Core

momapy.sbml.core

Core classes for SBML (Systems Biology Markup Language) maps.

This module provides dataclasses representing SBML model elements including compartments, species, reactions, and annotations using BioModels qualifiers.

Examples:

from momapy.sbml.core import Compartment, Species, Model
compartment = Compartment(name="cytosol")
species = Species(name="glucose", compartment=compartment)
model = Model(name="glycolysis", compartments={compartment}, species={species})

Classes:

Name	Description
`BQBiol`	BioModels.net biology qualifiers.
`BQModel`	BioModels.net model qualifiers.
`BiomodelQualifier`	Abstract base class for BioModels.net qualifiers.
`Compartment`	SBML compartment representing a bounded region.
`ModifierSpeciesReference`	Reference to a species that modifies a reaction.
`RDFAnnotation`	RDF annotation linking model elements to external resources.
`Reaction`	SBML reaction representing a biochemical transformation.
`SBML`	Root container for SBML documents.
`SBMLModel`	SBML model container.
`SBOTerm`	SBO (Systems Biology Ontology) term annotation.
`SBase`	Abstract base class for all SBML elements.
`SimpleSpeciesReference`	Base class for species references in reactions.
`Species`	SBML species representing a pool of entities.
`SpeciesReference`	Reference to a reactant or product species.

BQBiol

Bases: BiomodelQualifier

BioModels.net biology qualifiers.

These qualifiers describe the relationship between biological elements and external resources.

Attributes:

Name	Type	Description
`ENCODES`		The element encodes the resource.
`HAS_PART`		The element has the resource as a part.
`HAS_PROPERTY`		The element has the resource as a property.
`HAS_VERSION`		The element has the resource as a version.
`IS`		The element is exactly the resource.
`IS_DESCRIBED_BY`		The resource describes the element.
`IS_ENCODED_BY`		The element is encoded by the resource.
`IS_HOMOLOG_TO`		The element is homologous to the resource.
`IS_PART_OF`		The element is part of the resource.
`IS_PROPERTY_OF`		The element is a property of the resource.
`IS_VERSION_OF`		The element is a version of the resource.
`OCCURS_IN`		The process occurs in the resource.
`HAS_TAXON`		The element has the resource as a taxon.

BQModel

Bases: BiomodelQualifier

BioModels.net model qualifiers.

These qualifiers describe the relationship between the model and external resources such as publications or databases.

Attributes:

Name	Type	Description
`HAS_INSTANCE`		The resource is an instance of this model.
`IS`		The resource is exactly this model.
`IS_DERIVED_FROM`		The model is derived from the resource.
`IS_DESCRIBED_BY`		The resource describes the model.
`IS_INSTANCE_OF`		The model is an instance of the resource.

BiomodelQualifier

Bases: Enum

Abstract base class for BioModels.net qualifiers.

BioModels qualifiers are used in RDF annotations to describe the relationship between model elements and external resources.

Compartment `dataclass`

Compartment(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, outside: Optional[ForwardRef(Compartment, module=core)] = None)

Bases: SBase

SBML compartment representing a bounded region.

A compartment defines a container where species are located.

Attributes:

Name	Type	Description
`outside`	`Optional[ForwardRef(Compartment, module=core)]`	Optional outer compartment for hierarchical nesting.

Examples:

cytosol = Compartment(name="cytosol")
nucleus = Compartment(name="nucleus", outside=cytosol)

ModifierSpeciesReference `dataclass`

ModifierSpeciesReference(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species)

Bases: SimpleSpeciesReference

Reference to a species that modifies a reaction.

Modifier species influence reaction kinetics without being consumed or produced (e.g., catalysts, inhibitors).

RDFAnnotation `dataclass`

RDFAnnotation(*, id_: str = make_uuid4_as_str(), qualifier: BiomodelQualifier, resources: frozenset[str] = frozenset())

Bases: ModelElement

RDF annotation linking model elements to external resources.

Attributes:

Name	Type	Description
`qualifier`	`BiomodelQualifier`	The BioModels qualifier describing the relationship.
`resources`	`frozenset[str]`	Set of resource URIs linked to this annotation.

Examples:

from momapy.sbml.core import RDFAnnotation, BQBiol
annotation = RDFAnnotation(
    qualifier=BQBiol.IS,
    resources={"https://identifiers.org/chebi:4167"}
)

Reaction `dataclass`

Reaction(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[SpeciesReference] = frozenset(), products: frozenset[SpeciesReference] = frozenset(), modifiers: frozenset[ModifierSpeciesReference] = frozenset())

Bases: SBase

SBML reaction representing a biochemical transformation.

Reactions describe the conversion of reactants into products, potentially influenced by modifiers.

Attributes:

Name	Type	Description
`reversible`	`bool`	Whether the reaction can proceed in both directions.
`compartment`	`Compartment \| None`	Optional compartment where the reaction occurs.
`reactants`	`frozenset[SpeciesReference]`	Set of species consumed by the reaction.
`products`	`frozenset[SpeciesReference]`	Set of species produced by the reaction.
`modifiers`	`frozenset[ModifierSpeciesReference]`	Set of species that modify the reaction.

Examples:

reaction = Reaction(
    name="hexokinase",
    reversible=False,
    reactants={glucose_ref, atp_ref},
    products={g6p_ref, adp_ref}
)

SBML `dataclass`

SBML(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, xmlns: str = 'http://www.sbml.org/sbml/level3/version2/core', level: int = 3, version: int = 2, model: SBMLModel | None = None)

Bases: SBase

Root container for SBML documents.

Represents the top-level SBML element containing model metadata and the model definition.

Attributes:

Name	Type	Description
`xmlns`	`str`	XML namespace for the SBML version.
`level`	`int`	SBML level (version).
`version`	`int`	SBML version within the level.
`model`	`SBMLModel \| None`	The model contained in this SBML document.

Examples:

sbml = SBML(
    model=SBMLModel(name="glycolysis"),
    level=3,
    version=2
)

SBMLModel `dataclass`

SBMLModel(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartments: frozenset[Compartment] = frozenset(), species: frozenset[Species] = frozenset(), reactions: frozenset[Reaction] = frozenset())

Bases: SBase, Model

SBML model container.

Models aggregate compartments, species, and reactions into a complete biological system description.

Attributes:

Name	Type	Description
`compartments`	`frozenset[Compartment]`	Set of compartments in the model.
`species`	`frozenset[Species]`	Set of species in the model.
`reactions`	`frozenset[Reaction]`	Set of reactions in the model.

Examples:

model = SBMLModel(
    name="glycolysis",
    compartments={cytosol},
    species={glucose, atp, g6p},
    reactions={hexokinase}
)

SBOTerm `dataclass`

SBOTerm(*, id_: str = make_uuid4_as_str())

Bases: ModelElement

SBO (Systems Biology Ontology) term annotation.

SBO terms provide standardized vocabulary for describing model elements.

SBase `dataclass`

SBase(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None)

Bases: ModelElement

Abstract base class for all SBML elements.

SBase provides common attributes shared by all SBML components.

Attributes:

Name	Type	Description
`name`	`str \| None`	Human-readable name of the element.
`sbo_term`	`SBOTerm \| None`	Optional SBO term for semantic annotation.
`metaid`	`str \| None`	Optional metadata identifier for RDF annotations.

SimpleSpeciesReference `dataclass`

SimpleSpeciesReference(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species)

Bases: SBase

Base class for species references in reactions.

Attributes:

Name	Type	Description
`referred_species`	`Species`	The species being referenced.

Species `dataclass`

Species(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None)

Bases: SBase

SBML species representing a pool of entities.

A species represents a population of chemically identical entities (molecules, ions, etc.) located in a specific compartment.

Attributes:

Name	Type	Description
`compartment`	`Compartment \| None`	The compartment containing this species.

Examples:

compartment = Compartment(name="cytosol")
glucose = Species(name="glucose", compartment=compartment)

SpeciesReference `dataclass`

SpeciesReference(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species, stoichiometry: float | None = None)

Bases: SimpleSpeciesReference

Reference to a reactant or product species.

Attributes:

Name	Type	Description
`stoichiometry`	`float \| None`	Optional stoichiometric coefficient.

Examples:

species = Species(name="ATP", compartment=compartment)
ref = SpeciesReference(referred_species=species, stoichiometry=2)

Core

momapy.sbml.core

BQBiol

BQModel

BiomodelQualifier

Compartment dataclass

ModifierSpeciesReference dataclass

RDFAnnotation dataclass

Reaction dataclass

SBML dataclass

SBMLModel dataclass

SBOTerm dataclass

SBase dataclass

SimpleSpeciesReference dataclass

Species dataclass

SpeciesReference dataclass

Compartment `dataclass`

ModifierSpeciesReference `dataclass`

RDFAnnotation `dataclass`

Reaction `dataclass`

SBML `dataclass`

SBMLModel `dataclass`

SBOTerm `dataclass`

SBase `dataclass`

SimpleSpeciesReference `dataclass`

Species `dataclass`

SpeciesReference `dataclass`