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Posts: 122
Registered:
February 2010
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Re: why deletion of the outside attribute of compartment in SBML L3
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10 Jul '12 02:59
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Unfortunately for the time being you will have to encode this sort of information in a custom annotation, as the editors removed the attribute. Here the reasoning behind the decision:
http://sbml.org/Community/Wiki/SBML_Level_3_Core/No_outside_attribute
Since the information is quite useful it would make sense for different tools to agree on the same annotation to be used, so this information can be exchanged between tools. (Especially since no alternative package exists yet, or is in planning). An annotation like:
<outside xmlns="http://sbml.org/outsideinformation" compartment="compartmentSId" />
would suffice. it would be easy enough to translate this information when changing levels.
Cheers
Frank
> Dear all,
>
> I found out, that in SBML Level 3 the outside attribute of compartments
> was deleted.
>
> Is there a reason why the outside attribute was deleted? How can I now
> read out or set, which compartment is contained in another compartment?
> Or do I have to assume a parallel existence of the compartments, which
> (for me) makes no sense e.g. in case of a cell containing a nucleus.
>
> Thanks in advance!
> Stephanie Tscherneck
>
> --
> Stephanie Tscherneck, M. Sc.
> University of Tuebingen
> Center for Bioinformatics Tuebingen (ZBIT)
> Sand 1
> 72076 Tübingen
> Germany
>
> Phone: +49-7071-29-78987
> Fax: +49-7071-29-5091
>
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