From 1ac762319c2c6dd702f8a620b1cdfedb119c5e99 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Tue, 27 Jun 2023 12:00:47 +0200 Subject: [PATCH 1/2] Allow using observable IDs in `observableFormula` and `noiseFormula` 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 #https://github.com/PEtab-dev/PEtab/issues/543 --- doc/documentation_data_format.rst | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/doc/documentation_data_format.rst b/doc/documentation_data_format.rst index 64bf5a39..cfd9298a 100644 --- a/doc/documentation_data_format.rst +++ b/doc/documentation_data_format.rst @@ -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 @@ -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 From 05a374bf87d55d1439f90a473de24c4f5ff9ba9d Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 26 Jun 2024 17:24:50 +0200 Subject: [PATCH 2/2] Update doc/documentation_data_format.rst --- doc/documentation_data_format.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/documentation_data_format.rst b/doc/documentation_data_format.rst index 8cdfee13..f4d4272c 100644 --- a/doc/documentation_data_format.rst +++ b/doc/documentation_data_format.rst @@ -371,7 +371,7 @@ Detailed field description A noise model which accounts for relative and absolute contributions could, e.g., be defined as:: - noiseParameter1_observable_pErk + noiseParameter2_observable_pErk*pErk + noiseParameter1_observable_pErk + noiseParameter2_observable_pErk * observable_pErk with ``noiseParameter1_observable_pErk`` denoting the absolute and ``noiseParameter2_observable_pErk`` the relative contribution for the