利用Biopython 快速根据pmid 来下载参考文献信息
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利用Biopython 快速根据pmid 来下载参考文献信息
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之前用的常規爬蟲思路(import requests,from bs4 import BeautifulSoup)來下載文章題目,作者,來源等信息時,?偶爾會出現各種問題,有那個調試的時間,就自己根據biopython快速寫了一個腳本?,簡單好用。
# !bin/python # encoding:utf-8from Bio import Entrez from Bio import Medline Entrez.email = 'xxxx@qq.com' ref = open('ref.txt','w+') def downref(pmid):handle = Entrez.efetch(db="pubmed" , id=pmid , rettype="medline" , retmode="text")records = Medline.parse(handle)records = list(records) # records 是一個迭代器,所以只能訪問這些records一次。如果想保存這些records,需要把他們轉成列表。for record in records:print "title:" , record.get("TI" , "?")if len(record.get("AU" , "?"))>3: author = ','.join(record.get("AU" , "?")[0:3]) #如果名字很多時,作者名字取前三個print "authors:",authorelse:author =','.join(record.get("AU" , "?"))print "authors:",authorprint "source:" , record.get("SO" , "?")text = record.get("TI" , "?")+'\t'+ author +'\t' +record.get("SO" , "?") +'\n'ref.write(text)if __name__=="__main__":ids = ['21142915','25007187','27574448','16330681','24404132','22868256','23314736','18221820','24338217','17537913','19016765','22124095','18551042','17194903','22546611','22304580','22838950','21642870','19376514','20665488','24647007','23603345','23816762','19203783','25495407','21057378','22329723','21902499','21635146','24215845','22188361','19786980','21362365','21449681','24193570','17457342','19307503','20634689','17700593','23736036','20385995','25331073','24732178','20638924','21605004','22134350','17602053','20226083','18538455','18538445','24361227','16609362','18294295','21995462','26641474','18347181','26696550','19052714','18357466','24533712','23588304','19898482','2953022','26857783','20562211','19450125','15007088','16636344','23860526','20125120','24061601','25069034','20078613','19620936','27498158','25592234','24446315','19362955','16875718','22821704','17352537','18377430','19214144','23222202','24300978','22838949','23230131','16551864','24980784','27150640','25084203','22843789','20212519','16890579','26763541','22441531','21521023'] #可以讀文件來輸入pmidfor id in ids:downref(id)參考:https://blog.csdn.net/Cassiel60/article/details/90664558
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