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Updated BindingDB parser to correctly add all references to a 'public…
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…ations' edge property.
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@beaslejt
beaslejt committed Aug 11, 2023
1 parent e9cc03c commit 784a446
Showing 1 changed file with 137 additions and 54 deletions.
191 changes: 137 additions & 54 deletions parsers/BINDING/src/loadBINDINGDB.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import requests as rq
import pandas as pd
from decimal import Decimal
from numpy import nan

from parsers.BINDING.src.bindingdb_constraints import LOG_SCALE_AFFINITY_THRESHOLD #Change the binding affinity threshold here. Default is 10 uM Ki,Kd,EC50,orIC50
from Common.utils import GetData
Expand Down Expand Up @@ -32,6 +33,30 @@ class BD_EDGEUMAN(enum.IntEnum):
def negative_log(score): ### This function converts nanomolar concentrations into log-scale units (pKi/pKd/pIC50/pEC50). ###
return -(math.log10(score*(10**-9)))

def string_to_list(input, prefix: str):
#li = [prefix+item for item in input_list if not(math.isnan(item)) == True]
input = input.replace('[','').replace(']','')
li = input.split(", ")
li = [prefix+x for x in li if x != "nan"]
if li == None:
li = []
return li

def deduplicate_list(input_list):
return list(set(input_list))

def generate_dataframe_rows(df):
"""Generator function to yield each row of a pandas DataFrame.
Args:
df (pandas.DataFrame): The DataFrame to iterate over.
Yields:
pandas.Series: One row from the DataFrame as a pandas Series.
"""
for idx,row in df.iterrows():
yield idx,row

##############
# Class: Loading binding affinity measurements and sources from Binding-DB
# By: Michael Ramon & Jon-Michael Beasley
Expand Down Expand Up @@ -142,17 +167,19 @@ def parse_data(self) -> dict:

table = table.dropna(subset=["UniProt (SwissProt) Primary ID of Target Chain"])
table = table.dropna(subset=["PubChem CID"])
self.logger.info(f'About to group and aggregate ligand-protein pair data. This could take a while.')
table = table.groupby(["PubChem CID","UniProt (SwissProt) Primary ID of Target Chain"]).agg(list).reset_index()

self.logger.info(f'Done grouping data!')
# only keep 1000 entries for test mode
if self.test_mode:
table = table.head(1000)

measurements_list = []
does_it_bind_list = []
for idx,row in table.iterrows():
publications_store = []
for idx,row in generate_dataframe_rows(table):
if idx%10000 == 0:
self.logger.debug(idx,":",len(table))
self.logger.info(f"Processed {idx} of {len(table)} rows so far.")
does_it_bind = False
measurements_dict = {}
pKi_measurements = []
Expand All @@ -161,122 +188,177 @@ def parse_data(self) -> dict:
pEC50_measurements = []
kon_measurements = []
koff_measurements = []
publications_list = []
for i in range(len(row["Ki (nM)"])):

if type(row["Ki (nM)"][i]) == str:
measurement = {}
try:
value = round(negative_log(float(Decimal(str(row["Ki (nM)"][i]).replace('>','').replace('<','')))),3)
value = round(negative_log(float(Decimal(str(row["Ki (nM)"][i]).replace('>','').replace('<','')))),2)
if value > self.affinity_threshold:
does_it_bind = True
except:
value = "undefined"
measurement.update({"VALUE":value})
measurement.update({"affinity":value})
if type(row["PMID"][i]) == str:
pmid = row["PMID"][i]
measurement.update({"PMID":pmid})
pmid = "PMID:"+row["PMID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(pmid)
publications_list.append(pmid)
if type(row["PubChem AID"][i]) == str:
aid = row["PubChem AID"][i]
measurement.update({"PUBCHEM_AID":aid})
aid = "PUBCHEM.AID:"+row["PubChem AID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(aid)
publications_list.append(aid)
if type(row["Patent Number"][i]) == str:
patent = row["Patent Number"][i]
measurement.update({"PATENT_NUMBER":patent})
patent = "PATENT:"+row["Patent Number"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(patent)
publications_list.append(patent)
pKi_measurements = pKi_measurements + [measurement]

if type(row["Kd (nM)"][i]) == str:
measurement = {}
try:
value = round(negative_log(float(Decimal(str(row["Kd (nM)"][i]).replace('>','').replace('<','')))),3)
value = round(negative_log(float(Decimal(str(row["Kd (nM)"][i]).replace('>','').replace('<','')))),2)
if value > self.affinity_threshold:
does_it_bind = True
except:
value = "undefined"
measurement.update({"VALUE":value})
measurement.update({"affinity":value})
if type(row["PMID"][i]) == str:
pmid = row["PMID"][i]
measurement.update({"PMID":pmid})
pmid = "PMID:"+row["PMID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(pmid)
publications_list.append(pmid)
if type(row["PubChem AID"][i]) == str:
aid = row["PubChem AID"][i]
measurement.update({"PUBCHEM_AID":aid})
aid = "PUBCHEM.AID:"+row["PubChem AID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(aid)
publications_list.append(aid)
if type(row["Patent Number"][i]) == str:
patent = row["Patent Number"][i]
measurement.update({"PATENT_NUMBER":patent})
patent = "PATENT:"+row["Patent Number"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(patent)
publications_list.append(patent)
pKd_measurements = pKd_measurements + [measurement]

if type(row["IC50 (nM)"][i]) == str:
measurement = {}
try:
value = round(negative_log(float(Decimal(str(row["IC50 (nM)"][i]).replace('>','').replace('<','')))),3)
value = round(negative_log(float(Decimal(str(row["IC50 (nM)"][i]).replace('>','').replace('<','')))),2)
if value > self.affinity_threshold:
does_it_bind = True
except:
value = "undefined"
measurement.update({"VALUE":value})
measurement.update({"affinity":value})
if type(row["PMID"][i]) == str:
pmid = row["PMID"][i]
measurement.update({"PMID":pmid})
pmid = "PMID:"+row["PMID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(pmid)
publications_list.append(pmid)
if type(row["PubChem AID"][i]) == str:
aid = row["PubChem AID"][i]
measurement.update({"PUBCHEM_AID":aid})
aid = "PUBCHEM.AID:"+row["PubChem AID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(aid)
publications_list.append(aid)
if type(row["Patent Number"][i]) == str:
patent = row["Patent Number"][i]
measurement.update({"PATENT_NUMBER":patent})
patent = "PATENT:"+row["Patent Number"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(patent)
publications_list.append(patent)
pIC50_measurements = pIC50_measurements + [measurement]

if type(row["EC50 (nM)"][i]) == str:
measurement = {}
try:
value = round(negative_log(float(Decimal(str(row["EC50 (nM)"][i]).replace('>','').replace('<','')))),3)
value = round(negative_log(float(Decimal(str(row["EC50 (nM)"][i]).replace('>','').replace('<','')))),2)
if value > self.affinity_threshold:
does_it_bind = True
except:
value = "undefined"
measurement.update({"VALUE":value})
measurement.update({"affinity":value})
if type(row["PMID"][i]) == str:
pmid = row["PMID"][i]
measurement.update({"PMID":pmid})
pmid = "PMID:"+row["PMID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(pmid)
publications_list.append(pmid)
if type(row["PubChem AID"][i]) == str:
aid = row["PubChem AID"][i]
measurement.update({"PUBCHEM_AID":aid})
aid = "PUBCHEM.AID:"+row["PubChem AID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(aid)
publications_list.append(aid)
if type(row["Patent Number"][i]) == str:
patent = row["Patent Number"][i]
measurement.update({"PATENT_NUMBER":patent})
patent = "PATENT:"+row["Patent Number"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(pmid)
publications_list.append(patent)
pEC50_measurements = pEC50_measurements + [measurement]

if type(row["kon (M-1-s-1)"][i]) == str:
measurement = {}
try:
value = round(float(Decimal(str(row["kon (M-1-s-1)"][i]).replace('>','').replace('<',''))),3)
value = round(float(Decimal(str(row["kon (M-1-s-1)"][i]).replace('>','').replace('<',''))),2)
except:
value = "undefined"
measurement.update({"VALUE":value})
measurement.update({"affinity":value})
if type(row["PMID"][i]) == str:
pmid = row["PMID"][i]
measurement.update({"PMID":pmid})
pmid = "PMID:"+row["PMID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(pmid)
publications_list.append(pmid)
if type(row["PubChem AID"][i]) == str:
aid = row["PubChem AID"][i]
measurement.update({"PUBCHEM_AID":aid})
aid = "PUBCHEM.AID:"+row["PubChem AID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(aid)
publications_list.append(aid)
if type(row["Patent Number"][i]) == str:
patent = row["Patent Number"][i]
measurement.update({"PATENT_NUMBER":patent})
patent = "PATENT:"+row["Patent Number"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(patent)
publications_list.append(patent)
kon_measurements = kon_measurements + [measurement]

if type(row["koff (s-1)"][i]) == str:
measurement = {}
try:
value = round(float(Decimal(str(row["koff (s-1)"][i]).replace('>','').replace('<',''))),3)
value = round(float(Decimal(str(row["koff (s-1)"][i]).replace('>','').replace('<',''))),2)
except:
value = "undefined"
measurement.update({"VALUE":value})
measurement.update({"affinity":value})
if type(row["PMID"][i]) == str:
pmid = row["PMID"][i]
measurement.update({"PMID":pmid})
pmid = "PMID:"+row["PMID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(pmid)
publications_list.append(pmid)
if type(row["PubChem AID"][i]) == str:
aid = row["PubChem AID"][i]
measurement.update({"PUBCHEM_AID":aid})
aid = "PUBCHEM.AID:"+row["PubChem AID"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(aid)
publications_list.append(aid)
if type(row["Patent Number"][i]) == str:
patent = row["Patent Number"][i]
measurement.update({"PATENT_NUMBER":patent})
patent = "PATENT:"+row["Patent Number"][i]
if "publications" not in measurement.keys():
measurement.update({"publications":[]})
measurement["publications"].append(patent)
publications_list.append(patent)
koff_measurements = koff_measurements + [measurement]

if pKi_measurements != []:
Expand All @@ -291,7 +373,7 @@ def parse_data(self) -> dict:
measurements_dict.update({"kon(M-1-s-1)":pKi_measurements})
if koff_measurements != []:
measurements_dict.update({"koff(s-1)":pKi_measurements})

publications_store = publications_store + [deduplicate_list(publications_list)]
measurements_list = measurements_list + [measurements_dict]
if does_it_bind == True:
does_it_bind_list = does_it_bind_list + ["True"]
Expand All @@ -300,6 +382,7 @@ def parse_data(self) -> dict:

table['measurements'] = measurements_list
table['does_it_bind'] = does_it_bind_list
table['publications'] = publications_store
table = table[table['does_it_bind'] == "True"]

pandas_output_file_path = os.path.join(self.data_path, f"BindingDB_temp_table.tsv")
Expand All @@ -319,12 +402,12 @@ def parse_data(self) -> dict:
lambda line: {}, #Node 2 props
lambda line: {
"measurements":line[11],
PUBLICATIONS:[x for x in line[6] if type(x) == str]
PUBLICATIONS:line[13]
},
comment_character=None,
delim="\t",
has_header_row=True)

os.remove(pandas_output_file_path)
#os.remove(pandas_output_file_path)

return extractor.load_metadata

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