GOTerm Object¶

A PyGOTerm represents one term in the loaded Gene Ontology.

Main fields¶

Field	Type	Description
`id`	`str`	GO identifier (for example `GO:0006397`)
`name`	`str`	Human-readable label
`namespace`	`str`	One of `biological_process`, `molecular_function`, `cellular_component`
`definition`	`str`	GO definition text
`parents`	`list[str]`	Immediate `is_a` parents
`children`	`list[str]`	Immediate `is_a` children
`depth`	`int \| None`	Maximum distance to root
`level`	`int \| None`	Minimum distance to root
`is_obsolete`	`bool`	Obsolescence flag
`alt_ids`	`list[str]`	Alternate GO IDs
`replaced_by`	`str \| None`	Suggested canonical replacement for obsolete terms
`consider`	`list[str]`	Alternative replacements
`synonyms`	`list[str]`	Synonym strings
`xrefs`	`list[str]`	Cross-references
`relationships`	`list[tuple[str, str]]`	Additional relationships (for example `part_of`)
`comment`	`str \| None`	GO comment field

Example¶

import go3

go3.load_go_terms("go-basic.obo")
term = go3.get_term_by_id("GO:0006397")

print(term.id)
print(term.name)
print(term.namespace)
print(term.parents[:5])

API reference¶

class PyGOTerm¶

Bases: object

Python-exposed struct representing a GO term (for use in the Python API).

Fields¶

idstr: GO term identifier.
namestr: Human-readable name of the term.
namespacestr: Ontology namespace.
definitionstr: Textual definition of the term.
parentslist of str: List of parent GO term IDs.
childrenlist of str: List of child GO term IDs.
depthOptional[int]: Maximum distance to a root term.
levelOptional[int]: Minimum distance to a root term.
is_obsoletebool: True if the term is obsolete.
alt_idslist of str: Alternative GO IDs for this term.
replaced_byOptional[str]: If obsolete, the term that replaces this one.
considerlist of str: Suggested replacement terms if obsolete.
synonymslist of str: List of synonyms.
xrefslist of str: Cross-references to other databases.
relationshipslist of (str, str): Other relationships (e.g., part_of).
commentOptional[str]: Additional comments.

alt_ids¶

children¶

comment¶

consider¶

definition¶

depth¶

id¶

is_obsolete¶

level¶

name¶

namespace¶

parents¶

relationships¶

replaced_by¶

synonyms¶

xrefs¶