I have recently tried a few tools (MutationFinder, tmVar, PubTator etc.) that extract mutations from a given text. However, for my work I need something that will take a list of mutations as an input and return a list of pubmed id in which the mutations has been found.
Example input: mut_list = [Y702F, L483Y]
Example output: pub_list = [12215417, 18537569]
Can anyone give any idea?
Thanks!
You could use the pubmed API to query it directly. Typically I use Biopython for my pubmed queries. There are some good examples in the cookbook and on other SO posts.
This example from the cookbook link above has the guts of what you need. You will just have to iterate over your list. Depending on the number of queries you want to do you might have issues getting throttled by NCBI
In this example, we will query PubMed for all articles having to do with orchids (see section 2.3 for our motivation). We first check how many of such articles there are:
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com" # Always tell NCBI who you are
>>> handle = Entrez.egquery(term="orchid")
>>> record = Entrez.read(handle)
>>> for row in record["eGQueryResult"]: ...
if row["DbName"]=="pubmed": ...
print(row["Count"]) 463
Now we use the Bio.Entrez.efetch function to download the PubMed IDs of these 463 articles:
>>> from Bio import Entrez
>>> handle = Entrez.esearch(db="pubmed", term="orchid", retmax=463)
>>> record = Entrez.read(handle)
>>> handle.close()
>>> idlist = record["IdList"]
This returns a Python list containing all of the PubMed IDs of articles related to orchids
