Term

class Term(reference, definition=None, relationships=<factory>, _axioms=<factory>, properties=<factory>, parents=<factory>, intersection_of=<factory>, union_of=<factory>, equivalent_to=<factory>, disjoint_from=<factory>, synonyms=<factory>, xrefs=<factory>, namespace=None, is_obsolete=None, type='Term', builtin=None, is_anonymous=None, subsets=<factory>)[source]

Bases: Stanza

A term in OBO.

Attributes Summary

`builtin`
`definition`	A description of the entity
`disjoint_from`
`equivalent_to`
`intersection_of`
`is_anonymous`
`is_obsolete`	An annotation for obsolescence.
`namespace`	The sub-namespace within the ontology
`parents`	Relationships with the default "is_a"
`properties`
`reference`	The primary reference for the entity
`relationships`	Object properties
`subsets`
`synonyms`	Synonyms of this term
`type`
`union_of`
`xrefs`	Database cross-references, see `get_mappings()` for access to all mappings in an SSSOM-like interface

Methods Summary

`append_broad_match`(reference, *[, ...])	Append a broad match, also adding an xref.
`append_exact_match`(reference, *[, ...])	Append an exact match, also adding a cross-reference.
`append_narrow_match`(reference, *[, ...])	Append a narrow match, also adding an xref.
`append_related_match`(reference, *[, ...])	Append a related match, also adding an xref.
`append_see_also_uri`(uri)	Add a see also property.
`default`(prefix, identifier[, name])	Create a default term.
`extend_parents`(references)	Add a collection of parents to this entity.
`extend_relationship`(typedef, references)	Append several relationships.
`from_triple`(prefix, identifier[, name, ...])	Create a term from a reference.
`get_property`(prop)	Get a single property of the given key.
`get_property_literals`(prop)	Get properties from the given key.
`get_species`()	Get the species if it exists.
`iterate_obo_lines`(*, ontology_prefix, typedefs)	Iterate over the lines to write in an OBO file.
`set_species`(identifier[, name])	Append the from_species relation.

Attributes Documentation

Parameters:

reference (Reference)
definition (str | None)
relationships (RelationsHint)
_axioms (AnnotationsDict)
properties (PropertiesHint)
parents (list[Reference])
intersection_of (IntersectionOfHint)
union_of (UnionOfHint)
equivalent_to (list[Reference])
disjoint_from (list[Reference])
synonyms (list[Synonym])
xrefs (list[Reference])
namespace (str | None)
is_obsolete (bool | None)
type (StanzaType)
builtin (bool | None)
is_anonymous (bool | None)
subsets (list[Reference])

builtin: bool | None = None

definition: str | None = None: A description of the entity

disjoint_from: list[Reference] = <dataclasses._MISSING_TYPE object>

equivalent_to: list[Reference] = <dataclasses._MISSING_TYPE object>

intersection_of: IntersectionOfHint = <dataclasses._MISSING_TYPE object>

is_anonymous: bool | None = None

is_obsolete: bool | None = None: An annotation for obsolescence. By default, is None, but this means that it is not obsolete.

namespace: str | None = None: The sub-namespace within the ontology

parents: list[Reference] = <dataclasses._MISSING_TYPE object>: Relationships with the default “is_a”

properties: PropertiesHint = <dataclasses._MISSING_TYPE object>

reference: Reference = <dataclasses._MISSING_TYPE object>: The primary reference for the entity

relationships: RelationsHint = <dataclasses._MISSING_TYPE object>: Object properties

subsets: list[Reference] = <dataclasses._MISSING_TYPE object>

synonyms: list[Synonym] = <dataclasses._MISSING_TYPE object>: Synonyms of this term

type: StanzaType = 'Term'

union_of: UnionOfHint = <dataclasses._MISSING_TYPE object>

xrefs: list[Reference] = <dataclasses._MISSING_TYPE object>: Database cross-references, see get_mappings() for access to all mappings in an SSSOM-like interface

Methods Documentation

append_broad_match(reference, *, mapping_justification=None, confidence=None, contributor=None)[source]

Append a broad match, also adding an xref.

Parameters:

reference (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
mapping_justification (NormalizedNamableReference | None)
confidence (float | None)
contributor (NormalizedNamableReference | None)

Return type:

Self

append_exact_match(reference, *, mapping_justification=None, confidence=None, contributor=None)[source]

Append an exact match, also adding a cross-reference.

Parameters:

reference (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
mapping_justification (NormalizedNamableReference | None)
confidence (float | None)
contributor (NormalizedNamableReference | None)

Return type:

Self

append_narrow_match(reference, *, mapping_justification=None, confidence=None, contributor=None)[source]

Append a narrow match, also adding an xref.

Parameters:

reference (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
mapping_justification (NormalizedNamableReference | None)
confidence (float | None)
contributor (NormalizedNamableReference | None)

Return type:

Self

append_related_match(reference, *, mapping_justification=None, confidence=None, contributor=None)[source]

Append a related match, also adding an xref.

Parameters:

reference (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
mapping_justification (NormalizedNamableReference | None)
confidence (float | None)
contributor (NormalizedNamableReference | None)

Return type:

Self

append_see_also_uri(uri)[source]

Add a see also property.

Parameters:: uri (str)
Return type:: Self

classmethod default(prefix, identifier, name=None)[source]

Create a default term.

Parameters:

prefix (str)
identifier (str)
name (str | None)

Return type:

Self

extend_parents(references)[source]

Add a collection of parents to this entity.

Parameters:: references (Collection[NormalizedNamableReference])
Return type:: None

extend_relationship(typedef, references)[source]

Append several relationships.

Parameters:

typedef (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
references (Iterable[NormalizedNamableReference])

Return type:

None

classmethod from_triple(prefix, identifier, name=None, definition=None, **kwargs)[source]

Create a term from a reference.

Parameters:

prefix (str)
identifier (str)
name (str | None)
definition (str | None)
kwargs (Any)

Return type:

Term

get_property(prop)[source]

Get a single property of the given key.

Parameters:: prop (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
Return type:: str | None

get_property_literals(prop)[source]

Get properties from the given key.

Parameters:: prop (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
Return type:: list[str]

get_species(prefix: str = 'ncbitaxon', *, strict: Literal[True] = False) → NormalizedNamableReference[source]

get_species(prefix: str = 'ncbitaxon', *, strict: Literal[False] = False) → NormalizedNamableReference | None

Get the species if it exists.

Parameters:

prefix – The prefix to use in case the term has several species annotations.
strict – If true, raises when no species reference is available

Returns:

A species reference, if available

iterate_obo_lines(*, ontology_prefix, typedefs, synonym_typedefs=None, emit_object_properties=True, emit_annotation_properties=True)[source]

Iterate over the lines to write in an OBO file.

Parameters:

ontology_prefix (str)
typedefs (Mapping[ReferenceTuple, TypeDef])
synonym_typedefs (Mapping[ReferenceTuple, SynonymTypeDef] | None)
emit_object_properties (bool)
emit_annotation_properties (bool)

Return type:

Iterable[str]

set_species(identifier, name=None)[source]

Append the from_species relation.

Parameters:

identifier (str)
name (str | None)

Return type:

Self