Re: [sbml-annot] annotation spec

[Stefan H. <sh...@vb...>]

Hello All,

On 2/14/2011 4:56 PM, Nicolas Le novère wrote:
> On 14/02/11 21:33, Stefan Hoops wrote:
>
>> And he is correct with that. I even would say that any modification of
>> an SBML document is out of our hand. It is entirely possible that
>> someone changes the SBML Id or metaid or whatever unique attribute we
>> use to identify an SBML object. This will render all annotation using
>> this reference dangling as it talks about something non existing.
> I do not agree. That would be invalidating the SBML model and thus
> incorrect. It would be like changing the id of a species and making all
> formula invalid. A tool changing an id must take care of the consistency
> because the idref are part of SBML specification. Model merging is not part
> of the SBML specification.
>

I think we actually agree here too. In that we say that it is the 
modifier's (being it a tool or person) responsibility to create correct 
SBML. The problem here is that a tool unaware of the extension package 
might modify an SBML Id and correct all references within the L3 core to 
it. This would create a valid SBML L3 core model. However, the 
annotation package content will no be valid.

>> I think the only processing rule we might want stipulate is:
>> If a metaid (XMLId) is changed by a processing rule (e.g. through an
>> xml:include statement), all references to this Id within the annotation
>> package must be changed accordingly.
> Yes, we agree here.

Thanks,
Stefan




-- 
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax:   (540) 231-2606
Email: sh...@vb...