def query_associated_data(res, edge_type, col, target_or_source='target_id'):
associated_ids = []
for r in res:
if r['edge_type'] == edge_type:
associated_ids.append(r[target_or_source])
if len(associated_ids) == 0:
return []
query = {"identifier": {'$in': associated_ids}}
return list(query_data_find(query, col))
def query_compound_nodes():
search_string = input("Enter a compound to query(ID/value):")
regx = re.compile(search_string, re.IGNORECASE)
query = {
'$or': [{
"identifier": {
'$regex': regx
}
}, {
"value": {
'$regex': regx
}
}]
}
count = count_documents(query, db.compounds)
res = list(query_data_find(query, db.compounds))
if count > 1:
index = 1
for doc in res:
print(str(index) + ") " + doc['identifier'] + " - " + doc['value'])
index += 1
desired_index = None
while desired_index is None:
desired_index = input(
"\nMultiple results, select desired compound[1-" + str(count) +
"]:")
if not desired_index.isdigit() or int(desired_index) < 1 or int(
desired_index) > count:
print("Please enter # for one of the results above...")
desired_index = None
compound = res[int(desired_index) - 1]
elif count == 1:
compound = res[0]
else:
print("\nNo results found for query: '" + search_string + "'")
return
print("\nYou have selected:")
print(compound)
input("\nPress enter to query associated data with this compound...")
clear_screen()
print("Querying...")
edge_res = query_edges(compound['identifier'])
# Self
CrC = query_associated_data(edge_res, 'CrC', db.compounds)
# Outgoing Edges
CtD = query_associated_data(edge_res, 'CtD', db.diseases)
CpD = query_associated_data(edge_res, 'CpD', db.diseases)
CuG = query_associated_data(edge_res, 'CuG', db.genes)
CdG = query_associated_data(edge_res, 'CdG', db.genes)
CbG = query_associated_data(edge_res, 'CbG', db.genes)
clear_screen()
# Printing results
print("==== " + compound['identifier'] + " ====")
print("Name: " + compound['value'])
print("==== Self Edge ====")
print("Resembles (CrC):")
for resembling_compound in CrC:
print_associated_results(resembling_compound)
print("==== Outgoing Edge ====")
print("Treats Diseases (CtD):")
for treates in CtD:
print_associated_results(treates)
print("Palliates Diseases (CtD):")
for palliates in CpD:
print_associated_results(palliates)
print("Upregulates Gene (CuG):")
for upreg in CuG:
print_associated_results(upreg)
print("Downregulates Gene (CdG):")
for downreg in CdG:
print_associated_results(downreg)
print("Binds Gene (CbG):")
for binds in CbG:
print_associated_results(binds)
print("==== Incoming Edge ====")
print("*NONE*")
def query_edges(s_id):
query_string = {'$or': [{"source_id": s_id}, {"target_id": s_id}]}
return list(query_data_find(query_string, db.edges))
def query_gene_nodes():
search_string = input("Enter a gene to query(ID/value):")
regx = re.compile(search_string, re.IGNORECASE)
query = {
'$or': [{
"identifier": {
'$regex': regx
}
}, {
"value": {
'$regex': regx
}
}]
}
count = count_documents(query, db.genes)
res = list(query_data_find(query, db.genes))
if count > 1:
index = 1
for doc in res:
print(str(index) + ") " + doc['identifier'] + " - " + doc['value'])
index += 1
desired_index = None
while desired_index is None:
desired_index = input(
"\nMultiple results, select desired gene[1-" + str(count) +
"]:")
if not desired_index.isdigit() or int(desired_index) < 1 or int(
desired_index) > count:
print("Please enter # for one of the results above...")
desired_index = None
gene = res[int(desired_index) - 1]
elif count == 1:
gene = res[0]
else:
print("\nNo results found for query: '" + search_string + "'")
return
print("\nYou have selected:")
print(gene)
input("\nPress enter to query associated data with this gene...")
clear_screen()
print("Querying...")
edge_res = query_edges(gene['identifier'])
# Self
GrG = query_associated_data(edge_res, 'Gr>G', db.genes)
GcG = query_associated_data(edge_res, 'GcG', db.genes)
GiG = query_associated_data(edge_res, 'GiG', db.genes)
# Incoming Compound Edges
CuG = query_associated_data(edge_res, 'CuG', db.compounds, 'source_id')
CdG = query_associated_data(edge_res, 'CdG', db.compounds, 'source_id')
CbG = query_associated_data(edge_res, 'CbG', db.compounds, 'source_id')
# Incoming Disease Edges
DuG = query_associated_data(edge_res, 'DuG', db.diseases, 'source_id')
DdG = query_associated_data(edge_res, 'DdG', db.diseases, 'source_id')
DaG = query_associated_data(edge_res, 'DaG', db.diseases, 'source_id')
# Incoming Anatomy Edges
AuG = query_associated_data(edge_res, 'AuG', db.anatomy, 'source_id')
AdG = query_associated_data(edge_res, 'AdG', db.anatomy, 'source_id')
AeG = query_associated_data(edge_res, 'AeG', db.anatomy, 'source_id')
clear_screen()
# Printing results
print("==== " + gene['identifier'] + " ====")
print("Name: " + gene['value'])
print("==== Self Edge ====")
print("Regulates (Gr>G)")
for reg in GrG:
print_associated_results(reg)
print("Covaries (GcG)")
for cov in GcG:
print_associated_results(cov)
print("Interacts (GiG)")
for inter in GiG:
print_associated_results(inter)
print("==== Outgoing Edge ====")
print("*NONE*")
print("==== Incoming Compound Edge ====")
print("Upregulated by Compound (CuG):")
for upreg in CuG:
print_associated_results(upreg)
print("Downregulated by Compound (CdG):")
for downreg in CdG:
print_associated_results(downreg)
print("Binded by Compound (CbG):")
for binds in CbG:
print_associated_results(binds)
print("==== Incoming Disease Edge ====")
print("Upregulated by Disease (DuG):")
for upreg in DuG:
print_associated_results(upreg)
print("Downregulated by Disease (DdG):")
for downreg in DdG:
print_associated_results(downreg)
print("Associated by Disease (DaG):")
for assoc in DaG:
print_associated_results(assoc)
print("==== Incoming Anatomy Edge ====")
print("Upregulated by Anatomy (AuG):")
for upreg in AuG:
print_associated_results(upreg)
print("Downregulated by Anatomy (AdG):")
for downreg in AdG:
print_associated_results(downreg)
print("Expressed by Anatomy (AeG):")
for exp in AeG:
print_associated_results(exp)
def query_anatomy_nodes():
search_string = input("Enter an anatomy to query(ID/value):")
regx = re.compile(search_string, re.IGNORECASE)
query = {
'$or': [{
"identifier": {
'$regex': regx
}
}, {
"value": {
'$regex': regx
}
}]
}
count = count_documents(query, db.anatomy)
res = list(query_data_find(query, db.anatomy))
if count > 1:
index = 1
for doc in res:
print(str(index) + ") " + doc['identifier'] + " - " + doc['value'])
index += 1
desired_index = None
while desired_index is None:
desired_index = input(
"\nMultiple results, select desired anatomy[1-" + str(count) +
"]:")
if not desired_index.isdigit() or int(desired_index) < 1 or int(
desired_index) > count:
print("Please enter # for one of the results above...")
desired_index = None
anatomy = res[int(desired_index) - 1]
elif count == 1:
anatomy = res[0]
else:
print("\nNo results found for query: '" + search_string + "'")
return
print("\nYou have selected:")
print(anatomy)
input("\nPress enter to query associated data with this anatomy...")
clear_screen()
print("Querying...")
edge_res = query_edges(anatomy['identifier'])
# Outgoing Edges
AuG = query_associated_data(edge_res, 'AuG', db.genes)
AdG = query_associated_data(edge_res, 'AdG', db.genes)
AeG = query_associated_data(edge_res, 'AeG', db.genes)
# Incoming Edges
DlA = query_associated_data(edge_res, 'DlA', db.diseases, 'source_id')
clear_screen()
# Printing results
print("==== " + anatomy['identifier'] + " ====")
print("Name: " + anatomy['value'])
print("==== Self Edge ====")
print("*NONE")
print("==== Outgoing Edge ====")
print("Upregulates Gene (AuG):")
for upreg in AuG:
print_associated_results(upreg)
print("Downregulates Gene (AdG):")
for downreg in AdG:
print_associated_results(downreg)
print("Expresses Gene (AeG):")
for express in AeG:
print_associated_results(express)
print("==== Incoming Edge ====")
print("Localized by Diseases (DlA):")
for localized_by in DlA:
print_associated_results(localized_by)
def query_disease_nodes():
search_string = input("Enter a disease to query(ID/value):")
regx = re.compile(search_string, re.IGNORECASE)
query = {
'$or': [{
"identifier": {
'$regex': regx
}
}, {
"value": {
'$regex': regx
}
}]
}
count = count_documents(query, db.diseases)
res = list(query_data_find(query, db.diseases))
if count > 1:
index = 1
for doc in res:
print(str(index) + ") " + doc['identifier'] + " - " + doc['value'])
index += 1
desired_index = None
while desired_index is None:
desired_index = input(
"\nMultiple results, select desired disease[1-" + str(count) +
"]:")
if not desired_index.isdigit() or int(desired_index) < 1 or int(
desired_index) > count:
print("Please enter # for one of the results above...")
desired_index = None
disease = res[int(desired_index) - 1]
elif count == 1:
disease = res[0]
else:
print("\nNo results found for query: '" + search_string + "'")
return
print("\nYou have selected:")
print(disease)
input("\nPress enter to query associated data with this disease...")
clear_screen()
print("Querying...")
edge_res = query_edges(disease['identifier'])
# Self
DrD = query_associated_data(edge_res, 'DrD', db.diseases)
# Outgoing Edges
DlA = query_associated_data(edge_res, 'DlA', db.anatomy)
DuG = query_associated_data(edge_res, 'DuG', db.genes)
DdG = query_associated_data(edge_res, 'DdG', db.genes)
DaG = query_associated_data(edge_res, 'DaG', db.genes)
# Incoming Edges
CtD = query_associated_data(edge_res, 'CtD', db.compounds, 'source_id')
CpD = query_associated_data(edge_res, 'CpD', db.compounds, 'source_id')
clear_screen()
# Printing results
print("==== " + disease['identifier'] + " ====")
print("Name: " + disease['value'])
print("==== Self Edge ====")
print("Resembles (DrD):")
for resembling_diseases in DrD:
print_associated_results(resembling_diseases)
print("==== Outgoing Edge ====")
print("Localizes Anatomy (DlA):")
for localizes in DlA:
print_associated_results(localizes)
print("Upregulates Gene (DuG):")
for upreg in DuG:
print_associated_results(upreg)
print("Downregulates Gene (DdG):")
for downreg in DdG:
print_associated_results(downreg)
print("Associated with Gene (DaG):")
for assoc in DaG:
print_associated_results(assoc)
print("==== Incoming Edge ====")
print("Treated by Compound (CtD):")
for treated_by in CtD:
print_associated_results(treated_by)
print("Palliated by Compound (CpD):")
for palliated_by in CpD:
print_associated_results(palliated_by)