Usage

A python data model for OBO Graphs.

class Definition(*, val: str | None = None, xrefs: list[str] | None = None)

Represents a definition for a node.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class DomainRangeAxiom(*, predicateId: str, domainClassIds: list[str] | None = None, rangeClassIds: list[str] | None = None, allValuesFromEdges: list[Edge] | None = None, meta: Meta | None = None)

Represents a domain/range axiom.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Edge(*, sub: str, pred: str, obj: str, meta: Meta | None = None)

Represents an edge in an OBO Graph.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class EquivalentNodeSet(*, representativeNodeId: str, nodeIds: list[str], meta: Meta | None = None)

Represents a set of equivalent nodes.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class ExistentialRestrictionExpression(*, propertyId: str, fillerId: str)

Represents an existential restriction.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Graph(*, id: str | None = None, meta: Meta | None = None, nodes: list[Node] = <factory>, edges: list[Edge] = <factory>, equivalentNodesSets: list[EquivalentNodeSet] = <factory>, logicalDefinitionAxioms: list[LogicalDefinition] = <factory>, domainRangeAxioms: list[DomainRangeAxiom] = <factory>, propertyChainAxioms: list[PropertyChainAxiom] = <factory>)

A graph corresponds to an ontology.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

property name: str | None

Get the title.

property version: str | None

Get the version.

standardize(converter: curies.Converter, *, strict: bool = False) → StandardizedGraph

Standardize the graph.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class GraphDocument(*, graphs: list[Graph], meta: Meta | None = None)

Represents a list of OBO graphs.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

standardize(converter: curies.Converter) → StandardizedGraphDocument

Standardize the graph.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class LogicalDefinition(*, definedClassId: str, genusIds: list[str] | None = None, restrictions: list[ExistentialRestrictionExpression] | None = None, meta: Meta | None = None)

Represents a logical definition chain axiom.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Meta(*, definition: Definition | None = None, subsets: list[str] | None = None, xrefs: list[Xref] | None = None, synonyms: list[Synonym] | None = None, comments: list[str] | None = None, version: str | None = None, basicPropertyValues: list[Property] | None = None, deprecated: bool = False)

Represents the metadata about a node or ontology.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Node(*, id: str, lbl: str | None = None, meta: Meta | None = None, type: Literal['CLASS', 'PROPERTY', 'INDIVIDUAL'] | None = None, propertyType: Literal['ANNOTATION', 'OBJECT', 'DATA'] | None = None)

Represents a node in an OBO Graph.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Property(**data: Any)

Represent a property inside a metadata element.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class PropertyChainAxiom(*, predicateId: str, chainPredicateIds: list[str], meta: Meta | None = None)

Represents a property chain axiom.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedBaseModel

A standardized property.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

abstractmethod classmethod from_obograph_raw(obj: X, converter: Converter, *, strict: bool = False) → Self | None

Instantiate by standardizing a raw OBO Graph object.

abstractmethod to_raw(converter: Converter) → X

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedDefinition(*, value: str | None = None, xrefs: list[Reference] | None = None)

A standardized definition.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(definition: Definition | None, converter: Converter, *, strict: bool = False) → Self | None

Parse a raw object.

to_raw(converter: Converter) → Definition

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedDomainRangeAxiom(*, predicate: Reference, domains: list[Reference] = <factory>, ranges: list[Reference] = <factory>, all_values_from_edges: list[StandardizedEdge] = <factory>, meta: StandardizedMeta | None = None)

Represents a domain/range axiom.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(obj: DomainRangeAxiom, converter: Converter, *, strict: bool = False) → Self | None

Parse a raw object.

to_raw(converter: Converter) → DomainRangeAxiom

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedEdge(*, subject: Reference, predicate: Reference, object: Reference, meta: StandardizedMeta | None = None)

A standardized edge.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(edge: Edge, converter: Converter, *, strict: bool = False) → Self | None

Instantiate by standardizing a raw OBO Graph object.

to_raw(converter: Converter) → Edge

Create a raw object.

model_config = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedEquivalentNodeSet(*, node: Reference, equivalents: list[Reference] = <factory>, meta: StandardizedMeta | None = None)

Represents an equivalence set.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(obj: EquivalentNodeSet, converter: Converter, *, strict: bool = False) → Self | None

Parse a raw object.

to_raw(converter: Converter) → EquivalentNodeSet

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedExistentialRestriction(*, predicate: Reference, target: Reference)

Represents an existential restriction expression.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(obj: ExistentialRestrictionExpression, converter: Converter, *, strict: bool = False) → Self | None

Parse a raw object.

to_raw(converter: Converter) → ExistentialRestrictionExpression

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedGraph(*, id: str | None = None, meta: StandardizedMeta | None = None, nodes: list[StandardizedNode] = <factory>, edges: list[StandardizedEdge] = <factory>, equivalent_node_sets: list[StandardizedEquivalentNodeSet] = <factory>, logical_definition_axioms: list[StandardizedLogicalDefinition] = <factory>, domain_range_axioms: list[StandardizedDomainRangeAxiom] = <factory>, property_chain_axioms: list[StandardizedPropertyChainAxiom] = <factory>)

A standardized graph.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(graph: Graph, converter: Converter, *, strict: bool = False) → Self

Instantiate by standardizing a raw OBO Graph object.

to_raw(converter: Converter) → Graph

Create a raw object.

property name: str | None

Look up the name of the graph.

property version: str | None

Get the version.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedGraphDocument(*, graphs: list[StandardizedGraph], meta: StandardizedMeta | None = None)

A standardized graph document.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(graph_document: GraphDocument, converter: Converter, *, strict: bool = False) → Self

Instantiate by standardizing a raw OBO Graph Document object.

to_raw(converter: Converter) → GraphDocument

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedLogicalDefinition(*, node: Reference, geni: list[Reference] = <factory>, restrictions: list[StandardizedExistentialRestriction] = <factory>, meta: StandardizedMeta | None = None)

Represents a logical definition axiom.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(obj: LogicalDefinition, converter: Converter, *, strict: bool = False) → Self | None

Parse a raw object.

to_raw(converter: Converter) → LogicalDefinition

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedMeta(*, definition: StandardizedDefinition | None = None, subsets: list[Reference] | None = None, xrefs: list[StandardizedXref] | None = None, synonyms: list[StandardizedSynonym] | None = None, comments: list[str] | None = None, deprecated: bool = False, version_iri: str | None = None, properties: list[StandardizedProperty] | None = None)

A standardized meta object.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(meta: Meta | None, converter: Converter, flag: str = '', strict: bool = False) → Self | None

Instantiate by standardizing a raw OBO Graph object.

to_raw(converter: Converter) → Meta

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedNode(*, reference: Reference, label: str | None = None, meta: StandardizedMeta | None = None, type: Literal['CLASS', 'PROPERTY', 'INDIVIDUAL'] | None = None, property_type: Literal['ANNOTATION', 'OBJECT', 'DATA'] | None = None)

A standardized node.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(node: Node, converter: Converter, *, strict: bool = False) → Self | None

Instantiate by standardizing a raw OBO Graph object.

to_raw(converter: Converter) → Node

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedProperty

A standardized property.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(prop: Property, converter: Converter, *, strict: bool = False) → Self

Instantiate by standardizing a raw OBO Graph object.

to_raw(converter: Converter) → Property

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedPropertyChainAxiom(*, predicate: Reference, chain: list[Reference] = <factory>, meta: StandardizedMeta | None = None)

Represents a property chain axiom.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(obj: PropertyChainAxiom, converter: Converter, *, strict: bool = False) → Self | None

Parse a raw object.

to_raw(converter: Converter) → PropertyChainAxiom

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedSynonym(*, text: str, predicate: Reference, type: Reference | None = None, xrefs: list[Reference] | None = None)

A standardized synonym.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(synonym: Synonym, converter: Converter, *, strict: bool = False) → Self

Instantiate by standardizing a raw OBO Graph object.

to_raw(converter: Converter) → Synonym

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class StandardizedXref(*, reference: Reference)

A standardized database cross-reference.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

classmethod from_obograph_raw(xref: Xref, converter: Converter, *, strict: bool = False) → Self

Instantiate by standardizing a raw OBO Graph object.

to_raw(converter: Converter) → Xref

Create a raw object.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Synonym(**data: Any)

Represents a synonym inside an object meta.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class Xref(*, val: str)

Represents a cross-reference.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

guess_primary_graph(graph_document: GraphDocument, prefix: str) → Graph

guess_primary_graph(graph_document: StandardizedGraphDocument, prefix: str) → StandardizedGraph

Guess the primary graph from a graph document.

read(source: str | Path, *, timeout: int | float | None = None, squeeze: Literal[False] = True, encoding: str = None) → GraphDocument

read(source: str | Path, *, timeout: int | float | None = None, squeeze: Literal[True] = True, encoding: str = None) → Graph

Read an OBO Graph document.

Parameters:

• source – A file path or URL to an OBO Graph JSON

• timeout – The timeout for getting a URL

• squeeze – By default, will unpack the first graph from a graph document that only has a single graph and return a Graph object. If true and multiple graphs are received, will raise an error. Set this to false to return a GraphDocument containing all graphs.

• encoding – The encoding when reading a local filepath, passed to pystow.utils.safe_open()

• newline – The newline when reading a local filepath, passed to pystow.utils.safe_open()

Returns:

A graph or graph document

Raises:

ValueError – If squeeze is set to true and multiple graphs are received