Re: [Miase-discuss] miaseOM

[Dagmar K. <da...@eb...>]

Heho,
>> You are right. I did not put those changes in the UML so far, because I
>> actually couldn't remember the reason(s) to do that.
>> Can anyone explain again?
>>     
>
> Sorry ... explain what?
>   
I was looking at the part of the example file that specifies the output:
- why was the listOfVariables on the same level as listOfFigures and 
listOfColumns?
- why did we specify SBMLSymbolReferences and how did the ___TIME___ 
thing work?
... I am not sure if that bit was done shortly before the lunch break or 
what happened to me so that I really can't follow the XML file design at 
that point, so if someone of you could explain it again :) That would be 
nice.
Otherwise, I'll just put it in the OM and we'll see what people say and 
discuss it later on (hopefully South Africa meeting).
>> Concerning your remark on my data types: I think I didn't put any so
>> far actually (all being strings). Thought to fix that later on. But
>> suggestions are welcome :)
>>     
>
> Hm ... I am sure I saw a "positiveInteger" on those types :) 
>   
Well is there? ;) I actually decided to skip data types, but I might 
have been inconsistent on that!

>> Does anybody want to suggest an SBase like class for MIASE? How do we
>> name it and what attributes will it have?
>>     
> Actually, you could just take it as is from the SBML spec, strip the SBO
> term and call it SBase / MBase
>   
I'll do so. Go for MBase until further objection.
>   
>> Do we give the annotation element any specific structure or do we just
>> say: "Put the extra information in the annotation" and provide an
>> example of how to do it?
>>     
>
> I would say for right now we do not have to clarify that point :) ... ymmv
>   
ymmv?

Dagmar

-- 
Dagmar Köhn, EMBL - European Bioinformatics Institute, Computational Neurobiology Group, Hinxton, Cambridge, CB10 1DS, UK, http://www.ebi.ac.uk/compneur-srv/, da...@eb..., Tel: +441223494418