[SED-ML-discuss] Issues with ChangeXML

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

Hello all, 

I know at the Hackathon we were briefly talking about ChangeXML, and that it
should be included in SEDML Level 1 Version 1. So I finally had a detailed
look at the construct and tried to map out what implications it would have.
Currently we have one construct: 

<changeXML target="<xpath expression to model variable>" newXML="<some
really long unvalidatable string here that might or might not be XML>" />

I assume this to be a typo. If I remember it correctly from our discussions
this really should look like this: 

<changeXML target="<xpath expression to model variable>">
<newXML>
	<some new xml here, validatable with target namespace and bells and
whistles>
</newXML>
</changeXML>

Ok ... this basically would work ... so the next important thing to ask, is
what would we like to do with this. Basically three things: 

- adding new elements (i.e.: a degradation reaction to an existing species)
- replacing an element by something else (i.e.: a lumped reaction by its
individual steps)
- deleting elements (i.e.: removing a reaction step)

Previously we discussed, that we could delete elements by replacing a target
with an empty newXML block. If we look at the draft specification we find an
example, that shows that we could add a parameter to a model, by replacing
one parameter with itself and another one: 

1 <model [..]>
2 <listOfChanges>
3 <changeXML target="/sbml:sbml/sbml:model/sbml:listOfParameters
4 /sbml:parameter[@id='V_mT ']"
5 newXML="<parameter metaid="metaid_0000010" id="V_mT" value="0.7">
6 <parameter metaid="metaid_0000050" id="V_mT_2" value="4.6">" />
7 </listOfChanges>
8 </model>

I would very much prefer to keep the individual operations separate, either
by introducing an additional attribute 'operation' on the changeXML element:


1 <model [..]>
2 <listOfChanges>
3 <changeXML target="/sbml:sbml/sbml:model/sbml:listOfParameters"
4  operation="add">
5 <newXML>
6       <parameter xmlns="<sbmlnshere>" metaid="metaid_0000050" id="V_mT_2"
value="4.6">
7 </newXML>
8 </listOfChanges>
9 </model>

The advantage here is that it is much easier to apply changes from one model
to another, without artificially having to replace existing elements by
itself + whatever one wants to add in the first place. 

Similarly: 

<changeXML
target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V_mT
']"
  operation="delete"/>

would delete an element ... and so on ... alternatively if someone would
really be against the additional attribute, we could introduce differently
named elements like: 

<addXML target="<xpath>"><newXML> <stuff here/> </newXml> </addXML>
<removeXML target="xpath"/>

And changeXML would remain as is ... 


Let the floor be open for comments :) 

Cheers
Frank