Convert article title to pubmed ID

Question

[BIOTIN]

Hi,

Is any tool/method to convert article title to pubmed ID? Anyone know?

Thank you,

[dilrajk]

It didn't work for my file. I have around 98 Paper titles and I wanted to get the Pubmed id. I got the output showing "Not found" for all the titles.

[mohammadhassanj]

Hi, can I have your file to test the script?

Answer 1

[mohammadhassanj]

from lxml import etree
from requests import get
import sys
import os

url_for_get_id = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&field=title&term=\"{}\""
url_for_get_title = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={}&retmode=XML"

def xml_id_or_title_extractor(page):

   """extract the ids from page and return that as string"""

   content = etree.fromstring(page)
   root = content.getroottree()
   result = [item.text for item in root.xpath(xpath)]
   if len(result)<1:
       return "Not Found!!"
   return ",".join(result)

def write_to_file(_list):

    result = open("title_pubmedid_result.txt","a")

    for title in _list:
        try:
            title = title.strip()
            page = get(URL.format(title)).content
            _id = xml_id_or_title_extractor(page)
            result.write(_id + "\t" + title + "\n")
            print (title,"===>","OK")
        except:
            print("An Exception occurred!! on \n <{}>".format(title))
            result.write("ERROR" + "\t" + title + "\n")
    result.close()

def run(title_list):

    if len(sys.argv) > 2:
        path = os.getcwd()
        file_path = path+"/"+sys.argv[2]
        try:
            read_file = [item.strip() for item in open(file_path).readlines()]
            write_to_file(read_file)
        except FileNotFoundError:
            print ("your file is not exsists or input file not in same directory")
        except:
            print ("there is a problem with your input file")
    else:
        write_to_file(title_list)


if __name__ == "__main__":

    print ("the script is running\n")
    print ("this is a script to convert article paper to pubmedid and vice versa")
    print ("*"*20)

    if len(sys.argv)<2:
        print ("\nyour arguments are not enough !!\n \n Use this format : for example \n\n< python pubmedid_to_title.py -t2id your_file.txt> for reading from file\n\n\
        or \n\n< python pubmedid_to_title.py -t2id> for reading from a list")
        sys.exit()
    elif sys.argv[1] == "-t2id":
        URL = url_for_get_id
        xpath = "//Id"
        _id_or_title_list = ["Differentially Expressed miRNAs in Hepatocellular Carcinoma Target Genes in the Genetic Information Processing and Metabolism Pathways.",
        "miR-429 inhibits migration and invasion of breast cancer cells in vitro."]

    elif sys.argv[1] == "-id2t":
        URL = url_for_get_title
        xpath = "//ArticleTitle"
        _id_or_title_list = ["18456660","19196975"]
    else:
        print ("use -id2t for convert id to title or -t2id for convert title to id as first argument!! ")
        sys.exit()
    # suppose you have a list of paper's title, for example two titles or two id ==> _id_or_title_list list
    # you can edit it ...

    # if you wnat to read from a file, your file name come after it, be careful the script and file directory must be in same directory
    # also each line should be just one title
    # for example type this:
    # python title_to_pubmedid.py -t2id your_file.txt
    # first argument must be -t2id for convert titles to ides and -id2t for reverse search
    #SO YOU HAVE TWO CHICE: 1:READ FROM FILE 2:EDIT THE ABOVE LIST :D
    run(_id_or_title_list)

[WouterDeCoster]

Looking good! Thanks!

[alibjubran]

Thank you very much That was really helpful for me

Answer 2

[Ram]

You should be able to use eutils to query Pubmed with the title and get the PubmedID.

Also, try using biomaRt or reutils. They will help you work with the query output from NCBI as objects, which you can then use for further downstream analyses.

You'd just have to replicate this eutils query if you use reuils:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=p.R301X%20Mutation%20and%20Variable%20Phenotypic%20Appearance%20of%20Fabry%20Disease&retMode=json

This searches for the paper titled "p.R301X Mutation and Variable Phenotypic Appearance of Fabry Disease.", something I picked at random.

[BIOTIN]

Thank you so much! This is what I want~