diff --git a/doc/v2/documentation_data_format.rst b/doc/v2/documentation_data_format.rst index 699d2cae..1005c893 100644 --- a/doc/v2/documentation_data_format.rst +++ b/doc/v2/documentation_data_format.rst @@ -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: @@ -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