def get_connection_normalizing_count(gene_list, node_type_list):
# dictionary that keeps track of all connections from a gene to any node type
connection_dict = {}
for gene_symbol in gene_list:
gene_found = False
gene_query = ht.query(gene_symbol)['Gene']
for i in gene_query:
if (i['SYMBOL'].lower() == gene_symbol.lower()):
gene = i
gene_found = True
if (gene_found == True):
count = 0
input_object = gene
for x in node_type_list:
try:
## only look at direct connections
fc = FindConnection(input_obj=input_object,
output_obj=x,
intermediate_nodes=None)
fc.connect(verbose=False)
df = fc.display_table_view()
rows = df.shape[0]
count = count + rows
except:
print("gene " + str(gene_symbol) +
" for node intermediate " + str(x) + " failed")
connection_dict[gene_symbol] = count
else:
print(gene_symbol + ' could not be found')
connection_dict[gene_symbol] = 'Unknown'
return (connection_dict)
def setUpClass(cls):
ht = Hint()
cxcr4 = ht.query("CXCR4")["Gene"][0]
fc = FindConnection(input_obj=cxcr4,
output_obj="ChemicalSubstance",
intermediate_nodes=None)
fc.connect(verbose=True)
cls.response = fc.to_reasoner_std()
def setUp(self):
ht = Hint()
cxcr4 = ht.query('CXCR4')['Gene'][0]
fc = FindConnection(input_obj=cxcr4,
output_obj='ChemicalSubstance',
intermediate_nodes=None)
fc.connect(verbose=True)
self.response = fc.to_reasoner_std()
def test_one_filt(self):
ht = Hint()
input = ht.query('hyperphenylalaninemia')['Disease'][0]
filt = [{}, {'name': 'NodeDegree', 'count': 25}]
fc = FindConnection(input_obj=input,
output_obj='ChemicalSubstance',
intermediate_nodes=['Gene'],
filters=filt)
fc.connect()
self.assertEqual(27, len(fc.fc.G.nodes))
def test_no_filter(self):
ht = Hint()
input = ht.query('hyperphenylalaninemia')['Disease'][0]
filt = []
fc = FindConnection(input_obj=input,
output_obj='ChemicalSubstance',
intermediate_nodes=['Gene'],
filters=filt)
fc.connect()
for node, y in fc.fc.G.nodes(data=True):
self.assertTrue('filteredBy' not in y.keys())
def test_result_section(self):
"""Find connection between TMPRSS2 and pentamidine through all intermediate nodes """
tmprss2 = ht.query("TMPRSS2")["Gene"][0]
pentamidine = ht.query("pentamidine")["ChemicalSubstance"][0]
fc = FindConnection(
input_obj=tmprss2,
output_obj=pentamidine,
intermediate_nodes=["BiologicalEntity"],
registry=None,
)
fc.connect(verbose=True)
self.assertIn("PLXNA2", fc.fc.G)
def step_impl(context):
context.fc = FindConnection(input_obj=context.disease,
output_obj=context.chemical,
intermediate_nodes=['Gene'],
registry=reg)
context.fc.connect(verbose=True)
print(context.fc.fc.G)
def test_query_with_broken_intermediate_nodes(self):
"""For a query with long intermediate nodes, it might happen that one intermediate query returns 0 hits.
In this case, we should stop the code execution"""
mof = ht.query("Multiple Organ Failure")["Disease"][0]
fc = FindConnection(
mof,
output_obj="Gene",
intermediate_nodes=[
"BiologicalProcess",
"Cell",
"AnatomicalEntity",
"CellularComponent",
],
)
fc.connect()
self.assertGreater(len(fc.fc.G), 2)
def get_disease_to_gene_results(disease_input):
disease_to_gene_results = {}
#directly related
fc = FindConnection(input_obj=disease_input,
output_obj='Gene',
intermediate_nodes=None)
fc.connect(verbose=False)
disease_to_genes = fc.display_table_view()
disease_to_genes = disease_to_genes[~disease_to_genes['output_id'].str.
contains('UMLS')]
# keep track of number of occurrences from direct disease -> gene connection
print("running disease -> gene")
i = list(disease_to_genes["output_name"])
d = {x: i.count(x) for x in i}
sorted_disease_to_genes = {
k: v
for k, v in sorted(d.items(), key=lambda item: item[1])
}
disease_to_gene_results[
"sorted_disease_to_genes"] = sorted_disease_to_genes
# print("occurences of genes directly related to genes")
# print(disease_to_gene_results["sorted_disease_to_genes"])
one_step_genes_pub_counts = {}
for index, row in disease_to_genes.iterrows():
current_pubcount = 0
if (row["pred1_pubmed"] != None):
current_pubcount = current_pubcount + row["pred1_pubmed"].count(
",") + 1
if row["output_name"] in one_step_genes_pub_counts:
one_step_genes_pub_counts[
row["output_name"]] = one_step_genes_pub_counts[
row["output_name"]] + current_pubcount
else:
one_step_genes_pub_counts[row["output_name"]] = current_pubcount
disease_to_gene_results[
"one_step_genes_pub_counts"] = one_step_genes_pub_counts
disease_to_genes_list = list(reversed(list(
sorted_disease_to_genes.keys())))
disease_to_gene_results["disease_to_genes_list"] = disease_to_genes_list
return (disease_to_gene_results)
def predict_many(input_object, intermediate_node_list, output_type):
df_list = []
for inter in intermediate_node_list:
try:
print("Intermediate Node type running:")
print(inter)
fc = FindConnection(input_obj=input_object,
output_obj=output_type,
intermediate_nodes=[inter])
fc.connect(verbose=False)
df = fc.display_table_view()
rows = df.shape[0]
if (rows > 0):
df_list.append(df)
except:
print("FAILED")
if (len(df_list) > 0):
return pd.concat(df_list)
else:
return None
def get(self):
input_obj = self.get_query_argument('input_obj')
output_obj = self.get_query_argument('output_obj')
print("executing connect query: ", self.request.uri)
intermediate_nodes = self.get_query_argument('intermediate_nodes')
if type(input_obj) == str:
input_obj = tornado.escape.json_decode(input_obj)
if type(output_obj) == str:
output_obj = tornado.escape.json_decode(output_obj)
if type(intermediate_nodes) == str:
intermediate_nodes = ast.literal_eval(intermediate_nodes)
fc = FindConnection(input_obj=input_obj,
output_obj=output_obj,
intermediate_nodes=intermediate_nodes,
registry=reg)
fc.connect()
df = fc.display_table_view()
if df.empty:
res = []
else:
df = df[[
'input', 'pred1', 'pred1_api', 'node1_name', 'node1_type',
'pred2', 'pred2_api', 'output_name'
]]
df.drop_duplicates(inplace=True)
res = df.to_dict('records')
if res:
self.set_status(200)
self.write(
tornado.escape.json_encode({
'data': res,
'log': fc.fc.log
}))
self.finish()
return
else:
self.set_status(404)
self.write(json.dumps({'error': "Unable to find any connection"}))
self.finish()
return
def test_two_filt(self):
ht = Hint()
input = ht.query('hyperphenylalaninemia')['Disease'][0]
filt = [{
'name': 'NodeDegree',
'count': 20
}, {
'name': 'EdgeLabel',
'label': 'related_to'
}]
fc = FindConnection(input_obj=input,
output_obj='ChemicalSubstance',
intermediate_nodes=['Gene'],
filters=filt)
fc.connect()
self.assertEqual(52, len(fc.fc.G.nodes))
for node, y in fc.fc.G.nodes(data=True):
if node != 'mild hyperphenylalaninemia':
if y['type'] == 'Gene':
self.assertEqual('NodeDegree', y['filteredBy'])
elif y['type'] == 'ChemicalSubstance':
self.assertEqual('EdgeLabel', y['filteredBy'])
tbi = tbi_hint["Disease"][0]
print(tbi)
print()
# Find all potential representations of unipolar depression
depression_hint = ht.query("unipolar depression")
print(depression_hint)
print()
# Select the correct representation of depression
depression = depression_hint["Disease"][0]
print(depression)
print()
# help(FindConnection.__init__)
fc = FindConnection(input_obj=depression,
output_obj=tbi,
intermediate_nodes="BiologicalEntity")
# BTE finding connection
fc.connect(verbose=True)
print()
print("Displaying and filter results")
# Displaying and filter results
df = fc.display_table_view()
# because UMLS is not currently well-integrated in our ID-to-object translation system, removing UMLS-only entries here
patternDel = "^UMLS:C\d+"
filter = df.node1_id.str.contains(patternDel)
df = df[~filter]
fc.to_graphml("TBI.graphml")
fc.to_reasoner_std()
from biothings_explorer.hint import Hint
from biothings_explorer.user_query_dispatcher import FindConnection
ht = Hint()
ace2 = ht.query("ACE2")['Gene'][0]
# print(ace2)
fc = FindConnection(input_obj=ace2,
output_obj='DiseaseOrPhenotypicFeature',
intermediate_nodes='ChemicalSubstance')
fc.connect(verbose=True)
# save graphml file to test.graphml
output = fc.to_graphml("test.graphml")
from chp.core.query import Query
from chp.core.reasoner_std import ReasonerStdHandler
query_path = '/home/cyakaboski/src/python/projects/bkb-pathway-provider/tests/reasonerStdTests/sample_query.pk'
if os.path.exists(query_path):
with open(query_path, 'rb') as f_:
reasoner_std = pickle.load(f_)
else:
ht = Hint()
breast_cancer = ht.query('breast cancer')['Disease'][0]
tamoxifin = ht.query('tamoxifen')['ChemicalSubstance'][0]
fc = FindConnection(input_obj=breast_cancer,
output_obj=tamoxifin,
intermediate_nodes='Gene')
fc.connect(verbose=True)
reasoner_std = fc.to_reasoner_std()
#-- Add target node and edge to Query Graph
reasoner_std['query_graph']['nodes'].append({
'id': 't1',
'type': 'PhenotypicFeature',
'curie': 'CHPDART:SURVIVAL',
'operator': '>=',
'value': '365'
})
reasoner_std['probability_targets'] = [('Survival', '>=', '365')]
reasoner_std['reasoner_id'] = 'explorer'
# The angiotensin-converting enzyme 2, or ACE2 “receptor,” is the protein
# provides the entry point for the coronavirus to hook into and
# infect a wide range of human cells.
from biothings_explorer.user_query_dispatcher import FindConnection
from biothings_explorer.hint import Hint
ht = Hint()
ace2 = ht.query("ACE2")['Gene'][0]
fc = FindConnection(input_obj=ace2,
output_obj='ChemicalSubstance',
intermediate_nodes=['BiologicalEntity'])
fc.connect(
verbose=True
) # There was a KeyError: "equivalent_ids" on this line, will not move on from this example
def get_symtpom_prevalence(hp_symptom_dict, disease_name):
for key in hp_symptom_dict:
print(key)
edges_out_count = 0
# print("name: " + str(hp_symptom_dict[key]))
UMLS = ''
for y in ['PhenotypicFeature', 'Disease', 'BiologicalProcess']:
if y == 'PhenotypicFeature':
a = ht.query(key)[y]
if len(a) > 0:
b = a[0]
if 'UMLS' in b:
UMLS = b['UMLS']
try:
fc = FindConnection(input_obj=b,
output_obj='Gene',
intermediate_nodes=None)
fc.connect(verbose=False)
df = fc.display_table_view()
print('gene')
print(df.shape)
# print("phen")
# print(hp_symptom_dict[key])
# print(df.shape[0])
if (df.shape[0] > 0):
print("OKKKk")
df = df[df["output_name"] != disease_name]
edges_out_count = edges_out_count + df.shape[0]
print(edges_out_count)
except:
print("Nope")
try:
fc = FindConnection(input_obj=b,
output_obj='Disease',
intermediate_nodes=None)
fc.connect(verbose=False)
df = fc.display_table_view()
print(df.shape)
# print("phen")
# print(hp_symptom_dict[key])
# print(df.shape[0])
if (df.shape[0] > 0):
print("ok edge phen to dis")
df = df[df["output_name"] != disease_name]
edges_out_count = edges_out_count + df.shape[0]
print(edges_out_count)
except:
print("Nope")
if (y == 'Disease') | (y == 'BiologicalProcess'):
for z in hp_symptom_dict[key]["names"]:
if ((y == 'Disease') & (len(UMLS) > 0)):
try:
a = ht.query(UMLS)[y]
except:
a = []
# pass
else:
try:
a = ht.query(z)[y]
except:
a = []
# pass
# print(a)
for b in a:
if b['name'].lower() == z.lower():
# print('match')
# print(b)
# print(z)
try:
fc = FindConnection(input_obj=b,
output_obj='Gene',
intermediate_nodes=None)
fc.connect(verbose=False)
df = fc.display_table_view()
# print("BD")
# print(df.shape[0])
if (df.shape[0] > 0):
df = df[df["output_name"] != disease_name]
edges_out_count = edges_out_count + df.shape[
0]
except:
print("Nope")
try:
fc = FindConnection(input_obj=b,
output_obj='Disease',
intermediate_nodes=None)
fc.connect(verbose=False)
df = fc.display_table_view()
# print("BD")
# print(df.shape[0])
if (df.shape[0] > 0):
df = df[df["output_name"] != disease_name]
edges_out_count = edges_out_count + df.shape[
0]
except:
print("Nope")
print("edges out")
print(edges_out_count)
hp_symptom_dict[key]["edges_out_count"] = edges_out_count
return (hp_symptom_dict)
def step_impl(context):
context.fc = FindConnection(input_obj=context.gene,
output_obj="ChemicalSubstance",
intermediate_nodes=None,
registry=reg)
context.fc.connect(verbose=True)
def determined_genes_to_symptoms(gene_list, symptom_list):
# gene -> phenotypic feature nodes
print("Genes -> PhenotypicFeatures")
df_list = []
for x in gene_list:
# print(x)
try:
gene = ht.query(x)["Gene"][0]
fc = FindConnection(input_obj=gene,
output_obj='PhenotypicFeature',
intermediate_nodes=None)
fc.connect(verbose=False)
df = fc.display_table_view()
rows = df.shape[0]
if (rows > 0):
df_list.append(df)
except:
print(str(x) + " FAILED")
if (len(df_list) > 0):
top_gene_to_phenotypicFeature = pd.concat(df_list)
## Get names for HP ids
HP_ids = top_gene_to_phenotypicFeature[
top_gene_to_phenotypicFeature["output_name"].str.contains(
"HP:", regex=False)]["output_name"]
HP_ids = list(HP_ids)
HP_ids = list(dict.fromkeys(HP_ids))
# len(HP_ids)
HP_dict = {}
for x in HP_ids:
HP_ID = x.split(':')[1]
r = requests.get('https://biothings.ncats.io/hpo/phenotype/HP%3A' +
HP_ID)
res = r.json()
if (('_id' in res) & ('name' in res)):
HP_dict[res['_id']] = res['name'].lower()
phen_indices = get_similar_phen_indices(
list(top_gene_to_phenotypicFeature["output_name"]), symptom_list, 0.95,
HP_dict)
phen_top = top_gene_to_phenotypicFeature.iloc[phen_indices, :]
# phen_top = top_gene_to_phenotypicFeature
# phen_top
for index in range(phen_top.shape[0]):
# if("HP:" in row['output_name']):
# print(index)
if (phen_top.iloc[index]["output_name"] in HP_dict):
phen_top.iloc[index]["output_name"] = HP_dict[phen_top.iloc[index]
["output_name"]]
phen_top
# gene -> bioprocess
print("Genes -> Bioprocesses")
df_list = []
for x in gene_list:
# print(x)
try:
gene = ht.query(x)["Gene"][0]
fc = FindConnection(input_obj=gene,
output_obj='BiologicalProcess',
intermediate_nodes=None)
fc.connect(verbose=False)
df = fc.display_table_view()
rows = df.shape[0]
if (rows > 0):
df_list.append(df)
except:
print(str(x) + " FAILED")
if (len(df_list) > 0):
top_gene_to_bioprocesses = pd.concat(df_list)
go_ids = top_gene_to_bioprocesses[
top_gene_to_bioprocesses["output_name"].str.contains(
"go:", regex=False)]["output_name"]
go_ids = list(go_ids)
go_ids = list(dict.fromkeys(go_ids))
# len(go_ids)
go_dict = {}
for x in go_ids:
go_ID = x.split(':')[1]
r = requests.get('https://biothings.ncats.io/go_bp/geneset/GO%3A' +
go_ID)
res = r.json()
if ('name' in res):
go_dict[res['_id']] = res['name'].lower()
bp_indices = get_similar_bp_indices(
list(top_gene_to_bioprocesses["output_name"]), symptom_list, 0.95,
go_dict)
bioprocess_top = top_gene_to_bioprocesses.iloc[bp_indices, :]
# bioprocess_top = top_gene_to_bioprocesses
# Genes -> disease type "symptoms"
print("Genes -> Diseases")
df_list = []
for x in gene_list:
try:
gene = ht.query(x)["Gene"][0]
fc = FindConnection(input_obj=gene,
output_obj='Disease',
intermediate_nodes=None)
fc.connect(verbose=False)
df = fc.display_table_view()
rows = df.shape[0]
if (rows > 0):
df_list.append(df)
except:
print(str(x) + " FAILED")
if (len(df_list) > 0):
top_gene_to_diseases = pd.concat(df_list)
disease_indices = get_similar_disease_indices(
list(top_gene_to_diseases["output_name"]), symptom_list, 0.95)
relevant_top_gene_to_diseases = top_gene_to_diseases.iloc[
disease_indices, :]
# relevant_top_gene_to_diseases = top_gene_to_diseases
## make dataframe with all genes -> symptoms
all_gene_connections = pd.concat(
[bioprocess_top, phen_top, relevant_top_gene_to_diseases])
all_gene_connections["output_name"] = all_gene_connections[
"output_name"].str.lower()
return (all_gene_connections)
