go.rst

Gene Ontology

Provides access to Gene Ontology and its gene annotations.

Class References

Ontology()

Term()

id

The term id.

namespace

The namespace of the term.

def

The term definition (Note the use of trailing underscore to avoid conflict with a python keyword).

is_a

List of term ids this term is a subterm of (parent terms).

related

List of (rel_type, term_id) tuples with rel_type specifying the relationship type with term_id.

Annotations()

AnnotationRecord()

Usage

Load the ontology and print out some terms:

from orangecontrib.bioinformatics import go
ontology = go.Ontology()
term = ontology["GO:0097194"] # execution phase of apoptosis

# print a term
print(term)

# access fields by name
print(term.id, term.name)
# note the use of underscore due to a conflict with a python def keyword
print(term.def_)

Searching the annotation (part of code/go/gene_annotations.py)

code/go/gene_annotations.py

Term enrichment (part of code/go/enrichment.py)

code/go/enrichment.py