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
|
Curation Flags MIRIAM Standard.xls
Description: MS-Excel spreadsheet
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