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The specification documents for SBML.
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Need update for changes in SBO #227

Closed sbmlsecretary closed 2 years ago

sbmlsecretary commented 12 years ago

From Nicolas:

_____ Dear editors,

As described in the message http://sourceforge.net/mailarchive/forum.php?thread\_name=4D39AA77.3040102%40ebi.ac.uk&forum\_name=biomodels-net-discuss

we will imminently make a few changes in SBO root terms. Most of the changes are renaming, and none will affect the users at all. The SBML specification will have to change a bit though. Figures 21, 22, 24, 27 will have to be redone, but those are illustrative only and the temporary mismatches are innocuous. However, there is one change that affects (a little) the specification of the core. Table 6 contains:

Parameter quantitative parameter SBO:0000002 LocalParameter quantitative parameter SBO:0000002

We will create a root term 'systems description parameter'. 'quantitative parameter' then becomes a child of this new term. A sibbling will be 'qualitative parameter'. We though this solution better than renaming 'quantitative parameter' into 'systems description parameter' since it is less disruptive for users. Table 6 will then have to be rewritten as:

Parameter systems description parameter SBO:NEW LocalParameter systems description parameter SBO:NEW

(SBO:NEW is a placeholder for the real id, not yet assigned. Nick will mail you the ids when they are available).

The change of the table is not an emergency since at the moment, the specification does not allow to store qualitative parameter anyway (the value of a parameter is a double. So 'red', 'blue' and 'green' are not proper values for a parameter 'colour'. They have to be encoded numerically).

Best regards,

-- Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,

Reported by: mhucka

Original Ticket: sbml/sbml-specifications//226

sbmlsecretary commented 12 years ago

I am accepting this issue as valid.

Original comment by: ccmyers

sbmlsecretary commented 12 years ago

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

Original comment by: sarahkeating

sbmlsecretary commented 11 years ago

Original comment by: lenov

sbmlsecretary commented 10 years ago

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

On the basis of L3v1 already having made SBO updates, and the fact that we need to update SBO again for that, I'm setting this to 'accepted', and putting it on the L2v4 errata list (if it's not already there).

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

Adding L3v1 to this, as these SBO changes affect that, too. There's zero reason to update L2v4 and not update L3v1 at the same time.

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

This has now been changed in SVN for both L3v2 and L2v5, and will be incorporated into both forthcoming specifications.

Original comment by: luciansmith