#90 update SBO term PHYSICAL_STIMULATION

[Piero Dalle Pezze]

In Alias2SBO.cfg, the term PHYSICAL_STIMULATION is 21, but it should possibly be replaced with the number 459 (see http://www.ebi.ac.uk/sbo/main/display?open=-460&nodeId=460).

[Andreas Dräger]

Thanks for reporting this issue. Could you please tell a bit more how you run into this problem? Originally, the file Alias2SBO.cfg was used as a mapping between CellDesigner's graphical display and SBO terms. Some of CellDesigner's shapes etc. have no direct correspondence in the SBO. This is also reflected by the comments in the file Alias2SBO.cfg.

Now, if we change PHYSICAL_STIMULATION from SBO term 21 to 459, there would be a clash with TRANSLATIONAL_ACTIVATION. What we could do is, swap the SBO terms of both that are both not directly reflected in the SBO. However, tools that already rely on this scheme might experience different behavior.

Would this solve the problem or cause more problems?

[Piero Dalle Pezze]

We are working out a solution for a bug we found on a converter in SBFC and
we found that issue while checking the SBO term. We haven't yet solved the
bug though, so maybe there is an alternative without changing that term
number.

On 10 November 2015 at 08:29, "Andreas Dräger" <andreas-draeger@users.sf.net

wrote:

Thanks for reporting this issue. Could you please tell a bit more how you
run into this problem? Originally, the file Alias2SBO.cfg was used as a
mapping between CellDesigner's graphical display and SBO terms. Some of
CellDesigner's shapes etc. have no direct correspondence in the SBO. This
is also reflected by the comments in the file Alias2SBO.cfg.

Now, if we change PHYSICAL_STIMULATION from SBO term 21 to 459, there
would be a clash with TRANSLATIONAL_ACTIVATION. What we could do is, swap
the SBO terms of both that are both not directly reflected in the SBO.
However, tools that already rely on this scheme might experience different
behavior.

Would this solve the problem or cause more problems?

• [bugs:#90] http://sourceforge.net/p/jsbml/bugs/90/ update SBO term
  PHYSICAL_STIMULATION*

Status: unread
Group: jsbml 1.1
Created: Fri Oct 23, 2015 10:20 AM UTC by Piero Dalle Pezze
Last Updated: Fri Oct 23, 2015 10:20 AM UTC
Owner: nobody

In Alias2SBO.cfg, the term PHYSICAL_STIMULATION is 21, but it should
possibly be replaced with the number 459 (see
http://www.ebi.ac.uk/sbo/main/display?open=-460&nodeId=460).

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