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[cellml-discussion] Biological and other non-model citations inCellML metadata?


Chronological Thread 
  • From: david.nickerson at nus.edu.sg (David Nickerson)
  • Subject: [cellml-discussion] Biological and other non-model citations inCellML metadata?
  • Date: Thu, 29 Mar 2007 08:55:16 +0800
I think even with such a best practice specification the model
repository still needs to handle the case where there are multiple
primary references - a CellML representation of a model coupling
separate mechanics and electrophysiology models together would be an
obvious example.

As for more detailed citations, in the work I am doing I end up with
specific variables, components and equations referenced to different
articles. So in a CellML 1.1 model hierarchy there are many different
combinations of "primary" references possible depending on the
particular sub-models pulled into a specific experiment. The base model
has one primary reference but then I am adding various extra features to
the model which all have their own primary reference or making changes
to parameter values for various experiments etc.

I don't think the bio_entity or math_problem would be appropriate in
these instances.


Andre.


Andrew Miller wrote:
> Hi,
>
> As discussed at the last CellML meeting, there are some models which
> reference both the paper about the model, and a reference about the
> biology. Since there is no way to determine between them, this creates
> problems for CellML metadata processing tools which want to identify the
> paper about the model (such as the CellML repository). However, it would
> still be a good thing to include references about the biology /
> experiments on which a model is based, as well as papers on underlying
> mathematical techniques (and perhaps earlier papers?)
>
> The CellML Metadata specification already describes a predicate
> cmeta:bio_entity, and another cmeta:math_problem. Although the cmeta
> specification suggests that these be used to provide references to
> identifiers for the biological entity a part of the model relates to,
> and likewise for the mathematical problem, it would also be possible to
> create a list of references inside the resource targeted by the
> bio_entity or math_problem predicate.
>
> I would therefore suggest that the following be considered best practice:
> 1) Only refer to the paper about the model from the metadata for the model.
> 2) Any other papers should be in another resource referred to from the
> bio_entity and math_problem entities.
>
> Does anyone else have any opinion on this?
>
> Best regards,
> Andrew
>
> ||
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--
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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