From 8c5c6cfb04492138dc734361c128a26f143fe64d Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 26 Jan 2026 12:32:22 +0100 Subject: [PATCH 1/2] Remove SBML local parameter mapping As discussed during a recent PEtab editor meeting, we don't want to support SBML local parameters via the mapping table, as this just introduces unnecessary complexity. Instead of aliasing local parameters via the PEtab mapping table, they should just be implemented as global parameters in the SBML model to begin with. --- doc/v2/documentation_data_format.rst | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/doc/v2/documentation_data_format.rst b/doc/v2/documentation_data_format.rst index 699d2cae..660104e0 100644 --- a/doc/v2/documentation_data_format.rst +++ b/doc/v2/documentation_data_format.rst @@ -818,7 +818,6 @@ and *must not* include: - "Parameters" that are not *constant* entities (e.g., in an SBML model, the targets of *AssignmentRules* or *EventAssignments*) - Any parameters that do not have valid PEtab IDs - (e.g., SBML *local* parameters that are not mapped in the mapping table) it *may* include: @@ -1059,9 +1058,7 @@ Detailed field description not present in any model. This does not have to be a valid PEtab identifier. Rows with empty ``modelEntityId`` serve as annotations only. - For example, in SBML, local parameters may be referenced as - ``$reactionId.$localParameterId``, which are not valid PEtab IDs as they - contain a ``.`` character. Similarly, this table may be used to reference + This table may be used, for example, to reference specific species in a BNGL model that may contain many unsupported characters such as ``,``, ``(`` or ``.``. However, please note that IDs must exactly match the species names in the BNGL-generated network file, and no From 41a80b7b791001fac7597f957434bc9e61a85249 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 26 Jan 2026 18:52:25 +0100 Subject: [PATCH 2/2] .. --- doc/v2/documentation_data_format.rst | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/doc/v2/documentation_data_format.rst b/doc/v2/documentation_data_format.rst index 660104e0..1005c893 100644 --- a/doc/v2/documentation_data_format.rst +++ b/doc/v2/documentation_data_format.rst @@ -817,7 +817,10 @@ and *must not* include: - Parameters occurring as ``targetId`` in the *condition table* - "Parameters" that are not *constant* entities (e.g., in an SBML model, the targets of *AssignmentRules* or *EventAssignments*) -- Any parameters that do not have valid PEtab IDs +- Any parameters that do not have valid PEtab IDs. + (For example, *local parameters* in an SBML model, which are not globally + accessible, cannot be used in PEtab; if they are to be estimated or + changed, they must be converted to global parameters first.) it *may* include: