Re: [Miase-discuss] OM changed

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

Just a precision: The changes mentioned by Frank are not due to a recent 
inconsistency between OM and schema. All those changes where already 
present in the SVN repository as far as 5 month ago.

Until we have a formal specification (SBML-like) the authoritative public 
source should probably be the description given at CMSB:
http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/documents/publications/Koehn-CMSB2008.pdf

and the most recent version is (should be) at:
http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/documents/sed-om/

At the moment they are in sync.

Cheers

Dagmar Köhn wrote:
> Dear all,
> 
> concerning the mess with the OM and the XMLS. It is my  fault that they
> are not coherent, I didn't update the OM during the last time (although
> it should have been compliant with the paper). As we are changing the
> Schema back and forth, it felt a bit "useless" to do the same with the
> OM, but I understand the big confusion now.
> 
> We are currently trying to solve the problem by writing a UML2XMLS 
> converter that hopefully takes the OM in UML2 and produces updated 
> versions of the SED-ML XMLS. Hope to have that running until April so 
> that we can make changes more easily during the workshop.
> 
> I'd suggest to make the post-workshop version of both SED-ML XMLS and 
> UML2 a first official one for people to securely refer to!? Until then,
>  as Nicolas said, the schema versions should be considered unstable 
> versions open for discussion.
> 
> Dagmar
> 
> 
> Nicolas Le Novere wrote:
>> 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.
>> 
>> 
> 
> 
> ------------------------------------------------------------------------------
>  This SF.net email is sponsored by: SourcForge Community SourceForge
> wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword 
> _______________________________________________ Miase-discuss mailing
> list Mia...@li... 
> https://lists.sourceforge.net/lists/listinfo/miase-discuss


-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/