使用Rentrez解析pubmed中的作者和从属关系 [英] Using rentrez to parse out author and affiliation from pubmed

问题描述

我的总体目标是建立共同作者网络图。我有一份PubMed ID列表，这是我对共同作者网络图表感兴趣的唯一出版物。我无法弄清楚如何使用rentrez在查询中同时获得作者姓名和所属单位。我可以同时获得这两种信息，但是我的隶属关系列表比我的作者列表少300左右，因此显然有些人没有提供隶属关系，但我不知道是谁。有什么方法可以搜索作者和从属关系？ [当我在entrez_fetch中同时执行这两项操作时，它只是分别列出了作者和单位的列表，因此我仍然无法弄清哪个单位属于哪个作者。]

My overall goal is to build a co-author network graph. I have a list of PubMed ID's and these are the only publications I am interested in for the graphing of the co-author network. I can't figure out how to get both the Author names and respective affiliations together in my query using rentrez. I can get both information but my list of affiliations is about 300 less than my author list so obviously some did not provide affiliations but I can't figure out who. Any way to search for Author and affiliation combined? [When I did both in my entrez_fetch, it just gave me a list of authors and affiliations separately so I still can't figure out which affiliations belong with which authors.]

library(tidyverse)
library(rentrez)
library(XML)

trial<-entrez_fetch(db="pubmed", id=pub.list$PMID, rettype="xml", parsed=TRUE)
affiliations<-xpathSApply(trial, "//Affiliation", xmlValue)
first.names<-xpathSApply(trial, "//Author/ForeName", xmlValue)

一切正常，但我不知道哪个作者的隶属关系因其长度不同而有所不同。

This all works fine but I can't figure out which authors are with which affiliations since their lengths are different.

任何帮助将不胜感激。谢谢！

Any help would be greatly appreciated. Thanks!

推荐答案

您可以尝试以下方法：

xpathSApply(trial, "//Author", function(x) {
  author_name <- xmlValue(x[["LastName"]])
  author_affiliation <- xmlValue(x[["AffiliationInfo"]][["Affiliation"]])
  c(author_name,author_affiliation)
  })

通过在第一行中返回每个 // Author 节点。

It returns in the first row the last name of the authors and in the second row their affiliation by getting these values for each //Author node.

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