[cellml-discussion] Concerning the CellML Model Repository

[Tommy Yu]

David Nickerson wrote:
> Hi Tommy,
> 
> looks like a good starting point for some discussion. Just to help me 
> think through some of the issues, is there any chance you could add a 
> usage example illustrating how this system would deal with a model made 
> from the combination of a bunch of papers (i.e., a single model where 
> each component defines a new citation). I'm guessing this would be done 
> by adding each of the components as separate models and then importing 
> them into a single model?
> 

It depends on how the model is cited.

If the creator of the model that binds all the separate models together based his/her model on a published paper, that citation would be used.  If not, it can only reside inside the user's directory as a filename of his choice, that imports the other models.

Yes, creator of model would have to import the components.

> Another usage example that might be interesting to look at would be a 
> model author adding a local CellML 1.1 model hierarchy to a remote 
> repository and how all the import href's are handled in this case (i.e., 
> imports throughout the model hierarchy might consist of a mix of 
> relative, http, and file URLs).
> 

The model repository shouldn't be responsible for users importing from file:// and other non-existent URIs.  I will create detail use cases for this, but in the case of http URIs, I can think of checking for a pre-approved list of hostnames that models can be imported from.

> And another usage example might be the searching for models built using 
> a specific set of data. It will hopefully become standard practice to 
> annotate variable values with their source, where the source may be some 
> data from a different article than the model's publication.
> 

That's using the metadata, right?  If the creator of the model does annotate components properly (e.g. giving some comment to cmeta:id of some component of some file) it will be searchable (provided that the creator publishes that model).

Thanks for your inputs,
Tommy.

> 
> Thanks,
> David.
> 
> Tommy Yu wrote:
>> Hi,
>>
>> I have written down some of my thoughts on how the model repository could be put together.
>>
>> http://www.cellml.org/Members/tommy/repository_redesign.html
>>
>> It is still a pretty rough document.  The usage example section gives a rough outline on what I see people might be doing with the repository and how this design could address those issues, which I think it will be of interest to users.  It is not an exhaustive list, yet.
>>
>> I must also note the design outlined is quite a drastic departure from what we have now (it will be yet another new repository).  However, it is more true to the one envisioned before according to http://www.cellml.org/wiki/CellMLModelRepositories, except I have an addition layer that will assist in pulling content and drawing relationships between models.
>>
>> Feel free to take it apart and/or build on top of it.
>>
>> Cheers,
>> Tommy.
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