#123 Perturbing agent description

[HMi]

A recapture of a discussion with Nicolas about the description of perturbing agent in PD spec.

Huaiyu Mi wrote:
> >
> > perturbing agent in PD is an EPN, which means it is a continuent in
> > ontological term. The description in section 2.4.8 sounds like it can
> > represent processes, which are occurrents.

I see. The definition is:

"Biochemical networks can be affected by external infl uences. Those infl
uences can be well-defined physical perturbing agents, such as a light
pulse or a change in temperature; they can also be more complex and not
well-defined phenomena, for instance a biological process, an experimental
setup, or a mutation. For these situations, SBGN provides the perturbing
agent glyph. It is an EPN, and represents the amount to perturbing agent
applied to a process."

Should-we change it to something like:

"Biochemical networks can be affected by external influences. Those
influences can be the effect of well-defined physical perturbing agents,
such as a light pulse or a change in temperature; they can also be more
complex and not well-defined phenomena, for instance the outcome of a
biological process, an experimental setup, or a mutation. For these
situations, SBGN provides the perturbing agent glyph. It is an EPN, and
represents the amount to perturbing agent applied to a process."

?

[Nicolas Le Novère]

I believe your suggestion is fine.

[Stuart Moodie]

Added to spec.