Re: [Miase-discuss] annotation/notes element

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

> 
> ? The two variable glyphs carry the same attribute. But we nevertheless
> need to fork them. For parameter, we should rewrite the UML with only
> one glyph.
> 

(I counted taskReference / modelReference as attributes)

> >>> - changeAttribute: newValue should be of type xs:double
> >> Not sure, could I - for example - change
> >>
> >> <listOfProducts>
> >>      <speciesReference species="PZ"/>
> >>
> >> the species (XML) attribute "PZ" to some other species, e.g. to
> change
> >> the product in a reaction? Could that make sense? Or would we
> consider
> >> that as a completely different model then?
> >
> > right ... you actually could do that ... this does worry me a bit ...
> > i'd much rather that people would swap out whole reactions than
> fiddle
> > with products like that ... this seems like a sure way to create
> invalid
> > models ... no xs:double here then :)
> 
> I am with Frank here. This worries me a little as well. And actually, I
> remember that at one time changeAttribute was not called
> changeAttribute but changeValue. It could only change a numerical
> value. Then it became changeAttribute, which is actually a bit
> confusing with changeXML as well. 
> 

I've double checked my implementation, and indeed I did use string for
precisely the reason, that you might want to change some other attributes.
Here Xpath gives us all the freedom we want, or enough rope to hang
ourselves with. We could use it to set any attribute, like sbml Id, boundary
conditions, constant flags, relocate species and more. The problem with this
is that it might work fine for one model and cause lots of problems for
another model, partly because of for example default values in SBML (and I
know this is remedied by level 3).  

Lets create some examples first before changing the proposal, if we can come
up with a valid (and useful) case for keeping non-numerical values, then
perhaps it is worth keeping them. 

> To remove the problem and tackle the other confusions, what about
> renaming the three "modification types":
> 
> changeValue
> 
> replaceXML
> 
> computeValue
> 

Let us postpone renaming the types until we find more examples. 

Best
Frank

> ?
> 
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