>, Tommy Yu <tommy.yu at
>>>> auckland.ac.nz
>>>> <mailto:tommy.yu at auckland.ac.nz>>, David Nickerson
>>>> <d.nickerson at auckland.ac.nz <mailto:d.nickerson at auckland.ac.nz>>,
>>>> Peter
>>>> Hunter <p.hunter at auckland.ac.nz <mailto:p.hunter at auckland.ac.nz>>,
>>>> Randall Britten <r.britten at auckland.ac.nz
>>>> <mailto:r.britten at auckland.ac.nz>>
>>>> *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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