stonpy.model module

class stonpy.model.OntologyAF(value)

Bases: Enum

The ontology for AF

ACTIVITY = {'BIOLOGICAL_ACTIVITY', 'PHENOTYPE'}

ARC = {'EQUIVALENCE_ARC', 'LOGIC_ARC', 'NECESSARY_STIMULATION', 'NEGATIVE_INFLUENCE', 'POSITIVE_INFLUENCE', 'UNKNOWN_INFLUENCE'}

AUXILLIARY_UNIT = {'TERMINAL', 'UNIT_OF_INFORMATION'}

GLYPH = {'AND', 'BIOLOGICAL_ACTIVITY', 'COMPARTMENT', 'DELAY', 'NOT', 'OR', 'PHENOTYPE', 'SUBMAP', 'TAG', 'TERMINAL', 'UNIT_OF_INFORMATION'}

INFLUENCE = {'NECESSARY_STIMULATION', 'NEGATIVE_INFLUENCE', 'POSITIVE_INFLUENCE', 'UNKNOWN_INFLUENCE'}

LOGICAL_OPERATOR = {'AND', 'DELAY', 'NOT', 'OR'}

class stonpy.model.OntologyER(value)

Bases: Enum

The ontology for ER

ARC = {'ABSOLUTE_INHIBITION', 'ABSOLUTE_STIMULATION', 'ASSIGNMENT', 'EQUIVALENCE_ARC', 'INHIBITION', 'INTERACTION', 'LOGIC_ARC', 'MODULATION', 'NECESSARY_STIMULATION', 'STIMULATION'}

AUXILLIARY_UNIT = {'CARDINALITY', 'EXISTENCE', 'LOCATION', 'STATE_VARIABLE', 'TERMINAL', 'UNIT_OF_INFORMATION'}

ENTITY_NODE = {'AND', 'DELAY', 'ENTITY', 'NOT', 'OR', 'OUTCOME', 'PERTURBING_AGENT'}

GLYPH = {'AND', 'CARDINALITY', 'DELAY', 'ENTITY', 'EXISTENCE', 'IMPLICIT_XOR', 'INTERACTION_GLYPH', 'LOCATION', 'NOT', 'OR', 'OUTCOME', 'PERTURBING_AGENT', 'PHENOTYPE', 'STATE_VARIABLE', 'SUBMAP', 'TAG', 'TERMINAL', 'UNIT_OF_INFORMATION', 'VARIABLE_VALUE'}

INFLUENCE = {'ABSOLUTE_INHIBITION', 'ABSOLUTE_STIMULATION', 'INHIBITION', 'MODULATION', 'NECESSARY_STIMULATION', 'STIMULATION'}

INHIBITION = {'ABSOLUTE_INHIBITION', 'INHIBITION'}

INTERACTOR = {'ENTITY', 'OUTCOME'}

LOGICAL_OPERATOR = {'AND', 'DELAY', 'NOT', 'OR'}

RELATIONSHIP = {'ABSOLUTE_INHIBITION', 'ABSOLUTE_STIMULATION', 'ASSIGNMENT', 'INHIBITION', 'INTERACTION', 'MODULATION', 'NECESSARY_STIMULATION', 'PHENOTYPE', 'STIMULATION'}

STATEMENT = {'ASSIGNMENT', 'INTERACTION', 'PHENOTYPE'}

STATE_VARIABLE = {'EXISTENCE', 'LOCATION', 'STATE_VARIABLE'}

STIMULATION = {'ABSOLUTE_STIMULATION', 'NECESSARY_STIMULATION', 'STIMULATION'}

class stonpy.model.OntologyPD(value)

Bases: Enum

The ontology for PD

ARC = {'CATALYSIS', 'CONSUMPTION', 'EQUIVALENCE_ARC', 'INHIBITION', 'LOGIC_ARC', 'MODULATION', 'NECESSARY_STIMULATION', 'PRODUCTION', 'STIMULATION'}

AUXILLIARY_UNIT = {'CARDINALITY', 'COMPLEX_MULTIMER_SUBUNIT', 'COMPLEX_SUBUNIT', 'MACROMOLECULE_MULTIMER_SUBUNIT', 'MACROMOLECULE_SUBUNIT', 'NUCLEIC_ACID_FEATURE_MULTIMER_SUBUNIT', 'NUCLEIC_ACID_FEATURE_SUBUNIT', 'PHENOTYPE_SUBUNIT', 'SIMPLE_CHEMICAL_MULTIMER_SUBUNIT', 'SIMPLE_CHEMICAL_SUBUNIT', 'STATE_VARIABLE', 'TERMINAL', 'UNIT_OF_INFORMATION', 'UNSPECIFIED_ENTITY_SUBUNIT'}

EPN = {'COMPLEX', 'COMPLEX_MULTIMER', 'MACROMOLECULE', 'MACROMOLECULE_MULTIMER', 'NUCLEIC_ACID_FEATURE', 'NUCLEIC_ACID_FEATURE_MULTIMER', 'PERTURBING_AGENT', 'SIMPLE_CHEMICAL', 'SIMPLE_CHEMICAL_MULTIMER', 'SOURCE_AND_SINK', 'UNSPECIFIED_ENTITY'}

FLUX_ARC = {'CONSUMPTION', 'PRODUCTION'}

GLYPH = {'AND', 'ASSOCIATION', 'CARDINALITY', 'COMPARTMENT', 'COMPLEX', 'COMPLEX_MULTIMER', 'COMPLEX_MULTIMER_SUBUNIT', 'COMPLEX_SUBUNIT', 'DELAY', 'DISSOCIATION', 'EQUIVALENCE', 'GENERIC_PROCESS', 'MACROMOLECULE', 'MACROMOLECULE_MULTIMER', 'MACROMOLECULE_MULTIMER_SUBUNIT', 'MACROMOLECULE_SUBUNIT', 'NOT', 'NUCLEIC_ACID_FEATURE', 'NUCLEIC_ACID_FEATURE_MULTIMER', 'NUCLEIC_ACID_FEATURE_MULTIMER_SUBUNIT', 'NUCLEIC_ACID_FEATURE_SUBUNIT', 'OMITTED_PROCESS', 'OR', 'PERTURBING_AGENT', 'PHENOTYPE', 'PHENOTYPE_SUBUNIT', 'SIMPLE_CHEMICAL', 'SIMPLE_CHEMICAL_MULTIMER', 'SIMPLE_CHEMICAL_MULTIMER_SUBUNIT', 'SIMPLE_CHEMICAL_SUBUNIT', 'SOURCE_AND_SINK', 'STATE_VARIABLE', 'SUBMAP', 'TAG', 'TERMINAL', 'UNCERTAIN_PROCESS', 'UNIT_OF_INFORMATION', 'UNSPECIFIED_ENTITY', 'UNSPECIFIED_ENTITY_SUBUNIT'}

INHIBITION = {'INHIBITION'}

LOGICAL_OPERATOR = {'AND', 'DELAY', 'NOT', 'OR'}

MODULATION = {'CATALYSIS', 'INHIBITION', 'MODULATION', 'NECESSARY_STIMULATION', 'STIMULATION'}

MULTIMER = {'COMPLEX_MULTIMER', 'MACROMOLECULE_MULTIMER', 'NUCLEIC_ACID_FEATURE_MULTIMER', 'SIMPLE_CHEMICAL_MULTIMER'}

PROCESS = {'ASSOCIATION', 'DISSOCIATION', 'GENERIC_PROCESS', 'OMITTED_PROCESS', 'PHENOTYPE', 'UNCERTAIN_PROCESS'}

STIMULATION = {'CATALYSIS', 'NECESSARY_STIMULATION', 'STIMULATION'}

STOICHIOMETRIC_PROCESS = {'ASSOCIATION', 'DISSOCIATION', 'GENERIC_PROCESS', 'OMITTED_PROCESS', 'UNCERTAIN_PROCESS'}

SUBUNIT = {'COMPLEX_MULTIMER_SUBUNIT', 'COMPLEX_SUBUNIT', 'MACROMOLECULE_MULTIMER_SUBUNIT', 'MACROMOLECULE_SUBUNIT', 'NUCLEIC_ACID_FEATURE_MULTIMER_SUBUNIT', 'NUCLEIC_ACID_FEATURE_SUBUNIT', 'PHENOTYPE_SUBUNIT', 'SIMPLE_CHEMICAL_MULTIMER_SUBUNIT', 'SIMPLE_CHEMICAL_SUBUNIT', 'UNSPECIFIED_ENTITY_SUBUNIT'}

class stonpy.model.STONEnum(value)

Bases: Enum

The Enum for the labels, relationship types and properties names used in stonpy’s data model

ABSOLUTE_INHIBITION = 'AsboluteInhibition'

ABSOLUTE_INHIBITION_SHORTCUT = 'ABSOLUTE_INHIBITS'

ABSOLUTE_STIMULATION = 'AsboluteStimulation'

ABSOLUTE_STIMULATION_SHORTCUT = 'ABSOLUTE_STIMULATES'

ACTIVITY = 'Activity'

AND = 'AndOperator'

ANNOTATION = 'Annotation'

ARC = 'Arc'

ARCGROUP = 'Arcgroup'

ASSIGNMENT = 'Assignment'

ASSIGNMENT_SHORTCUT = 'IS_ASSIGNED_TO'

ASSOCIATION = 'Association'

AUXILLIARY_UNIT = 'AuxilliaryUnit'

BBOX = 'Bbox'

BIOLOGICAL_ACTIVITY = 'BiologicalActivity'

CARDINALITY = 'Cardinality'

CARDINALITY_PROP = 'cardinality'

CATALYSIS = 'Catalyzis'

CATALYSIS_SHORTCUT = 'CATALYZES'

CLASS = 'class'

CLONE = 'clone'

CLONE_LABEL = 'cloneLabel'

COLLECTION_NS = 'collection_ns'

COMPARTMENT = 'Compartment'

COMPARTMENT_ORDER = 'compartmentOrder'

COMPLEX = 'Complex'

COMPLEX_MULTIMER = 'ComplexMultimer'

COMPLEX_MULTIMER_SUBUNIT = 'ComplexMultimerSubunit'

COMPLEX_SUBUNIT = 'ComplexSubunit'

CONSUMPTION = 'Consumption'

CONSUMPTION_SHORTCUT = 'CONSUMES'

DELAY = 'DelayOperator'

DISSOCIATION = 'Dissociation'

END = 'End'

ENTITY = 'Entity'

ENTITY_NODE = 'EntityNode'

EPN = 'Epn'

EQUIVALENCE = 'EquivalenceOperator'

EQUIVALENCE_ARC = 'EquivalenceArc'

EQUIVALENCE_ARC_SHORTCUT = 'HAS_INPUT'

EXISTENCE = 'Existence'

EXTENSION = 'extension'

FLUX_ARC = 'FluxArc'

GENERIC_PROCESS = 'GenericProcess'

GLYPH = 'Glyph'

H = 'h'

HAS_ANNOTATION = 'HAS_ANNOTATION'

HAS_ARC = 'HAS_ARC'

HAS_ARCGROUP = 'HAS_ARCGROUP'

HAS_BBOX = 'HAS_BBOX'

HAS_CARDINALITY = 'HAS_CARDINALITY'

HAS_END = 'HAS_END'

HAS_EXISTENCE = 'HAS_EXISTENCE'

HAS_GLYPH = 'HAS_GLYPH'

HAS_LABEL = 'HAS_LABEL'

HAS_LOCATION = 'HAS_LOCATION'

HAS_NEXT = 'HAS_NEXT'

HAS_OUTCOME = 'HAS_OUTCOME'

HAS_PORT = 'HAS_PORT'

HAS_RESOURCE = 'HAS_RESOURCE'

HAS_SOURCE = 'HAS_SOURCE'

HAS_START = 'HAS_START'

HAS_STATE_VARIABLE = 'HAS_STATE_VARIABLE'

HAS_SUBUNIT = 'HAS_SUBUNIT'

HAS_TARGET = 'HAS_TARGET'

HAS_TERMINAL = 'HAS_TERMINAL'

HAS_UNIT_OF_INFORMATION = 'HAS_UNIT_OF_INFORMATION'

HAS_VALUE = 'HAS_VALUE'

ID = 'id'

IMPLICIT_XOR = 'ImplicitXor'

INFLUENCE = 'Influence'

INHIBITION = 'Inhibition'

INHIBITION_SHORTCUT = 'INHIBITS'

INTERACTION = 'Interaction'

INTERACTION_ARCGROUP = 'InteractionArcgroup'

INTERACTION_GLYPH = 'InteractionGlyph'

INTERACTION_SHORTCUT = 'INTERACTS_WITH'

INTERACTOR = 'Interactor'

IS_IN_COMPARTMENT = 'IS_IN_COMPARTMENT'

LABEL = 'Label'

LABEL_PROP = 'label'

LANGUAGE = 'language'

LOCATION = 'Location'

LOGICAL_OPERATOR = 'LogicalOperator'

LOGIC_ARC = 'LogicArc'

LOGIC_ARC_SHORTCUT = 'HAS_INPUT'

MACROMOLECULE = 'Macromolecule'

MACROMOLECULE_MULTIMER = 'MacromoleculeMultimer'

MACROMOLECULE_MULTIMER_SUBUNIT = 'MacromoleculeMultimerSubunit'

MACROMOLECULE_SUBUNIT = 'MacromoleculeSubunit'

MAP = 'Map'

MAP_ID = 'id'

MODULATION = 'Modulation'

MODULATION_SHORTCUT = 'MODULATES'

MULTIMER = 'Multimer'

NECESSARY_STIMULATION = 'NecessaryStimulation'

NECESSARY_STIMULATION_SHORTCUT = 'NECESSARY_STIMULATES'

NEGATIVE_INFLUENCE = 'NegativeInfluence'

NEGATIVE_INFLUENCE_SHORTCUT = 'NEGATIVELY_INFLUENCES'

NEXT = 'Next'

NOT = 'NotOperator'

NOTES = 'notes'

NUCLEIC_ACID_FEATURE = 'NucleicAcidFeature'

NUCLEIC_ACID_FEATURE_MULTIMER = 'NucleicAcidFeatureMultimer'

NUCLEIC_ACID_FEATURE_MULTIMER_SUBUNIT = 'NucleicAcidFeatureMultimerSubunit'

NUCLEIC_ACID_FEATURE_SUBUNIT = 'NucleicAcidFeatureSubunit'

OMITTED_PROCESS = 'OmittedProcess'

OR = 'OrOperator'

ORDER = 'order'

ORIENTATION = 'orientation'

OUTCOME = 'Outcome'

PERTURBING_AGENT = 'PerturbingAgent'

PHENOTYPE = 'Phenotype'

PHENOTYPE_SUBUNIT = 'PhenotypeSubunit'

PORT = 'Port'

POSITIVE_INFLUENCE = 'PositiveInfluence'

POSITIVE_INFLUENCE_SHORTCUT = 'POSITIVELY_INFLUENCES'

PREFIX = 'prefix'

PROCESS = 'Process'

PRODUCTION = 'Production'

PRODUCTION_SHORTCUT = 'PRODUCES'

QUALIFIER = 'qualifier'

QUALIFIER_NS = 'qualifier_ns'

QUALIFIER_URI = 'qualifier_uri'

RELATIONSHIP = 'Relationship'

RESOURCE = 'Resource'

SIMPLE_CHEMICAL = 'SimpleChemical'

SIMPLE_CHEMICAL_MULTIMER = 'SimpleChemicalMultimer'

SIMPLE_CHEMICAL_MULTIMER_SUBUNIT = 'SimpleChemicalMultimerSubunit'

SIMPLE_CHEMICAL_SUBUNIT = 'SimpleChemicalSubunit'

SOURCE_AND_SINK = 'EmptySet'

START = 'Start'

STATEMENT = 'Statement'

STATE_VARIABLE = 'StateVariable'

STIMULATION = 'Stimulation'

STIMULATION_SHORTCUT = 'STIMULATES'

STOICHIOMETRIC_PROCESS = 'StoichiometricProcess'

SUBMAP = 'Submap'

SUBUNIT = 'Subunit'

TAG = 'Tag'

TERMINAL = 'Terminal'

TEXT = 'text'

UI_TYPE = 'type'

UNCERTAIN_PROCESS = 'UncertainProcess'

UNIT_OF_INFORMATION = 'UnitOfInformation'

UNKNOWN_INFLUENCE = 'UnknownInfluence'

UNKNOWN_INFLUENCE_SHORTCUT = 'INFLUENCES'

UNSPECIFIED_ENTITY = 'UnspecifiedEntity'

UNSPECIFIED_ENTITY_SUBUNIT = 'UnspecifiedEntitySubunit'

URI = 'uri'

VALUE = 'value'

VARIABLE = 'variable'

VARIABLE_VALUE = 'VariableValue'

W = 'w'

X = 'x'

Y = 'y'