利用pubmedR实现doi搜索

Question

尝试使用这里和这里方法从doi列表中提取作者的隶属关系，但没有找到任何关于使用pubmedR进行doi搜索的信息。已经调查过转换语法，但也没有运气。请帮帮忙！谢谢

Answer 1

lol发现了这一点[ 这个职位是的一个伟大的帮助]，并希望为将来可能有同样问题的其他人发帖子。最后使用了easypubmed包而不是tho

library(easyPubMed)

#loading list of DOIs
dois <- read.csv("dois.csv")

#convering dois to their associated PMID's 
pmids <- lapply(dois, get_pubmed_ids)

#using pmid's to extract abstract & article information as an xml thing
abstracts <- c()
for (i in c(1:length(pmids))){
  if (is.character(pmids[[i]][["IdList"]][["Id"]])==TRUE){
  abstracts[i] <- fetch_pubmed_data(pmids[[i]])
  }
}
abstracts <-as.list(abstracts) 

#making the xml thing readable by R
readAbstracts <- c()
for (i in c(1:length(abstracts))){
  if (is.na(abstracts[[i]]) == FALSE){
    readAbstracts[[i]] <- read_xml(abstracts[[i]]) 
  }
}

#now extracting desired information from the abstracts object
 <- data.frame()
for (i in c(1:length(pmids)){
  if (is.na(abstracts[[i]]) == FALSE && length(pmids[[i]]$IdList)<2){
    index <- i
    curRent <- readAbstracts[[i]] 
    pmid    <- xml2::xml_find_first( curRent, ".//PMID") %>% xml2::xml_text()
    title    <- xml2::xml_find_first( curRent, ".//ArticleTitle") %>% xml2::xml_text()
    authors <- paste( 
      xml2::xml_find_all( curRent, ".//AuthorList/Author/LastName") %>% xml2::xml_text(),
      xml2::xml_find_all( curRent, ".//AuthorList/Author/ForeName") %>% xml2::xml_text(),
      sep = ", " )
    affiliate <- xml2::xml_find_all( curRent, ".//AuthorList/Author/AffiliationInfo[1]/Affiliation") %>% xml2::xml_text()
    if(is.na(affiliate[1])==TRUE){
      affiliate <- NA
    }
    if(is.na(authors[1])==TRUE){
      authors <- NA
    }
    if(length(authors)>length(affiliate)){
      authors <- authors[c(1:length(affiliate))]
    }
    df <- data.frame( pmid = pmid, title=title, authors = authors, affiliate = affiliate, i = i)
    extractedInfo <-  rbind(extractedInfo, df)
    }
}

然后，您可以使用各种方法来格式化“extractedInfo”，以满足您的需要。干杯