Ontology API

Ontology loading and traversal functions.

Core functions

load_go_terms(path=None)

  • Loads GO terms from an OBO file.

  • If path is omitted, GO3 downloads go-basic.obo.

  • Replaces the in-process ontology cache.

get_term_by_id(go_id)

  • Returns a go3.PyGOTerm object.

  • Raises ValueError if the term does not exist.

ancestors(go_id)

  • Returns all ancestors of go_id (including the term itself).

common_ancestor(go_id1, go_id2)

  • Returns common ancestors between two terms.

deepest_common_ancestor(go_id1, go_id2)

  • Returns the deepest common ancestor (MICA-like depth criterion).

  • Raises ValueError if either GO ID is missing.

Example

import go3

go3.load_go_terms("go-basic.obo")

term = go3.get_term_by_id("GO:0006397")
print(term.name)

ancs = go3.ancestors("GO:0006397")
print(len(ancs))

common = go3.common_ancestor("GO:0006397", "GO:0008380")
print(len(common))

dca = go3.deepest_common_ancestor("GO:0006397", "GO:0008380")
print(dca)

Notes for developers

  • Ontology data is cached globally within the Python process.

  • Loading a new ontology refreshes dependent internal caches.

  • For reproducible analyses, keep ontology version fixed across runs.

API reference

ancestors(go_id)

Returns the list of all ancestors in the ontology for the given GO Term.

Parameters:

go_id (str) – GO term ID.

Returns:

List of IDs of all the ancestors in the ontology.

Return type:

list of str

common_ancestor(go_id1, go_id2)

Returns the list of all the common ancestors in the ontology for the given GO Terms.

Parameters:

  • go_id1 (str) – GO term ID 1.

  • go_id2 (str) – GO term ID 2.

Returns:

List of IDs of all the common ancestors in the ontology.

Return type:

list of str

deepest_common_ancestor(go_id1, go_id2)

Returns the deepest common ancestor in the ontology for the given GO Terms.

Parameters:

  • go_id1 (str) – GO term ID 1.

  • go_id2 (str) – GO term ID 2.

Returns:

ID of the deepest common ancestor in the ontology.

Return type:

Option<String>

get_term_by_id(go_id)

Get the PyGOTerm object for a given GO term ID.

Raises:

ValueError – If the GO term does not exist in the ontology.

load_go_terms(path=None)

Load GO terms from an OBO file and cache them globally.

Parameters:

path (Optional[str]) – Optional path to the OBO file.

Returns:

List of GO terms as Python objects.

Return type:

list of PyGOTerm