通过PMC ID自动批量下载PubMed文献

 2025.3.13更新

更新代码如下：

加入了添加文件名后PMID的功能，如不需要可自行删去pmid相关变量

import pandas as pd
from bs4 import BeautifulSoup
import requests
from fake_useragent import UserAgent


def download(pmc_id, filename, pmid):
    url = 'https://www.ncbi.nlm.nih.gov/pmc/articles/' + str(pmc) + "/"
    ua = UserAgent()
    headers = {'User-Agent': ua.firefox}
    request = requests.get(url, headers=headers)
    bs = BeautifulSoup(request.content, 'lxml')
    download_url = bs.find_all(attrs={'class': "usa-link display-flex usa-tooltip"})
    download_link = download_url[1].get('href')
    print(download_link)
    download_url = "https://pmc.ncbi.nlm.nih.gov/articles" + "/" + pmc + "/" + download_link
    print(filename)
    print(download_url)
    r = requests.get(download_url, headers=headers)
    with open("The Path You Want to Store These/Papers/"+filename+"_"+ str(pmid) + ".pdf", 'wb') as f:
        f.write(r.content)


# Read the excel file containing the list of papers
df = pd.read_excel('The Path Where Your Paper List is Located/Demo_Paper_List.xlsx', header=None)
df.columns = ['Title', 'PMCNum', "PMID"]

# Drop rows with missing values
PMC = df.dropna(axis=0, how='any')
print(PMC)
PMCNum = PMC['PMCNum']
TitleO = list(PMC['Title'])
PMID = list(PMC['PMID'])

# Remove special characters from the title
Title = []
for i in TitleO:
    table = i.maketrans(':"/', '   ')
    Title.append(i.translate(table))

# Download the papers
failed_titles = []
for m, pmc in enumerate(PMCNum):
    file = Title[m]
    pmid = PMID[m]
    try:
        download(filename=file, pmc_id=pmc, pmid=pmid)
    except Exception as e:
        print(f"Error downloading {pmc} for title '{Title[m]}': {e}")
        failed_titles.append(Title[m])
        continue

# Print the titles that failed to download
if failed_titles:
    print("Failed to download the following titles:")
    for title in failed_titles:
        print(title)

---

原回答：

1.首先需要准备需要下载文献的PMC ID（必须），和文献的题目（非必须，为了给下载的文献命名）

2.准备一个Excel表格，包括题目和PMC ID（若无题目则取1、2、3......）

格式如下图（左右顺序不能颠倒，若某项有缺失值则在程序中自动删除该行）

将表格命名为 PMCNum.xlsx，并将其与py文件放在同一文件夹中

3.安装Python及相应包

包括bs4、requests、fake_useragent、pandas

在cmd中输入：

pip install xxx

即可安装

如：

pip install bs4

4.运行代码

import pandas as pd
from bs4 import BeautifulSoup
import requests
from fake_useragent import UserAgent


def download(pmc_id, filename):
    url = 'https://www.ncbi.nlm.nih.gov/pmc/articles/' + str(pmc) + "/"
    ua = UserAgent()
    headers = {'User-Agent': ua.firefox}
    request = requests.get(url, headers=headers)
    bs = BeautifulSoup(request.content, 'lxml')
    download_url = bs.find_all(attrs={'class': "int-view"})
    download_link = download_url[1].get('href')
    download_url = "https://www.ncbi.nlm.nih.gov" + download_link
    print(filename)
    print(download_url)
    r = requests.get(download_url, headers=headers)
    with open(filename, 'wb') as f:
        f.write(r.content)


# 读取Excel文件
df = pd.read_excel('PMCNum.xlsx', header=None)
df.columns = ['Title', 'PMCNum']

# 去除包含空值的行
PMC = df.dropna(axis=0, how='any')
PMCNum = PMC['PMCNum']
TitleO = list(PMC['Title'])

# 处理标题中的特殊字符
Title = []
for i in TitleO:
    table = i.maketrans(':"/', '   ')
    Title.append(i.translate(table))

# 下载PDF文件，并记录下载失败的标题
failed_titles = []
for m, pmc in enumerate(PMCNum):
    file = Title[m] + '.pdf'
    try:
        download(pmc_id=pmc, filename=file)
    except Exception as e:
        print(f"Error downloading {pmc} for title '{Title[m]}': {e}")
        failed_titles.append(Title[m])
        continue

# 输出下载失败的标题
if failed_titles:
    print("Failed to download the following titles:")
    for title in failed_titles:
        print(title)

5.所有文件下载到了同一文件夹中，由于某些原因下载失败的文献在程序完成后显示，可以手动下载。（亲测成功率达到80%以上）