#226 Need update for changes in SBO

[Michael Hucka]

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,

[Chris Myers]

I am accepting this issue as valid.

[Sarah Keating]

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

[Lucian Smith]

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).

[Lucian Smith]

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.

[Lucian Smith]

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