Term

class pyobo.Term(reference, definition=None, provenance=<factory>, relationships=<factory>, properties=<factory>, parents=<factory>, synonyms=<factory>, xrefs=<factory>, xref_types=<factory>, alt_ids=<factory>, namespace=None, is_obsolete=None)

Bases: Referenced

A term in OBO.

Attributes Summary

definition	A description of the entity
is_obsolete	An annotation for obsolescence.
namespace	The sub-namespace within the ontology

Methods Summary

append_alt(alt)	Add an alternative identifier.
append_comment(value)	Add a comment relationship.
append_exact_match(reference)	Append an exact match, also adding an xref.
append_parent(reference)	Add a parent to this entity.
append_property(prop, value)	Append a property.
append_provenance(reference)	Add a provenance reference.
append_relationship(typedef, reference)	Append a relationship.
append_see_also(reference)	Add a see also relationship.
append_synonym(synonym[, type])	Add a synonym.
append_xref(reference)	Append an xref.
auto(prefix, identifier)	Create a term from a reference.
extend_parents(references)	Add a collection of parents to this entity.
extend_relationship(typedef, references)	Append several relationships.
from_curie(curie[, name])	Create a term directly from a CURIE and optional name.
from_triple(prefix, identifier[, name, ...])	Create a term from a reference.
get_properties(prop)	Get properties from the given key.
get_property(prop)	Get a single property of the given key.
get_relationship(typedef)	Get a single relationship of the given type.
get_relationships(typedef)	Get relationships from the given type.
get_species([prefix])	Get the species if it exists.
iterate_obo_lines()	Iterate over the lines to write in an OBO file.
iterate_properties()	Iterate over pairs of property and values.
iterate_relations()	Iterate over pairs of typedefs and targets.
set_species(identifier[, name])	Append the from_species relation.

Attributes Documentation

definition: Optional[str] = None

A description of the entity

is_obsolete: Optional[bool] = None

An annotation for obsolescence. By default, is None, but this means that it is not obsolete.

namespace: Optional[str] = None

The sub-namespace within the ontology

Methods Documentation

append_alt(alt)

Add an alternative identifier.

Return type:

None

append_comment(value)

Add a comment relationship.

Return type:

Term

append_exact_match(reference)

Append an exact match, also adding an xref.

append_parent(reference)

Add a parent to this entity.

Return type:

Term

append_property(prop, value)

Append a property.

Return type:

None

append_provenance(reference)

Add a provenance reference.

Return type:

None

append_relationship(typedef, reference)

Append a relationship.

Return type:

None

append_see_also(reference)

Add a see also relationship.

Return type:

Term

append_synonym(synonym, type=None)

Add a synonym.

Return type:

None

append_xref(reference)

Append an xref.

Return type:

None

classmethod auto(prefix, identifier)

Create a term from a reference.

Return type:

Term

extend_parents(references)

Add a collection of parents to this entity.

Return type:

None

extend_relationship(typedef, references)

Append several relationships.

Return type:

None

classmethod from_curie(curie, name=None)

Create a term directly from a CURIE and optional name.

Return type:

Term

classmethod from_triple(prefix, identifier, name=None, definition=None)

Create a term from a reference.

Return type:

Term

get_properties(prop)

Get properties from the given key.

Return type:

List[str]

get_property(prop)

Get a single property of the given key.

Return type:

Optional[str]

get_relationship(typedef)

Get a single relationship of the given type.

Return type:

Optional[Reference]

get_relationships(typedef)

Get relationships from the given type.

Return type:

List[Reference]

get_species(prefix='NCBITaxon')

Get the species if it exists.

Parameters:

prefix (str) – The prefix to use in case the term has several species annotations.

Return type:

Optional[Reference]

iterate_obo_lines()

Iterate over the lines to write in an OBO file.

Return type:

Iterable[str]

iterate_properties()

Iterate over pairs of property and values.

Return type:

Iterable[Tuple[str, str]]

iterate_relations()

Iterate over pairs of typedefs and targets.

Return type:

Iterable[Tuple[TypeDef, Reference]]

set_species(identifier, name=None)

Append the from_species relation.