diff --git a/docs/model.md b/docs/model.md
index e08cff7..dc635b1 100644
--- a/docs/model.md
+++ b/docs/model.md
@@ -75,8 +75,8 @@ This page provides comprehensive information about the structure and components
## Ontologies
-- [schema](https://schema.org/)
- [OBO](http://purl.obolibrary.org/obo/)
+- [schema](https://schema.org/)
## Types
@@ -497,12 +497,7 @@ __species_id__* `string`
- The identifier for the described reactant.
-__init_conc__* `float`
-
-- Initial concentration of the measurement data. This must be the same as the first data point in the
-
-
-__conc_unit__* [`UnitDefinition`](#unitdefinition)
+__data_unit__* [`UnitDefinition`](#unitdefinition)
- SI unit of the data that was measured.
@@ -517,9 +512,14 @@ __data_type__* `string`
- Type of data that was measured (e.g. concentration)
-__prep_conc__ `float`
+__prepared__ `float`
+
+- Amount of the reactant before the measurement. This field should be used for specifying the prepared amount of a species in the reaction mix. Not to be confused with
+
+
+__initial__ `float`
-- Concentration of the reactant before the measurement. This field should be used for specifying the prepared concentration of a species in the reaction mix. Not to be confused with init_conc, specifying the concentration at the first data point from the
+- Initial amount of the measurement data. This must be the same as the first data point in the
__data__* `list[float]`
diff --git a/python/pyenzyme/dataclass_models.py b/python/pyenzyme/dataclass_models.py
index e0eab13..7001626 100644
--- a/python/pyenzyme/dataclass_models.py
+++ b/python/pyenzyme/dataclass_models.py
@@ -721,11 +721,11 @@ class Measurement:
def add_to_species_data(
self,
species_id: str,
- init_conc: float,
- conc_unit: UnitDefinition,
+ data_unit: UnitDefinition,
time_unit: UnitDefinition,
data_type: str,
- prep_conc: Optional[float] = None,
+ prepared: Optional[float] = None,
+ initial: Optional[float] = None,
data: list[float] = [],
time: list[float] = [],
is_simulated: bool = False,
@@ -733,11 +733,11 @@ def add_to_species_data(
):
params = {
"species_id": species_id,
- "init_conc": init_conc,
- "conc_unit": conc_unit,
+ "data_unit": data_unit,
"time_unit": time_unit,
"data_type": data_type,
- "prep_conc": prep_conc,
+ "prepared": prepared,
+ "initial": initial,
"data": data,
"time": time,
"is_simulated": is_simulated,
@@ -755,11 +755,13 @@ def add_to_species_data(
@dataclass
class MeasurementData:
species_id: str
- init_conc: float
- conc_unit: UnitDefinition
+ data_unit: UnitDefinition
time_unit: UnitDefinition
data_type: str
- prep_conc: Optional[float] = field(
+ prepared: Optional[float] = field(
+ default=None, metadata=config(exclude=lambda x: x is None)
+ )
+ initial: Optional[float] = field(
default=None, metadata=config(exclude=lambda x: x is None)
)
data: List[float] = field(default_factory=list)
diff --git a/python/pyenzyme/pydantic_models.py b/python/pyenzyme/pydantic_models.py
index e73eff9..9c3b412 100644
--- a/python/pyenzyme/pydantic_models.py
+++ b/python/pyenzyme/pydantic_models.py
@@ -104,8 +104,8 @@ class EnzymeMLDocument(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"name": "schema:title",
"references": {
"@id": "schema:citation",
@@ -505,8 +505,8 @@ class Creator(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"given_name": "schema:givenName",
"family_name": "schema:familyName",
"mail": "schema:email",
@@ -603,8 +603,8 @@ class Vessel(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
@@ -708,8 +708,8 @@ class Protein(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@type": "@id",
},
@@ -821,8 +821,8 @@ class Complex(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
@@ -929,8 +929,8 @@ class SmallMolecule(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
@@ -1040,8 +1040,8 @@ class Reaction(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
@@ -1168,8 +1168,8 @@ class ReactionElement(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"species_id": {
"@type": "@id",
},
@@ -1269,8 +1269,8 @@ class Equation(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"species_id": {
"@type": "@id",
},
@@ -1430,8 +1430,8 @@ class Parameter(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
@@ -1533,8 +1533,8 @@ class Measurement(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
@@ -1625,11 +1625,11 @@ def add_type_term(
def add_to_species_data(
self,
species_id: str,
- init_conc: float,
- conc_unit: UnitDefinition,
+ data_unit: UnitDefinition,
time_unit: UnitDefinition,
data_type: str,
- prep_conc: Optional[float] = None,
+ prepared: Optional[float] = None,
+ initial: Optional[float] = None,
data: list[float] = [],
time: list[float] = [],
is_simulated: bool = False,
@@ -1637,11 +1637,11 @@ def add_to_species_data(
):
params = {
"species_id": species_id,
- "init_conc": init_conc,
- "conc_unit": conc_unit,
+ "data_unit": data_unit,
"time_unit": time_unit,
"data_type": data_type,
- "prep_conc": prep_conc,
+ "prepared": prepared,
+ "initial": initial,
"data": data,
"time": time,
"is_simulated": is_simulated,
@@ -1661,11 +1661,11 @@ class MeasurementData(BaseModel):
) # type: ignore
species_id: str
- init_conc: float
- conc_unit: UnitDefinition
+ data_unit: UnitDefinition
time_unit: UnitDefinition
data_type: str
- prep_conc: Optional[float] = Field(default=None)
+ prepared: Optional[float] = Field(default=None)
+ initial: Optional[float] = Field(default=None)
data: list[float] = Field(default_factory=list)
time: list[float] = Field(default_factory=list)
is_simulated: bool = False
@@ -1685,8 +1685,8 @@ class MeasurementData(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"species_id": {
"@type": "@id",
},
@@ -1786,8 +1786,8 @@ class UnitDefinition(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
},
)
@@ -1916,8 +1916,8 @@ class BaseUnit(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
},
)
@@ -2011,8 +2011,8 @@ class EqVariable(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@type": "@id",
},
@@ -2110,8 +2110,8 @@ class EqParameter(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
- "schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
+ "schema": "https://schema.org/",
"id": {
"@type": "@id",
},
diff --git a/schemes/enzymeml.json b/schemes/enzymeml.json
index afbc7fc..2fa9d0e 100644
--- a/schemes/enzymeml.json
+++ b/schemes/enzymeml.json
@@ -82,62 +82,6 @@
},
"description": "This is the root object that composes all objects found in an EnzymeML document. It also includes general metadata such as the name of the document, when it was created/modified, and references to publications, databases, and arbitrary links to the web.",
"definitions": {
- "Complex": {
- "title": "Complex",
- "type": "object",
- "properties": {
- "id": {
- "title": "id",
- "description": "Unique identifier of the complex.",
- "term": "schema:identifier",
- "type": "string"
- },
- "name": {
- "title": "name",
- "term": "schema:name",
- "type": "string"
- },
- "constant": {
- "title": "constant",
- "type": "boolean"
- },
- "participants": {
- "title": "participants",
- "description": "Array of IDs the complex contains",
- "type": "array",
- "items": {
- "type": "string"
- }
- }
- },
- "description": "This object describes complexes made of reactants and/or proteins that were used or produced in the course of the experiment."
- },
- "Creator": {
- "title": "Creator",
- "type": "object",
- "properties": {
- "given_name": {
- "title": "given_name",
- "description": "Given name of the author or contributor.",
- "term": "schema:givenName",
- "type": "string"
- },
- "family_name": {
- "title": "family_name",
- "description": "Family name of the author or contributor.",
- "term": "schema:familyName",
- "type": "string"
- },
- "mail": {
- "title": "mail",
- "description": "Email address of the author or contributor.",
- "term": "schema:email",
- "type": "string"
- }
- },
- "description": "The creator object contains all information about authors that contributed to the resulting document.",
- "term": "schema:person"
- },
"Measurement": {
"title": "Measurement",
"type": "object",
@@ -218,6 +162,62 @@
},
"description": "This object describes an ordinary differential equation that is part of the kinetic model."
},
+ "Complex": {
+ "title": "Complex",
+ "type": "object",
+ "properties": {
+ "id": {
+ "title": "id",
+ "description": "Unique identifier of the complex.",
+ "term": "schema:identifier",
+ "type": "string"
+ },
+ "name": {
+ "title": "name",
+ "term": "schema:name",
+ "type": "string"
+ },
+ "constant": {
+ "title": "constant",
+ "type": "boolean"
+ },
+ "participants": {
+ "title": "participants",
+ "description": "Array of IDs the complex contains",
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ }
+ },
+ "description": "This object describes complexes made of reactants and/or proteins that were used or produced in the course of the experiment."
+ },
+ "Creator": {
+ "title": "Creator",
+ "type": "object",
+ "properties": {
+ "given_name": {
+ "title": "given_name",
+ "description": "Given name of the author or contributor.",
+ "term": "schema:givenName",
+ "type": "string"
+ },
+ "family_name": {
+ "title": "family_name",
+ "description": "Family name of the author or contributor.",
+ "term": "schema:familyName",
+ "type": "string"
+ },
+ "mail": {
+ "title": "mail",
+ "description": "Email address of the author or contributor.",
+ "term": "schema:email",
+ "type": "string"
+ }
+ },
+ "description": "The creator object contains all information about authors that contributed to the resulting document.",
+ "term": "schema:person"
+ },
"SmallMolecule": {
"title": "SmallMolecule",
"type": "object",
@@ -270,6 +270,46 @@
},
"description": "This object describes the reactants that were used or produced in the course of the experiment."
},
+ "Reaction": {
+ "title": "Reaction",
+ "type": "object",
+ "properties": {
+ "id": {
+ "title": "id",
+ "description": "Unique identifier of the reaction.",
+ "term": "schema:identifier",
+ "type": "string"
+ },
+ "name": {
+ "title": "name",
+ "description": "Name of the reaction.",
+ "type": "string"
+ },
+ "reversible": {
+ "title": "reversible",
+ "description": "Whether the reaction is reversible or irreversible",
+ "type": "boolean"
+ },
+ "kinetic_law": {
+ "$ref": "#/definitions/Equation"
+ },
+ "species": {
+ "type": "array",
+ "items": {
+ "$ref": "#/definitions/ReactionElement"
+ }
+ },
+ "modifiers": {
+ "title": "modifiers",
+ "description": "List of reaction elements that are not part of the reaction but influence it.",
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ }
+ },
+ "description": "This object describes a chemical or enzymatic reaction that was investigated in the course of the experiment. All species used within this object need to be part of the data model."
+ },
"Protein": {
"title": "Protein",
"type": "object",
@@ -363,46 +403,6 @@
},
"description": "This object describes vessels in which the experiment has been carried out. These can include any type of vessel used in biocatalytic experiments.",
"term": "OBO:OBI_0400081"
- },
- "Reaction": {
- "title": "Reaction",
- "type": "object",
- "properties": {
- "id": {
- "title": "id",
- "description": "Unique identifier of the reaction.",
- "term": "schema:identifier",
- "type": "string"
- },
- "name": {
- "title": "name",
- "description": "Name of the reaction.",
- "type": "string"
- },
- "reversible": {
- "title": "reversible",
- "description": "Whether the reaction is reversible or irreversible",
- "type": "boolean"
- },
- "kinetic_law": {
- "$ref": "#/definitions/Equation"
- },
- "species": {
- "type": "array",
- "items": {
- "$ref": "#/definitions/ReactionElement"
- }
- },
- "modifiers": {
- "title": "modifiers",
- "description": "List of reaction elements that are not part of the reaction but influence it.",
- "type": "array",
- "items": {
- "type": "string"
- }
- }
- },
- "description": "This object describes a chemical or enzymatic reaction that was investigated in the course of the experiment. All species used within this object need to be part of the data model."
}
}
}
\ No newline at end of file
diff --git a/schemes/enzymeml.shex b/schemes/enzymeml.shex
index abe70a4..814188c 100644
--- a/schemes/enzymeml.shex
+++ b/schemes/enzymeml.shex
@@ -1,7 +1,7 @@
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX enzml: <http://www.enzymeml.org/v2/>
-PREFIX schema: <https://schema.org/>
PREFIX OBO: <http://purl.obolibrary.org/obo/>
+PREFIX schema: <https://schema.org/>
enzml:EnzymeMLDocument {
schema:title xsd:string {
diff --git a/schemes/enzymeml.xsd b/schemes/enzymeml.xsd
index 18dd692..62afc51 100644
--- a/schemes/enzymeml.xsd
+++ b/schemes/enzymeml.xsd
@@ -616,14 +616,7 @@
</xs:documentation>
</xs:annotation>
</xs:element>
- <xs:element name="init_conc" type="xs:float">
- <xs:annotation>
- <xs:documentation>
- Initial concentration of the measurement data. This must be the same as the first data point in the
- </xs:documentation>
- </xs:annotation>
- </xs:element>
- <xs:element name="conc_unit" type="UnitDefinitionType">
+ <xs:element name="data_unit" type="UnitDefinitionType">
<xs:annotation>
<xs:documentation>
SI unit of the data that was measured.
@@ -644,10 +637,17 @@
</xs:documentation>
</xs:annotation>
</xs:element>
- <xs:element name="prep_conc" type="xs:float">
+ <xs:element name="prepared" type="xs:float">
+ <xs:annotation>
+ <xs:documentation>
+ Amount of the reactant before the measurement. This field should be used for specifying the prepared amount of a species in the reaction mix. Not to be confused with
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="initial" type="xs:float">
<xs:annotation>
<xs:documentation>
- Concentration of the reactant before the measurement. This field should be used for specifying the prepared concentration of a species in the reaction mix. Not to be confused with init_conc, specifying the concentration at the first data point from the
+ Initial amount of the measurement data. This must be the same as the first data point in the
</xs:documentation>
</xs:annotation>
</xs:element>
diff --git a/typescript/src/index.ts b/typescript/src/index.ts
index 50f686c..4dc27de 100644
--- a/typescript/src/index.ts
+++ b/typescript/src/index.ts
@@ -390,27 +390,25 @@ export const MeasurementCodec = D.lazy("Measurement", () => D.struct({
time course data.
* @param species_id - The identifier for the described reactant.
- * @param init_conc - Initial concentration of the measurement data. This must be the same
- as the first data point in the
- * @param conc_unit - SI unit of the data that was measured.
+ * @param data_unit - SI unit of the data that was measured.
* @param time_unit - Time unit of the replicate.
* @param data_type - Type of data that was measured (e.g. concentration)
- * @param prep_conc - Concentration of the reactant before the measurement. This field
- should be used for specifying the prepared concentration
- of a species in the reaction mix. Not to be confused with
- init_conc, specifying the concentration at the first data
- point from the
+ * @param prepared - Amount of the reactant before the measurement. This field should be
+ used for specifying the prepared amount of a species in
+ the reaction mix. Not to be confused with
+ * @param initial - Initial amount of the measurement data. This must be the same as the
+ first data point in the
* @param data - Data that was measured.
* @param time - Time steps of the replicate.
* @param is_simulated - Whether or not the data has been generated by simulation.
**/
export interface MeasurementData extends JsonLd {
species_id: string;
- init_conc: number;
- conc_unit: UnitDefinition;
+ data_unit: UnitDefinition;
time_unit: UnitDefinition;
data_type: string;
- prep_conc?: number | null;
+ prepared?: number | null;
+ initial?: number | null;
data: number[];
time: number[];
is_simulated: boolean;
@@ -418,11 +416,11 @@ export interface MeasurementData extends JsonLd {
export const MeasurementDataCodec = D.lazy("MeasurementData", () => D.struct({
species_id: D.string,
- init_conc: D.number,
- conc_unit: UnitDefinitionCodec,
+ data_unit: UnitDefinitionCodec,
time_unit: UnitDefinitionCodec,
data_type: D.string,
- prep_conc: D.nullable(D.number),
+ prepared: D.nullable(D.number),
+ initial: D.nullable(D.number),
data: D.array(D.number),
time: D.array(D.number),
is_simulated: D.boolean,