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Remove SBML local parameter mapping #663

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Remove SBML local parameter mapping #663

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Remove SBML local parameter mapping
dweindl Jan 26, 2026
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dweindl Jan 26, 2026
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10 changes: 5 additions & 5 deletions doc/v2/documentation_data_format.rst
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Expand Up @@ -817,8 +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
(e.g., SBML *local* parameters that are not mapped in the mapping table)
- 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:

Expand Down Expand Up @@ -1059,9 +1061,7 @@ 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
Expand Down