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Allow using observable IDs in observableFormula and noiseFormula
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Following up on #543 and the discussion during the last PEtab editor meeting:
There was general consent to allow using observableIDs in the `noiseFormula` column in the observables table.

What was not discussed explicitly:
* Should all observable IDs be allowed, or only the current one?
* If so, should it be allowed to use observable IDs inside `observableFormula`?

CC @PEtab-dev/petab-editors

Closes ##543
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dweindl committed Jun 27, 2023
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10 changes: 8 additions & 2 deletions doc/documentation_data_format.rst
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Expand Up @@ -340,7 +340,9 @@ Detailed field description
Observation function as plain text formula expression.
May contain any symbol defined in the SBML model (including model time ``time``)
or parameter table. In the simplest case just an SBML species ID
or an ``AssignmentRule`` target.
or an ``AssignmentRule`` target. Additionally, any observable ID
introduced in the observable table may be referenced, but circular definitions
must be avoided.

May introduce new parameters of the form ``observableParameter${n}_${observableId}``,
which are overridden by ``observableParameters`` in the measurement table
Expand All @@ -362,7 +364,11 @@ Detailed field description
observable.

Alternatively, some formula expression can be provided to specify
more complex noise models. A noise model which accounts for relative and
more complex noise models. The formula may reference any uniquely identifiable
model entity with PEtab-compatible identifier or any observable ID
specified in the observable table.

A noise model which accounts for relative and
absolute contributions could, e.g., be defined as::

noiseParameter1_observable_pErk + noiseParameter2_observable_pErk*pErk
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