Examples

Basic Term Similarity

import go3
go3.load_go_terms()
annots = go3.load_gaf("goa_human.gaf")
counter = go3.build_term_counter(annots)
sim = go3.semantic_similarity("GO:0006397", "GO:0008380", "resnik", counter)
print("Resnik similarity:", sim)

Batch Similarity

list1 = ["GO:0006397", "GO:0008380"]
list2 = ["GO:0008380", "GO:0006397"]
sims = go3.batch_similarity(list1, list2, "lin", counter)
print(sims)

Gene-to-Gene Similarity

sim = go3.compare_genes("BRCA1", "CASP8", "BP", "topoicsim", "bma", counter)
print("TopoICSim gene similarity:", sim)

Error Handling

try:
    sim = go3.compare_genes("FAKEGENE", "BRCA1", "BP", "resnik", "bma", counter)
except ValueError as e:
    print("Error:", e)