Re: [Miase-discuss] sed-ml library?

[Frank B. <fbergman@u.washington.edu>]

Hello again :) 

> 
> In my opinion it should not and so far it does not have one ... But
> people might have a different opinion? Does anyone see a need to have
> an
> id for the curves?

As described in my previous mail we might not have right now, but that does
not mean we should preclude people from doing it. 

> 
> Hmm, I would keep the ids where they are as there are (up to now) quite
> a few elements without id... unless another identifiableSedBase class
> would make life far easier for you!?
> 

Definitely, I can't see any harm done with having an id (maybe even a name)
in the base class. 

> 
> The fact that we are not allowing SBML models to be embedded in the
> SED-ML files does not change a thing. The actual problem with referring
> to external sources which might address different versions of (even
> curated) models remains. Imho we cannot get around having either a
> "version" attribute in the <model> element or making sure the model
> resources we allow for reference have unambigious URIs for each version
> of the models ;-)

I honestly think this is making live much more difficult. If I read a
description file which tells me the models is at: 

http://modelrepository.net/interestingModel.xml

I know exactly what to do and how to get it. Even if your give me a
biomodels urn. That is all well. Now if you start and say, "oh but take
version X" ... then I cannot automatically resolve it anymore. I don't know
how to go to the source repository and request a different version. And I
don't see how you can unambiguously describe how models and versions are to
be kept on all repositories. But again, this is a non-issue. At the time of
writing, the software tool knows exactly which model was run, so the tool
can make sure the description is correct. 



Frank