Should explain compartment 'outside' doesn't impact size

[sbmlsecretary]

As discussed in the recent thread on sbml-discuss, the spec is silent on whether a compartment 'outside' of another needs to have a size encompassing the inner compartment. Should we add a sentence to the spec in the relevant section about this?

Reported by: mhucka

Original Ticket: "sbml/sbml-specifications//106":https://sourceforge.net/p/sbml/sbml-specifications//106

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I am accepting this issue as valid.

Original comment by: shoops

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Yes, we should :)

It should state that the attribute outside does no have any mathematical implication. This means especially that no deduction can be made about the sizes of a compartment outside another.

Original comment by: shoops

[sbmlsecretary]

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I accept this issue as valid, however NOT as phrased by Mike. The compartment "outside" another does NOT *contain* the inner one. The relation is a surrounding, not a containment. We have to clarify that. Therefore the size of a compartment 'outside' of another certainely not need to have a size encompassing the inner compartment. That has been a recurrent misunderstanding of a the spec throughout the years.

Original comment by: lenov

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I am accepting this issue as valid.

Original comment by: lenov

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This needs clarification since Nicolas and the spec are totally opposite. Nicolas says the outside does *not* contain the inner compartment. However the paragraph on the outside attribute uses the word containment and implies that it does.

Original comment by: sarahkeating

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I am accepting this issue as valid.

Original comment by: sarahkeating

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I have tried to get rid of this word (containment) for a long time. It was always intended as in "the plasma membrane *contains* the cell content" or "the plastic bag *contains* the shopping". But this is really confusing. I apologise for not having been more proactive as an editor. I should have rewritten the relevant parts of the spec. Sarah, the spec and I are certainly not opposite. A species can only belong to one compartment. That totally rules out a compartment that would encompass another one. Furthermore, all the transport examples of the spec clearly explain how to compute the changes in concentrations using "my" interpretation. And I am not aware of any software that got confused. But some modellers are. Hence we need to fix the relevant parts of the spec. A very easy fix is to replace any "contains" by "surrounds" and "containment" by "surrounding".

Original comment by: lenov

[sbmlsecretary]

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In my opinion the attribute outside should be deprecated. The intend for this attribute was to confer semantic information to the user for which we have now much better means. Please note that this term had and will not carry any information, which will be used or needed during simulation, therefore getting rid of it would be best.

Original comment by: shoops

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Stefan,

I entirely agree with the deprecation. This metadata should not be part of SBML but should be externalised. Once we have a geometry extension, it can be part of it. But at the moment, I do not see how it is different from, let's say CellDesigner annotation. It is useful, but does not belong to SBML. It does not affect the way we interpret a model.

Original comment by: lenov

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We need to explain that the optional attribute only contains semantic information, which does not impact the simulation at all, in other words we do not enforce any relation ship between the dimension and/or size of inside and outside.

Original comment by: shoops

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• status: open --> pending

Original comment by: lenov

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This Tracker item was closed automatically by the system. It was previously set to a Pending status, and the original submitter did not respond within 180 days (the time period specified by the administrator of this Tracker).

Original comment by: sf-robot

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• status: pending --> closed

Original comment by: sf-robot

[sbmlsecretary]

• status: closed --> pending

Original comment by: mhucka

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In any case we should clarify that the attribute has no impact on the recommended mathematical interpretation. We should also clarify that the "inside" compartment is not a part of the "outside" compartment.

I also think it should be deprecated.

Original comment by: s_sahle

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Regarding the deprecation: I think that's ok, and I would like to argue that we also don't need to have a vote on it, because we can argue that it's something in preparation for L3 geometry, where it would be irrelevant.

Do the rest of you agree, or should we put the deprecation issue to a vote?

Original comment by: mhucka

[sbmlsecretary]

• status: pending --> open

Original comment by: mhucka

[sbmlsecretary]

• status: open --> pending

Original comment by: mhucka

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I've logged a separate issue for the action of deprecating the 'outside' attribute. It is issue #2025244.

Original comment by: mhucka

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• status: pending --> open

Original comment by: mhucka

[sbmlsecretary]

• status: open --> pending

Original comment by: mhucka

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I've logged a separate issue for the action of deprecating the 'outside' attribute. It is issue #2025244.

Original comment by: mhucka

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• milestone: 678078 --> Rejected/No_action
• status: pending --> closed

Original comment by: lenov

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I close this item since it results from a misunderstanding (a compartment outside of another does definitively not contain it) and another item has been open that will supersede this one.

Original comment by: lenov