add ModifierElement and extend DataTypes

Author: JR-1991

specifications/v2.md

@@ -16,6 +16,14 @@ EnzymeML is a data exchange format that supports the comprehensive documentation
 
 The EnzymeMLDocument is the root object that serves as a container for all components of an enzymatic experiment. It includes essential metadata about the document itself, such as its title and creation/modification dates, as well as references to related publications and databases. Additionally, it contains comprehensive information about the experimental setup, including reaction vessels, proteins, complexes, small molecules, reactions, measurements, equations, and parameters.
 
+- **version**
+  - Type: string
+  - Description: The version of the EnzymeML Document.
+  - Pattern: "^(\\d+)\\.\\d+$"
+  - Default: "2.0"
+- description
+  - Type: string
+  - Description: Description of the EnzymeML Document.
 - **name**
   - Type: string
   - Description: Title of the EnzymeML Document.
@@ -209,6 +217,9 @@ The SmallMolecule object represents small chemical compounds that participate in
 - inchikey
   - Type: string
   - Description: Hashed International Chemical Identifier (InChIKey) encoding of the small molecule.
+- synonymous_names
+  - Type: string[]
+  - Description: List of synonymous names for the small molecule.
 - references
   - Type: Identifier[]
   - Description: List of references to publications, database entries, etc. that describe or reference the small molecule.
@@ -243,7 +254,7 @@ The Reaction object represents a chemical or enzymatic reaction and holds the di
   - Type: ReactionElement[]
   - Description: List of products that are part of the reaction.
 - modifiers
-  - Type: Identifier[]
+  - Type: ModifierElement[]
   - Description: List of reaction elements that are not part of the reaction but influence it.
 
 ### ReactionElement
@@ -260,6 +271,18 @@ This object is part of the `Reaction` object and describes a species (SmallMolec
   - Default: 1.0
   - ExclusiveMinimum: 0
 
+### ModifierElement
+
+The ModifierElement object represents a species that is not part of the reaction but influences it.
+
+- **species_id**
+  - Type: Identifier
+  - Description: Internal identifier to either a protein or reactant defined in the EnzymeML Document.
+  - Term: schema:identifier
+- **role**
+  - Type: ModifierRole
+  - Description: Role of the modifier in the reaction.
+
 ## Modelling
 
 The Modelling section contains objects that describe the mathematical models used to analyze the experimental data. This includes equations, variables, and parameters that define the kinetic models used to describe the reactions. There are multiple types of equations that can be used to describe a reaction. In the following is a table that describes the different types of equations and their usage:
@@ -411,6 +434,20 @@ This object describes a single entity of a measurement, which corresponds to one
 
 ## Enumerations
 
+### ModifierRole
+
+These values are used to determine the role of a modifier in a reaction.
+
+```python
+SOLVENT = "solvent"
+BIOCATALYST = "biocatalyst"
+CATALYST = "catalyst"
+BUFFER = "buffer"
+ADDITIVE = "additive"
+INHIBITOR = "inhibitor"
+ACTIVATOR = "activator"
+```
+
 ### EquationType
 
 These values are used to determine the type of equation. ODE equations describe the rate of change of species over time, assignment equations define algebraic relationships between variables, initial assignments set starting values, and rate laws define reaction kinetics.
@@ -433,5 +470,7 @@ CONVERSION = "conversion"
 PEAK_AREA = "peakarea"
 TRANSMITTANCE = "transmittance"
 FLUORESCENCE = "fluorescence"
-AMOUNT = "amount'
+AMOUNT = "amount"
+YIELD = "yield"
+TURNOVER = "turnover"
 ```