polyphenol_pubmed

Tiny script to query pubmed using the phenol explorer database

%pip install pymed from pymed import PubMed import pandas as pd from IPython.display import Markdown, display import regex as re from google.colab import files

import numpy as np

def printmd(string): display(Markdown(string))

#!wget https://github.com/compchemeric/polyphenol_pubmed/blob/main/natural-compounds-classification.csv %ls

mols = pd.read_csv('natural-compounds-classification.csv', sep=";") print(mols)
mollist = mols['Compound Name'].tolist()

if True: number_of_pubs = [] for mol in mollist:

query_words = ['ampk', mol]

pubmed = PubMed(tool="MyTool", email="my@email.address")

#print(mol)

try:
  results = pubmed.query(f'{query_words[0]} "{query_words[1]}"[Title/Abstract]', max_results=500)
  number_of_pubs.append(len(list(results)))
except: 
  print('error with pubmed query')
  number_of_pubs.append(np.nan)

np.save('n_pubs.npy', number_of_pubs)

n_pubs = np.load('n_pubs.npy')

d = {'Molecules': mollist, 'Publications': n_pubs}

df = pd.DataFrame(d) df.sort_values('Publications', ascending=False, inplace=True) print(df.head(100))

if True: for i,article in enumerate(results): article_id = article.pubmed_id title = article.title for word in query_words: title = re.sub(f'{word}', f'{word}', title)

publication_date = article.publication_date
abstract = article.abstract
authors = article.authors
journal = article.journal

printmd(f'{title} {publication_date} {journal}')