Re: [Miase-discuss] OM changed

[Nicolas Le N. <le...@eb...>]

Frank Bergmann wrote:

> I've had another look at the OM + example. As it turns out it has changed in
> some places from what we initially discussed. If possible I'd rather like to
> discuss changes on this list first, before they get taken as granted. Some
> of the changes have been renaming of attributes. Those are breaking changes
> for all of us with working prototypes and deserve to be discussed: 
> 

Frank,

I am deeply sorry. This comes from the unfortunate fact that during half a year, the OM on Sourceforge was not updated. Those changes were largely discussed, sometimes on the list, sometimes on more restricted discussion. Most of them date back to the time of CCB in March 2008. They were all present in the report on SED-ML we made for CMSB08 last October (attached), that has been available since the summer for instance from the project webpage.

The problem is that SED-ML is not yet stable, and therefore there is not a precise date that corresponds to a given version of the OM. That is indeed a big mess, and we will change that ASAP by setting a numbering system.

> - i.e: XPath -> target, or listOfColumns -> listOfDataSets ...

Those where early changes. The XPath is the value of the attribute. Its meaning is a target. It would be like calling the attribute id "string". ListOfColumns implied a specific disposition in space rather than a type of information.
 
> Other changes do require discussion, as I'm not quite sure what to do with
> them: 
> 
> Previously logX and logY were properties of a Plot2D, as facility of
> creating a log plot. In the current version those attributes are now
> properties of the *individual* curves of the plot. Is this really necessary?

Yes, we found examples where curves with linear and log Y where plotted together. 

> Does it make sense to paint those together? And what is supposed to be on
> the axis, the logged values or the uhm not-logged ones?

You have plenty of plots with several axis, for instance on the left and on the right.

> Or previously we had Parameter values defined as real-numbered values, now
> they are strings. 

I do not remember when this happened, and actually did not notice. I find this odd and I agree we should discuss it.
 
> Finally some of the classes that were previously under discussion, hence
> marked white are now no longer marked. 

It is just a coloring trick I believe. 

> 	I.e: ChangeMath, here I'm not sure what the list of variables, or
> list of parameters would be? I thought this would be a special case of
> changeXML, where I just swap out one snippet of MathML by another one. But I
> would not know what to do with variables and parameters in that case. 

This is a big misunderstanding. ChangeXML is used to replace a piece of the model by something else. One can replace the value of an attribute, or an element etc.

ChangeMath COMPUTES a change. For instance, you can compute the new value for an attribute of model A based on the value of an attribute of model B and an external parameter. Therefore the listOfVariables use an XPath.

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust 
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