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Dear CellML community,

First of all, sorry for having be silent so long. We indeed read the
exchanges about curation, and enjoyed them. It is nice to see that the
various communities are committed to increase the quality of the
quantitative models. We do not have much advice to give. The best we can
do is to describe the procedure we use to curate our own models in
BioModels Database. Hopefully you will find some reusable ideas. And if
you have any comment, suggestion or criticism, they are most welcome!

Users can currently submit models in CellML and SBML (VCML is coming).
All the models are then converted to SBML, which is our internal format.
Using libSBML, we check the syntax of the files. If a model is incorrect,
it is rejected. Therefore, we accept only syntactically correct SBML
files. The models are then entered in the curation pipeline. The first
curation step is the consistency check. This is done by libSBML, which
checks that all the rules listed in the SBML spec are fulfilled (e.g.
units consistency, coherence of symbols etc.). Once a model is dubbed
consistent, the export formats are generated (CellML, SciLab, XPP, BioPAX,
GIF, SVG). The model can then be moved to the non-curated branch, or
downloaded for further curation. The latter step is the verification of
MIRIAM compliance. The curator checks that the structure of the model
reflects the one described in the paper, that all the values are correct,
and finally that one can reproduce published results *using different
software than the one used by the authors*. If the model passes MIRIAM
checks, it can be moved to the curated branch for annotation.

We release the models publicly twice a year.

I hope those explanations are clear enough. We remain available for any
additional details.

Various additional information can be found at:
http://www.ebi.ac.uk/compneur-srv/biomodels/doc/curation.html
http://www.ebi.ac.uk/compneur-srv/biomodels/doc/annotation.html

Best regards,

The BioModels Database team


--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: +44(0)1223494468, Mob: +44(0)7833147074
http://www.ebi.ac.uk/~lenov, AIM:nlenovere, MSN:nlenovere at hotmail.com

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• [cellml-discussion] curation of BioModels Database, Nicolas Le Novere, 07/18/2007
  • [cellml-discussion] curation of BioModels Database, David Nickerson, 07/18/2007
    • [cellml-discussion] curation of BioModels Database, Nicolas Le Novere, 07/19/2007
      • [cellml-discussion] curation of BioModels Database, David Nickerson, 07/19/2007
  • [cellml-discussion] curation of BioModels Database, Matt , 07/19/2007
    • [cellml-discussion] curation of BioModels Database, Nicolas Le Novere, 07/20/2007

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