使用biopython搜索带有术语列表的PubMed

Question

我在pandas dataframe列中有一系列术语，我想用这些术语搜索PubMed，以了解它们在文献中出现的频率。我正在尝试调整Entrez biopython代码来完成这项任务，但不确定如何继续，因为我使用的代码似乎是针对单个搜索项，而不是数据帧。这是我到目前为止得到的结果，它返回HTTPError:HTTPError 500:Internal Server Error。提前感谢您的建议

from Bio import Medline
import pandas as pd
import time
Entrez.email =myemail@mail.com

# return a list of the PMIDs that match your search term

def getPubMedIDs(searchstring,maxrecords):
    IDlist=[]
    if not maxrecords > 100000: #maximum possible = 100,000 records
        handle = Entrez.esearch(db="pubmed", term=searchstring, retmax = maxrecords) 
        result = Entrez.read(handle)
        IDlist= result["IdList"]
        handle.close()

    return IDlist
# get MEDLINE data records for each PMID and store in a dataframe
# searchPMIDlist was created by getPubMedIDs function
# this will only get the first 10000 records from your PMID list

def getPubMeddata(searchPMIDlist,dataframename):

    # a trick to remove duplicates from the PMID list using set and list
    searchPMIDlist = list(set(searchPMIDlist))

    # for displaying number of records processed
    counter=0

    # get MEDLINE data records
    fetchhandle = Entrez.efetch(db="pubmed", id=searchPMIDlist, rettype="medline", retmode="text")
    fetchresult = Medline.parse(fetchhandle)

    # parse the dictionary of returned records
    for record in fetchresult: 
        if "PMID" not in record: # if there's no PMID in this record (rare), skip it
            continue

        PT=''
        if "PT" in record: # if there's a pub type list in this record, store it
            PT=record["PT"]
        TI=''
        if "TI" in record: # if there's a title in this record, store it
            TI=record["TI"]
        AB=''
        if "AB" in record: # if there's an abstract in this record, store it
            AB=record["AB"]
        MH=''
        if "MH" in record:
            MH=record["MH"]

        # put the data you found into a new row in the dataframe
        # you might want to collect different data for your purposes
        dataframename = dataframename.append({'PMID': record["PMID"],
                                              'PT': PT,
                                              'Title': TI,
                                              'Abstract': AB,
                                              'MeSH': MH,
                                              'AbLength': len(AB)}, ignore_index=True)

        # if we've processed 100 new records, display number of records processed
        counter += 1
        if not counter % 100:
            print(counter, "records processed")

    time.sleep(5) # wait time between repeated fetches
    fetchhandle.close()

    return dataframename


myPMIDlist=[]
searchstring=allresultsdf['New Term'] #allresultsdf is dataframe containing terms I am searching, New Term is the column

myPMIDlist = getPubMedIDs(searchstring, 3000)
print("Search string:", searchstring)
print("Total PMIDs found:",len(myPMIDlist))```