The mapping of SBO terms must be significantly revised

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SBML L2V2R1 Pages & lines: all of Section 5 Description:

(The following was originally written by Nicolas.)

From: Nicolas Le Novere <lenov@ebi.ac.uk> Sender: sbml-editors-bounces@caltech.edu To: The SBML Editors mailing list <sbml-editors@caltech.edu> Subject: Re: [sbml-editors] SBO extension Date: Tue, 12 Dec 2006 09:43:12 +0000 (GMT)

On Tue, 12 Dec 2006, Michael Hucka wrote:

> A couple of things: > > 1) I have already forgotten, and apparently didn't write > down, the reason for the addition of an sboTerm on the > event delay. Could you elaborate?

It is more than the event delay.

During the Forum last October, a discussion erupted on the fact that the sboTerm on reaction (modelling framework) was necessary to understand properly the meaning of the kineticLaw. The result of the discussion (thanks to Andrew and his ability to transform any controversy into constructive work) was that the modelling framework being specified in the element "semantics" of the SBO MathML, it was not necessary to repeat it in the SBML. On the contrary, we should use the sboTerm of reaction to link with the branch "event" of SBO, adding the missing semantics to link SBML reaction and SBGN processes.

Then, going on, we noticed that it was silly to annotate then element "event" with an SBO term representing a mathematical expression. An SBML event is not a mathematical expression. Therefore the SBO term should represent an event as well. On the contrary there was no SBO term on event triggers and event delays.

The basic rule is simple: Every SBML element that carry a "math" field should carry an sboTerm pointing to a mathematical expression.

Finally, since we were talking about interfacing SBML and SBGN, it was natural to takle the problem of species, that have no sboTerm (speciesReference have). So now, it is quite clear and simple really. There is an obvious map between SBML, BioPAX and SBGN in the non-mathematical area, and the original SBO annotate the math-related elements. E.g. for an enzymatic reaction (this is an example, not supposed to represent every enzymatic reaction):

SBML SBO SBGN BioPAX model continuous compartment compartment compartment dbxref GO Cell Component species E polypeptide macromolecule protein species S simple chemical simple chemical small molecule species P simple chemical simple chemical small molecule reaction catalysis positive modulation catalysis speciesRef S substrate speciesRef P product modSpeciesRef E catalyst kineticLaw Henri-Michaelis-Menten

> 2) It would indeed require a schema change. And you know > what my response to that will be ;-).

But the situation is different. IMHO, we cannot leave the spec as it is. It will jeopardise not only the use of SBO terms on events, but also block any tentative of using SBO to interface SBML, BioPAX and SBGN.

Regarding the schema change, it is very minimal and entirely backward compatible. We will need to rewrite significantly the section 5 though. But that doesn't affect the description of SBML in section 4, except for some of the UML diagrams.

Reported by: mhucka

Original Ticket: "sbml/sbml-specifications//8":https://sourceforge.net/p/sbml/sbml-specifications//8

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• priority: 5 --> 9

Original comment by: mhucka

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• status: open --> pending

Original comment by: mhucka

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Logged In: YES user_id=343670 Originator: YES

I agree with the proposed change and that it should be done.

Original comment by: mhucka

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• assigned_to: nobody --> lenov
• status: pending --> open

Original comment by: mhucka

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• status: open --> pending

Original comment by: mhucka

[sbmlsecretary]

Logged In: YES user_id=641982 Originator: NO

I agree with the proposed change and that it should be done.

Original comment by: sarahkeating

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Logged In: YES user_id=862059 Originator: NO

I agree with the proposed change and that it should be done.

Original comment by: shoops

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• milestone: 678078 --> Accepted:_Changes_with_conformance_implications

Original comment by: lenov

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• status: pending --> closed

Original comment by: lenov