How to traverse to GO children and descendants¶

Traverse immediate children or all descendants with or without user-specified optional relationships

Children and Descendants described
Code to get Children and Descendants
- Get children through is_a relationship
- Get children through is_a relationship and optional relationship, part_of.
- Get descendants through is_a relationship
- Get descendants through is_a relationship and optional relationship, part_of.

Children and Descendants¶

Children¶

Children are terms directly below a GO term

Descendants¶

Descendants are all terms below a GO term in the hierarchy

import os
from goatools.obo_parser import GODag

# Load a small test GO DAG and all the optional relationships,
# like 'regulates' and 'part_of'
godag = GODag('../tests/data/heartjogging.obo',
              optional_attrs={'relationship'})

Get children through is_a relationship¶

Direct children through is_a relationship only

GO_ID = 'GO:0003143'  # embryonic heart tube morphogenesis
goterm = godag[GO_ID]

# Get direct children through is_a
children_isa = [child.item_id for child in goterm.children]
print('{GO} children (is_a): {C}'.format(
    GO=GO_ID,
    C=children_isa))

Get children through is_a relationship and optional relationship, part_of¶

Direct children through is_a and part_of relationships

from goatools.godag.go_tasks import get_go2children

optional_relationships = {"part_of"}
# Note: GODag inherits from dict, so we pass godag directly
go2children_partof = get_go2children(godag, optional_relationships)
print("{GO} children (is_a + part_of): {C}".format(
    GO=GO_ID,
    C=go2children_partof.get(GO_ID, set())))

Get descendants through is_a relationship¶

All descendants through is_a only

# Using GOTerm method
descendants_isa = goterm.get_all_children()
print('{GO} descendants (is_a): {D}'.format(
    GO=GO_ID,
    D=sorted(descendants_isa)))

Get descendants through is_a relationship and optional relationship, part_of¶

All descendants through is_a and part_of relationships

from goatools.godag.go_tasks import get_go2descendants

go2descendants_partof = get_go2descendants(godag.values(), optional_relationships)
print('{GO} descendants (is_a + part_of): {D}'.format(
    GO=GO_ID,
    D=sorted(go2descendants_partof.get(GO_ID, set()))))

Alternative: Use GOTerm.get_all_lower() for all relationships¶

This method automatically includes all relationship types

# Get all descendants through is_a and ALL relationships
all_lower = goterm.get_all_lower()
print('{GO} descendants (is_a + all relationships): {D}'.format(
    GO=GO_ID,
    D=sorted(all_lower)))

# Show the additional descendants found through relationships
additional = all_lower - descendants_isa
if additional:
    print("\nAdditional descendants through relationships:")
    for goid in sorted(additional):
        desc_term = godag[goid]
        print(f"  {goid}: {desc_term.name}")

Summary¶

To get descendants with relationships in GOAtools:

Load GO DAG with relationships: Use optional_attrs={'relationship'} when loading
For a single GO term:
- goterm.get_all_children() - descendants through is_a only
- goterm.get_all_lower() - descendants through is_a + all relationships
For multiple GO terms (batch processing):
- get_go2descendants(godag.values(), relationships=None) - is_a only
- get_go2descendants(godag.values(), relationships=True) - is_a + all relationships
- get_go2descendants(godag.values(), relationships={'part_of'}) - is_a + selected relationships
For hierarchy visualization: Use wr_hier.py -r command-line tool