根据GSE号在NCBI批量获取文献

如今，在ncbi查找文献已经成为了读研必不可少的技能之一，今天记录下根据GSE号批量在ncbi获取文献
需要安装biopython

安装方法：pip install biopython
biopython教程：https://biopython-cn.readthedocs.io/zh_CN/latest/cn/chr09.html

1、查看ncbi当前所有的数据库

from Bio import Entrez
hd_info = Entrez.einfo()
# 获取所有数据库列表
read_info = Entrez.read(hd_info)
for db in read_info['DbList']:
    print (db)

2、根据gse号批量获取文献

from Bio import Entrez
from Bio import Medline
from Bio import Geo
import csv
# 参数设置
Entrez.email = "[e-mail]" #告诉ncbi你是谁
Entrez.tool  = "abcd"

# GEO.csv文件为一列数据全部为gse号
list1=[]
with open('GEO.csv', encoding='utf-8')as f:
    f_csv = csv.reader(f)
    for i, rows in enumerate(f_csv):
        if i >= 1:
            list1.append(rows)
    for t in list1:
        print(t)
        # uid为gse的uid号，取了第一个 gds为gse所在的geo库的名字
        handle = Entrez.esearch(db="gds", term=t)
        record = Entrez.read(handle)
        uid = record["IdList"][0]
        # print(uid)
        # print(record)
        # print(record["Count"])
        # print(record["IdList"][0])
        # print(record["IdList"])

        read_elink = Entrez.read(Entrez.elink(dbfrom="gds", db="pubmed", id=uid))
        print ("LinkSetDb: ", read_elink[0]["LinkSetDb"])
        # 查看所有相关的目标库
        for lsd in read_elink[0]["LinkSetDb"]:
            print (lsd["DbTo"], lsd["LinkName"], len(lsd["Link"]))
        # 查看相关的所有文献 pmid
        for link in read_elink[0]["LinkSetDb"][0]["Link"]:
            mid = link["Id"]
            print(mid)

        # 根据gse号的pmid获取对应文献
        # 用 efetch下载
        hd_efetch = Entrez.efetch(db="pubmed", id=mid, rettype="medline", retmode="text", )
        parse_medline = Medline.parse(hd_efetch)
        with open("mouse_pubmed.xls", "a") as file:
            file.write("title\tauthors\tsource\tPubMed\n")
            for i, ele in enumerate(list(parse_medline)):
                line = ele['TI'] + "\t" + ",".join(ele['AU']) + "\t" + ele['SO'] + "\t" + ele['PMID'] + "\n"
                file.write(line)
                print(i, line)
       #有的文章作者很多，比如encode计划等，这种文章再批量获取时，需要把’AU‘作者去掉，不然总会报错