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


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  • From: c.lloyd at auckland.ac.nz (Catherine Lloyd)
  • Subject: [cellml-discussion] Fwd: [Fwd: Fwd: Curation flags]
  • Date: Thu, 3 Jun 2010 13:26:09 +0100
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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