python - 使用 entrez 和 biopython 在 medline 数据库中搜索标题

Question

我正在尝试搜索标题中包含特定单词的论文。更准确地说，是 2010 年至 2015 年间发表的论文中的病毒或病毒一词。这是我的代码:

import re
from Bio import Medline

handle = Entrez.esearch(db="pubmed",  # database to search
                    term="2010[Date - Publication]:2015[Date - Publication]"
                    )
record = Entrez.read(handle)
handle.close()

pmid_list = record["IdList"] #list of records

handle = Entrez.efetch(db="pubmed", id=pmid_list, rettype="medline",     retmode="text")
records = Medline.parse(handle)

titles = [] # start with empty list of titles
for record in records:
    ti_list = record['TI'] #titles
    for title in ti_list:
        if title == "virus" and title not in titles: #searching viral/virus
        titles.append(title)

print('Publications with viral or virus in the title:')
for record in records:
    print(" ", title)

如果我简单地打印(记录['TI']，那么我会在我的搜索查询中得到所有标题的列表。但是，我无法搜索特定的词。我认为我的错误可能在于“if title == "virus"(因为显然没有论文会单独使用这个词作为标题)。

我很困。有没有更好的方法可以在我查询的论文标题中搜索这个词？

谢谢。

编辑:更新代码(仍然没有运气)

import re
from Bio import Medline

handle = Entrez.esearch(db="pubmed",  # database to search
                    term="2010[Date - Publication]:2015[Date - Publication]"
                    )
record = Entrez.read(handle)
handle.close()

pmid_list = record["IdList"] #list of records

from Bio import Medline
handle = Entrez.efetch(db="pubmed", id=pmid_list, rettype="medline",     retmode="text")
records = Medline.parse(handle)

r = re.compile(r"\bvir(al|us)\b")
titles = set()  # start with empty list of titles
for record in records:
    ti_list = record['TI']  # titles
    for title in ti_list:
        if r.search(title):  #
            titles.add(title)

print('Publications with viral or virus in the title:')
for record in records:
     print(" ", title)

新代码:

import re
from Bio import Medline
handle = Entrez.efetch(db="pubmed", id=pmid_list, rettype="medline", retmode="text", 
                       term="2010[Date - Publication]:2015[Date - Publication]")
records = Medline.parse(handle)
titles = []
for record in records:
    ti_list = record['TI']
    for title in ti_list:
        titles.append(title)
handle.close()
for title in titles:
    print(title)

Answer 1

如果要匹配子字符串，请使用 in 查看标题中是否包含任何单词:

words  = ("viral","virus")
if any(w in title for w in words) and title not in titles: #

但是您似乎想过滤记录，获取任何包含病毒或病毒的记录标题:

st  = {"viral","virus"}

filtered_records = [ record for record in records if any(w in st for w in record['TI'] )]

如果你想匹配子字符串并使用模式，那么你实际上需要使它成为一个正则表达式，"vir(al|us)" 只是你代码中的一个字符串:

import re

r = re.compile("vir(al|us)")
filtered_records = [record for record in records if any(r.search(w) for w in record['TI'])]

您自己的循环中的正则表达式将转到您的 if 所在的位置:

import re

r = re.compile(r"vir(al|us)")
if r.search(title) and title not in titles: 
      .......

如果您不希望病毒等匹配，请为您的正则表达式使用单词边界:

r = re.compile(r"\bvir(al|us)\b")

您还应该将标题设为一个不能有重复项的集合，这是一个使用您自己的代码的工作示例:

r = re.compile(r"\bvir(al|us)\b")
titles = set()  # start with empty list of titles
for record in records:
    ti_list = record['TI']  # titles
    for title in ti_list:
        if r.search(title):  #
            titles.add(title)

可以成为集合推导:

r = re.compile(r"\bvir(al|us)\b")

titles = {title for record in records for title in record['TI']  if r.search(title)} # titles

因为 record['TI'] 返回一个字符串而不是一个列表:

r = re.compile(r"\bvir(al|us)\b")
titles = set() 
for record in records:
    title = record['TI']  # title is a str not a list
    if r.search(title):  #
           titles.add(title)

对 set comp 或任何其他示例执行相同的操作。