Biochemical Space

Rule

Rule is reaction with generalised components. Components of a rule, also called entities, may refer to more than one entity of a reaction. This link forms a hierarchy of entities. Therefore the reaction can be seen as a special case of the rule. This approach is so-called rule-based modelling.

Attributes of a rule:

1. Name - unique identifier of the rule
2. Equation - expression of the rule *
3. Modifier - set of entities which are mandatory in order to apply the rule
4. Classification - short description of general functionality of the rule
5. Description - detailed characterization of the rule
6. Annotation - links to databases with appropriate annotations *
7. Organisms - set of organisms where the rule might occur *
8. Notes - additional information

* mandatory (cannot be empty)

Moreover, rule detail provides:

• explicit enumeration of substrates and products,
• classification of the rule in process hierarchy,
• schematical visualisation.