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.

Example

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.
Model	SBML model container.
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.
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.

Example

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

Model dataclass

Model(*, 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.

Example

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

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.

Example

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.

Example

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: Model | 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	Model | None	The model contained in this SBML document.

Example

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

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.

Example

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: int | None = None)

Bases: SimpleSpeciesReference

Reference to a reactant or product species.

Attributes:

Name	Type	Description
stoichiometry	int | None	Optional stoichiometric coefficient.

Example

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