Python Ontology.from_ndex Examples

Example #1

File: Ont_Metrics_3.py Project: joreynajr/synapse_ontology

def Generate_Ontology_File(Term):
    ndex_server = 'http://public.ndexbio.org'
    go_human = Ontology.from_ndex(
        'http://public.ndexbio.org/v2/network/16565851-4bfc-11e9-9f06-0ac135e8bacf'
    )
    ont = go_human.focus(Term)
    ont.to_table('custom_ontology.txt')
    return ont

Example #2

File: find_input_genes_1.py Project: KarenYuanMei/SynSig

def GO_Focus(Term):
    ndex_server = 'http://public.ndexbio.org'
    ndex_user, ndex_pass = '******', 'Synapse'
    go_human = Ontology.from_ndex(
        'http://public.ndexbio.org/v2/network/16565851-4bfc-11e9-9f06-0ac135e8bacf'
    )
    go_genes = go_human.genes
    subont = go_human.focus(Term)
    subont_genes = subont.genes
    return go_genes, subont_genes

Example #3

def find_GO_score_matrix():
	ndex_server ='http://public.ndexbio.org' 
	ndex_user, ndex_pass = '******', 'Synapse'
	go_human = Ontology.from_ndex('http://public.ndexbio.org/v2/network/16565851-4bfc-11e9-9f06-0ac135e8bacf')

	print (go_human)
	sim, genes=go_human.flatten()

	sim_df = pd.DataFrame(sim, index=genes, columns=genes)
	return sim_df