GeneProductRef¶
The leaf of an association: one gene product the reaction depends on.
A gene product reference is where an association names a gene. It carries the identifier of a gene product of the model and nothing else, so it is the place at which the tree of a reaction meets the list of the genes.
The report makes it an element of its own because the reference is where the file writes the identifier: the link to the gene product starts here, and the same gene may be named by several references of one reaction.
Attributes¶
| attribute | type | required | meaning | specification |
|---|---|---|---|---|
| geneProduct | SIdRef |
required | the gene product this leaf of the association names | fbc v3 3.11 |
Every element of a model also carries the common attributes of SBase.
geneProduct
The attribute is required and names a gene product of the same model. The report shows the identifier the reference writes and links the gene product behind it.
2020904(error): The attribute 'fbc:geneProduct' on a <GeneProductRef> must be of the data type 'SIdRef'.2020908(error): The attribute 'fbc:geneProduct' on a <GeneProductRef> if set, must refer to 'id' of a <GeneProduct> in the <Model>.
Validation rules¶
2020901(error): A <GeneProductRef> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a <GeneProductRef>.2020902(error): A <GeneProductRef> object may have the optional SBML Level 3 Core subobjects for notes and annotations. No other elements from the SBML Level 3 Core namespace are permitted on a <GeneProductRef>.2020903(error): A <GeneProductRef> object must have the required attribute 'fbc:geneProduct' and may have the optional attribute 'fbc:id'. No other attributes from the SBML Level 3 Flux Balance Constraints namespace are permitted on a <> object.
Related elements¶
- GeneProduct: a gene or one of its products which the reactions of the model depend on
- GeneProductAssociation: the genes a reaction needs, as the tree of operators over them
- And: the associations below it are all needed at once
- Or: one of the associations below it suffices
Specification¶
SBML Level 3 Package: Flux Balance Constraints, Version 3 Release 1, Section 3.11 (Olivier and Bergmann, COMBINE specification).