def test_issue2():
ob = Orangeboard(master_rel_is_directed, debug=True)
node = ob.add_node('omim_disease',
'OMIM:603933',
desc='sickle-cell anemia',
seed_node_bool=True)
expand_omim_disease(ob, node)
def test_description_uniprot():
ob = Orangeboard(master_rel_is_directed, debug=True)
node = ob.add_node('uniprot_protein', 'P68871', desc='HBB', seed_node_bool=True)
print(ob.__str__())
expand_uniprot_protein(ob, node)
ob.neo4j_set_url() # use default url
ob.neo4j_set_auth() # use default username/password
ob.neo4j_push()
def test_microrna():
ob = Orangeboard(master_rel_is_directed, debug=True)
ob.add_node('omim_disease', 'OMIM:613074', desc='deafness', seed_node_bool=True)
expand_all_nodes(ob)
expand_all_nodes(ob)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_issue3():
ob = Orangeboard(master_rel_is_directed, debug=True)
disease_node = ob.add_node('disont_disease',
'DOID:9352',
desc='foo',
seed_node_bool=True)
expand_all_nodes(ob)
expand_all_nodes(ob)
expand_all_nodes(ob)
def test_disease_to_go():
ob = Orangeboard(debug=False)
ob.set_dict_reltype_dirs({'affects': True})
bne = BioNetExpander(ob)
node = bne.add_node_smart('disease', 'DOID:906', seed_node_bool=True, desc='peroxisomal disease')
bne.expand_disease(node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_go_bp_microrna():
ob = Orangeboard(debug=False)
ob.set_dict_reltype_dirs({'targets': True})
bne = BioNetExpander(ob)
microrna_node = bne.add_node_smart('microRNA', 'NCBIGene:406991', seed_node_bool=True, desc='test microrna')
bne.expand_microrna(microrna_node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_go_term():
ob = Orangeboard(debug=False)
ob.set_dict_reltype_dirs({'targets': True})
bne = BioNetExpander(ob)
go_node = bne.add_node_smart('biological_process', 'GO:1904685', seed_node_bool=True, desc='test biological process')
bne.expand_biological_process(go_node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_metabolite_to_protein():
ob = Orangeboard(debug=False)
ob.set_dict_reltype_dirs({'physically_interacts_with': True})
bne = BioNetExpander(ob)
node = bne.add_node_smart('metabolite', 'KEGG:C00190', seed_node_bool=True, desc='UDP-D-xylose')
bne.expand_metabolite(node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_go_bp_protein():
ob = Orangeboard(debug=False)
ob.set_dict_reltype_dirs({'targets': True})
bne = BioNetExpander(ob)
protein_node = bne.add_node_smart('protein', 'Q75MH2', seed_node_bool=True, desc='IL6')
bne.expand_protein(protein_node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_issue6():
ob = Orangeboard(master_rel_is_directed, debug=True)
ob.add_node('omim_disease',
'OMIM:605027',
desc='LYMPHOMA, NON-HODGKIN, FAMILIAL',
seed_node_bool=True)
expand_all_nodes(ob)
expand_all_nodes(ob)
expand_all_nodes(ob)
def test_issue7():
ob = Orangeboard(master_rel_is_directed, debug=True)
ob.add_node('omim_disease',
'OMIM:605275',
desc='NOONAN SYNDROME 2; NS2',
seed_node_bool=True)
expand_all_nodes(ob)
expand_all_nodes(ob)
expand_all_nodes(ob)
def test_anatomy_to_go():
ob = Orangeboard(debug=False)
ob.set_dict_reltype_dirs({'capable_of': True})
bne = BioNetExpander(ob)
node = bne.add_node_smart('anatomical_entity', 'UBERON:0000171', seed_node_bool=True, desc='respiration organ')
bne.expand_disease(node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_mondo_liver():
ob = Orangeboard(debug=False)
ob.set_dict_reltype_dirs({'gene_associated_with_condition': True,
'has_phenotype': True})
bne = BioNetExpander(ob)
node = bne.add_node_smart('disease', 'MONDO:0005359', seed_node_bool=True, desc='drug-induced liver injury')
bne.expand_disease(node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_add_mim():
ob = Orangeboard(master_rel_is_directed, debug=True)
node = ob.add_node('omim_disease', 'OMIM:603903', desc='sickle-cell anemia', seed_node_bool=True)
expand_omim_disease(ob, node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_description_disont2():
ob = Orangeboard(master_rel_is_directed, debug=True)
node = ob.add_node('disont_disease', 'DOID:9352', desc='foobar', seed_node_bool=True)
expand_disont_disease(ob, node)
ob.neo4j_set_url() # use default url
ob.neo4j_set_auth() # use default username/password
ob.neo4j_push()
def test_anatomy_1():
ob = Orangeboard(master_rel_is_directed, debug=True)
mir96 = ob.add_node('ncbigene_microrna', 'NCBIGene:407053', desc='MIR96', seed_node_bool=True)
expand_ncbigene_microrna(ob, mir96)
ob.neo4j_set_url() # use default url
ob.neo4j_set_auth() # use default username/password
ob.neo4j_push()
def test_expand_pharos_drug():
ob = Orangeboard(master_rel_is_directed, debug=True)
lovastatin = ob.add_node('pharos_drug', 'lovastatin', desc='lovastatin', seed_node_bool=True)
expand_pharos_drug(ob, lovastatin)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_anatomy_3():
ob = Orangeboard(master_rel_is_directed, debug=True)
mkd = ob.add_node('phenont_phenotype', 'HP:0000003', desc='Multicystic kidney dysplasia', seed_node_bool=True)
expand_phenont_phenotype(ob, mkd)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_anatomy_2():
ob = Orangeboard(master_rel_is_directed, debug=True)
hmox1 = ob.add_node('uniprot_protein', 'P09601', desc='HMOX1', seed_node_bool=True)
expand_uniprot_protein(ob, hmox1)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_issue_228():
ob = Orangeboard(debug=False)
bne = BioNetExpander(ob)
bne.add_node_smart('disease', 'MONDO:0005359', seed_node_bool=True, desc='drug-induced liver injury')
bne.add_node_smart('protein', 'Q59F02', seed_node_bool=True, desc='PMM2')
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_issue_269():
ob = Orangeboard(debug=False)
bne = BioNetExpander(ob)
chem_node = bne.add_node_smart('chemical_substance',
'CHEMBL521', seed_node_bool=True,
desc='Ibuprofen')
bne.expand_chemical_substance(chem_node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_issue_235():
ob = Orangeboard(debug=False)
bne = BioNetExpander(ob)
omim_node = bne.add_node_smart('disease',
'OMIM:105150', seed_node_bool=True,
desc='CEREBRAL AMYLOID ANGIOPATHY, CST3-RELATED')
bne.expand_genetic_condition(omim_node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_issue_237():
ob = Orangeboard(debug=False)
bne = BioNetExpander(ob)
chem_node = bne.add_node_smart('chemical_substance',
'KWHRDNMACVLHCE-UHFFFAOYSA-N', seed_node_bool=True,
desc='ciprofloxacin')
bne.expand_chemical_substance(chem_node)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def test_double_proteins():
ob = Orangeboard(debug=False)
bne = BioNetExpander(ob)
bne.add_node_smart('protein', 'Q59F02', seed_node_bool=True, desc='PMM2')
bne.add_node_smart('protein', 'H3BV55', seed_node_bool=True, desc='PMM2')
bne.add_node_smart('protein', 'A0A0S2Z4J6', seed_node_bool=True, desc='PMM2')
bne.add_node_smart('protein', 'H3BV34', seed_node_bool=True, desc='PMM2')
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def make_rels_file(filename='rels.csv', separator=','):
assert ':' not in separator
query_result = run_cypher('match (n)-[r]-(m) return n.UUID, m.UUID, r')
rels_file = open(filename, 'w')
for record in query_result:
source_node_uuid = record[0]
target_node_uuid = record[1]
rel = record[2]
rel_properties = rel.properties
reltype = rel.type
reltype_dir = BioNetExpander.MASTER_REL_IS_DIRECTED[reltype]
sourcedb = rel_properties['sourcedb']
rel_key = Orangeboard.make_rel_dict_key(source_node_uuid, target_node_uuid, reltype_dir)
if rel_key not in rels_set:
rels_set.add(rel_key)
rels_file.write('rel' + separator + source_node_uuid + separator + target_node_uuid + separator + sourcedb + ':' + reltype + '\n')
rels_file.close()
def test_issue9():
ob = Orangeboard(master_rel_is_directed, debug=True)
node1 = ob.add_node('uniprot_protein', 'P16887', desc='HBB')
node2 = ob.add_node('uniprot_protein', 'P09601', desc='HMOX1')
ob.add_rel('interacts_with', 'reactome', node1, node2)
ob.neo4j_set_url()
ob.neo4j_set_auth()
ob.neo4j_push()
def bigtest():
genetic_condition_mim_id = 'OMIM:603903' # sickle-cell anemia
target_disease_disont_id = 'DOID:12365' # malaria
## cerebral malaria: 'DOID:014069'
# genetic_condition_mim_id = 'OMIM:219700' # cystic fibrosis
# target_disease_disont_id = 'DOID:1498' # cholera
# genetic_condition_mim_id = 'OMIM:305900' # glucose-6-phosphate dehydrogenase (G6PD)
# target_disease_disont_id = 'DOID:12365' # malaria
# genetic_condition_mim_id = 'OMIM:607786' # proprotein convertase, subtilisin/kexin-type, 9 (PCSK9)
# target_disease_disont_id = 'DOID:13810' # familial hypercholesterolemia
# genetic_condition_mim_id = 'OMIM:184745' # kit ligard
# target_disease_disont_id = 'DOID:2841' # asthma
ob = Orangeboard(master_rel_is_directed, debug=True)
## add the initial target disease into the Orangeboard, as a 'disease ontology' node
disease_node = ob.add_node('disont_disease',
target_disease_disont_id,
desc='malaria',
seed_node_bool=True)
print('----------- first round of expansion ----------')
expand_all_nodes(ob)
print('----------- second round of expansion ----------')
expand_all_nodes(ob)
print('----------- third round of expansion ----------')
expand_all_nodes(ob)
print('total number of nodes: ' + str(ob.count_nodes()))
print('total number of edges: ' + str(ob.count_rels()))
## add the initial genetic condition into the Orangeboard, as a 'MIM' node
mim_node = ob.add_node('omim_disease',
genetic_condition_mim_id,
desc='sickle-cell anemia',
seed_node_bool=True)
print('----------- first round of expansion ----------')
expand_all_nodes(ob)
print('----------- second round of expansion ----------')
expand_all_nodes(ob)
print('----------- third round of expansion ----------')
expand_all_nodes(ob)
print('total number of nodes: ' + str(ob.count_nodes()))
print('total number of edges: ' + str(ob.count_rels()))
# push the entire graph to neo4j
ob.neo4j_set_url() # use default url
ob.neo4j_set_auth() # use default username/password
ob.neo4j_push()
from BioNetExpander import BioNetExpander
from QueryNCBIeUtils import QueryNCBIeUtils
from QuerySciGraph import QuerySciGraph
from QueryDisont import QueryDisont
from ParsePhenont import ParsePhenont
from QueryChEMBL import QueryChEMBL
import pandas
import timeit
import argparse
## configure requests package to use the "orangeboard.sqlite" cache
requests_cache.install_cache('orangeboard')
## create an Orangeboard object
ob = Orangeboard(debug=True)
## configure the Orangeboard for Neo4j connectivity
ob.neo4j_set_url()
ob.neo4j_set_auth()
master_rel_is_directed = {
'disease_affects': True,
'is_member_of': True,
'is_parent_of': True,
'gene_assoc_with': True,
'phenotype_assoc_with': True,
'interacts_with': False,
'controls_expression_of': True,
'is_expressed_in': True,
'targets': True
import requests_cache
import sys
from Orangeboard import Orangeboard
from BioNetExpander import BioNetExpander
import pandas
import os
import re
#requests_cache.install_cache('orangeboard')
# specifiy the path of orangeboard database
pathlist = os.path.realpath(__file__).split(os.path.sep)
RTXindex = pathlist.index("RTX")
dbpath = os.path.sep.join([*pathlist[:(RTXindex + 1)], 'data', 'orangeboard'])
requests_cache.install_cache(dbpath)
ob = Orangeboard(debug=True)
ob.neo4j_set_url()
ob.neo4j_set_auth()
bne = BioNetExpander(ob)
q1_diseases_dict = {
'DOID:11476': 'osteoporosis',
'DOID:526': 'HIV infectious disease',
'DOID:1498': 'cholera',
'DOID:4325': 'Ebola hemmorhagic fever',
'DOID:12365': 'malaria',
'DOID:10573': 'Osteomalacia',
'DOID:13810': 'hypercholesterolemia',
'DOID:9352': 'type 2 diabetes mellitus',
'DOID:2841': 'asthma',
return list(map(__get_in_degree, path.nodes))
def get_all_out_degrees_in_path(self, path):
# `MATCH (s)-[r]->() WHERE s.UUID IN $uuid_lst RETURN count(r)` does not preserve the order of $uuid_lst
# So here make a query for each node in the path
def __get_out_degree(node):
query = "MATCH (s)-[r]->() WHERE s.UUID = $uuid RETURN count(r) AS out_degree"
stmt_resp = self.orangeboard.neo4j_run_cypher_query(
query, parameters={'uuid': node.properties['UUID']})
return stmt_resp.single()['out_degree']
return list(map(__get_out_degree, path.nodes))
if __name__ == '__main__':
ob = Orangeboard(debug=False)
master_rel_is_directed = {
'disease_affects': True,
'is_member_of': True,
'is_parent_of': True,
'gene_assoc_with': True,
'phenotype_assoc_with': True,
'interacts_with': False,
'controls_expression_of': True,
'is_expressed_in': True,
'targets': True
}
ob.set_dict_reltype_dirs(master_rel_is_directed)
ob.neo4j_set_url()