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Hi all,

Just wanted to see what people think about using the BioModels
qualifiers (http://biomodels.net/index.php?s=Qualifiers) in CellML
models? i.e., following the SBML annotation specification (see section 6
of the SBML level 2 version 2 specification).

The reason I ask is that I am starting to look at how to reference
external data, for example to justify a parameter value or provide
experimental data for use in making a graph. At least for these examples
the http://biomodels.net/model-qualifiers/isDescribedBy qualifier seems
quite appropriate - where the referenced resource could be a journal
publication to justify a parameter value or a reference to some
experimental data.

Before progressing too far with this, I thought I'd better check. One
problem I can see immediately is that the
http://biomodels.net/model-qualifiers/is and/or
http://biomodels.net/biology-qualifiers/is qualifiers are pretty much
the same as the cmeta:bio_entity already defined in the CellML Metadata
Specification. So is there already something in the CellML metadata
specification that will let me reference arbitrary (possibly external)
resources? Is it ok to just use the BioModels qualifiers that we want
without supporting them all? Or is there some other way to achieve the
same result?

I know Carey did some initial work looking at using the XML Resource
Directory Description Language (RDDL, www.rddl.org) to reference
external data. To make full use of this (especially in regard to model
curation), I think we would need to define our own natures (roles) and
purposes (arcroles) - which would essentially result in the same
metadata as using the BioModels qualifiers but with different namespaces.


David.

--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: david.nickerson at nus.edu.sg

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• [cellml-discussion] BioModels qualifiers in CellML and references to external data, David Nickerson, 12/28/2006
  • [cellml-discussion] BioModels qualifiers in CellML and references to external data, Andrew Miller, 12/29/2006
    • [cellml-discussion] BioModels qualifiers in CellML andreferences to external data, David Nickerson, 12/29/2006

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