How to interpret the ec2pathway.pkl file (e.g., enzyme and pathway labels)?

[jolespin]

I've loaded the file into Python but I can't figure out how to interpret the results inside. I'm assuming the rows are compounds and columns are pathways but how can I get the labels of enzymes and pathways?

import pickle
with open("/Users/jolespin/Databases/Pathway2Vec/ec2pathway.pkl", "rb") as f:
    ec2pathway = pickle.load(f)
    # DeprecationWarning: Please use `lil_matrix` from the `scipy.sparse` namespace, the `scipy.sparse.lil` namespace is deprecated.
    
type(ec2pathway) 
# scipy.sparse._lil.lil_matrix

ec2pathway.data
# array([list([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
#        list([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
#        list([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
#        ..., list([]), list([1, 1, 1, 1, 1, 1, 1, 1]), list([1, 1])],
#       dtype=object)

df = pd.DataFrame(ec2pathway.todense())
print(df.shape)
# (6378, 2526)

df[0][lambda x: x != 0]

# 3579    1
# 3667    1
# 3678    1
# 3681    1
# Name: 0, dtype: int32