saMNG_main.py

"""
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                       Version 3, 29 June 2007

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<http://www.gnu.org/licenses/>.

  The GNU General Public License does not permit incorporating your program
into proprietary programs.  If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library.  If this is what you want to do, use the GNU Lesser General
Public License instead of this License.  But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.

Title: Single Article Mesh Graph Network
Author: Akshay Shirsath
Logo Icon Source: www.flaticon.com
"""
############################################
############## Libraries ###################

# Web Application
import streamlit as st
import streamlit.components.v1 as components
from PIL import Image
import os 

# Fetching PubMed article metadata
from Bio import Entrez
from Bio import Medline
import numpy as np

import networkx as nx
from pyvis.network import Network

############################################
########### Custom Function ################

@st.cache
def pubmedData(pmid):
    """
    Returns PubMed data associated with PMID
    """
    Entrez.email = 'akishirsath@gmail.com'

    handle = Entrez.efetch(
      db="pubmed", 
      id=pmid, 
      rettype="medline", 
      retmode="text")

    records = Medline.parse(handle)
    records = list(records)[0]
    
    return records

def removeSpecialChar(string):
    """
    Removes special characters from given string
    """
    special_characters = ['!','#','$','%','@','[',']',' ',']','_', "*", ","]
    
    for i in special_characters:
        string = string.replace(i,' ').strip()
    
    return string

############################################
################## Main ####################

# Logo
image = Image.open('saMNG_logo.png')
st.image(image, use_column_width=True)

st.markdown("This web application visualizes MeSH terms in the PubMed article as Network-Graph representation.")

expander_bar = st.expander("About Site")
expander_bar.markdown("""
* **version 1.8**
* **Python Libraries:** streamlit, pyvis, networkx, biopython.
* **Data source:** PubMed Entrez
* **Author:** Akshay Shirsath   
* **Compare Two Topics:** [Click-Here](https://tcmng.herokuapp.com/)
""")

st.subheader('Enter PubMed Article URL')
default_url = "https://pubmed.ncbi.nlm.nih.gov/21371747/"
user_url = st.text_input('Replace below URL:', default_url)

pmid = user_url.split('/')[3]

if st.button('Show Graph'):

	st.spinner()
	with st.spinner(text=f'Fetching {pmid} PMID data...'):
		pubmed_data = pubmedData(pmid)
		
		title = pubmed_data.get('TI')

		authors = pubmed_data.get('AU')

		source = pubmed_data.get('SO')

		mesh = pubmed_data.get('MH')



	st.subheader('Article Info')
	text = ", ".join(authors)+" | "+title+" | "+source
	st.info(text)

	graph_components = dict()
	unique_words = set()

	for terms in mesh:
	    process_string = removeSpecialChar(terms)
	    clean_string = [word.strip() for word in process_string.split("/")]
	    
	    if len(clean_string)>1:
	        secondary_node = clean_string[0]
	        tertiary_nodes = clean_string[1:]
	        graph_components[secondary_node] = tertiary_nodes
	        
	        for word in clean_string:
	            unique_words.add(word.strip())
	    else:
	        secondary_node = clean_string[0]
	        graph_components[secondary_node] = "None"
	        unique_words.add(secondary_node)

	num_unique_words = len(unique_words)        


	paper_title = pubmed_data['TI']
	no_words_paper_title= len(paper_title.split())
	sentence_break = int(np.floor(no_words_paper_title/2))
	part_one = "-".join(paper_title.split(' ')[:sentence_break])
	part_two = "-".join(paper_title.split(' ')[sentence_break:])
	root_node = part_one + "\n" + part_two

	G = nx.Graph()

	G.add_node(root_node, size=24, title=f"PMID-{pmid}", color="#00ACEA")

	G.add_nodes_from(graph_components.keys(), size=16, color="#FEDB41")


	for key in graph_components.keys():
	    values = graph_components.get(key)
	    G.add_edge(root_node, key, weight=1.5)
	    if isinstance(values, list) and len(values)!=0:
	        for value in values:
	            G.add_node(value, color="#00EFD1")
	            G.add_edge(key, value)
	            
	    if isinstance(values, str) and values!='None':
	        G.add_node(values, color="#00EFD1")
	        G.add_edge(key, values)

	nt = Network(height="500px", width="65%", bgcolor='#dcdde1', font_color='#2f3640')
	nt.from_nx(G)
	nt.set_options("""
	var options = {
	  "physics": {
	    "barnesHut": {
	      "gravitationalConstant": -7700,
	      "centralGravity": 0,
	      "springLength": 120
	    },
	    "minVelocity": 0.75
	  }
	}
	""")

	nt.write_html(f'{pmid}.html')
	
	st.subheader('MeSH Graph')
	st.info('NOTE: Interact with mouse')

	HtmlFile = open(f"{pmid}.html", 'r', encoding='utf-8')
	source_code = HtmlFile.read() 
	components.html(source_code, height = 1200, width=1100)

try:
    os.remove(f'{pmid}.html')
except OSError:
    pass	

st.stop()