Question

我正在尝试从NCBI xml文件解析某些子节点的xmlValue。但是，对于某些PM.ID，Root node <PubmedArticleSet>具有不同的信息w.r.t发布的记录，PubmedBookArticle和PubmedArticle。我想传递一个条件，if(xmlName(fetch.pubmed) == PubmedBookArticle提取某些值elseif (xmlName(fetch.pubmed) == PubmedArticle提取其他值。最后，使用与其PMID相对应的值创建dataframe。这似乎很简单，但(xmlName(fetch.pubmed)抛出错误no applicable method for 'xmlName' applied to an object of class "c('XMLInternalDocument', 'XMLAbstractDocument')"感谢任何帮助，谢谢

<?xml version="1.0"?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2015//EN" "http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_150101.dtd">
<PubmedArticleSet>
  <PubmedBookArticle>
    <BookDocument>
      <PMID Version="1">25506969</PMID>
      <ArticleIdList>
        <ArticleId IdType="bookaccession">NBK259188</ArticleId>
      </ArticleIdList> ....

   ...... </BookDocument>
  </PubmedBookArticle>

  <PubmedArticle>
    <MedlineCitation Status="Publisher" Owner="NLM">
      <PMID Version="1">25013473</PMID>
      <DateCreated>
        <Year>2014</Year>
        <Month>7</Month>
        <Day>11</Day>
      </DateCreated>....

    ....</MedlineCitation>
    </PubmedArticle>
</PubmedArticleSet>

我的代码在

下面

library(XML)
library(rentrez)

PM.ID <- c("25506969"," 25032371","   24983039","24983034","24983032","24983031",
"26386083","26273372","26066373","25837167",
 "25466451","25013473")
# rentrez function to retrieve XMl file for above PIMD
fetch.pubmed <- entrez_fetch(db = "pubmed", id = PM.ID,
                             rettype = "xml", parsed = T)
# If empty records, return NA
FindNull <- function(x,x1child){
  res <- xpathSApply(x,x1child,xmlValue)
  if (length(res) == 0){
    out <- NA
  }else {
    out <- res
  }
  out
}

# extract contents from xml file
    xpathSApply(fetch.pubmed,"//PubmedArticle",FindNull,x1child = './/ArticleTitle')

    xpathSApply(fetch.pubmed,"//PubmedBookArticle",FindNull,x1child = './/BookTitle')

如何在循环中获取上面的代码，以便我可以在每次搜索中满足条件时检索PubmedArticle和PubmedBookArticle中的值？

Answer 1

有几种方法可以做到这一点，但我可能会为书籍和文章获得单独的节点集。

table( xpathSApply(fetch.pubmed, "/PubmedArticleSet/*", xmlName) )
    PubmedArticle PubmedBookArticle 
                6                 6 

books <- getNodeSet(fetch.pubmed, "/PubmedArticleSet/PubmedBookArticle")

data.frame( pmid = sapply(books, function(x) xpathSApply(x, ".//PMID", xmlValue)),
           title = sapply(books, function(x) xpathSApply(x, ".//BookTitle", xmlValue))
)

      pmid                                                                                                      title
1 25506969                                                     Probe Reports from the NIH Molecular Libraries Program
2 25032371                                                       Understanding Climate’s Influence on Human Evolution
3 24983039 Assessing the Effects of the Gulf of Mexico Oil Spill on Human Health: A Summary of the June 2010 Workshop
4 24983034                                                  In the Light of Evolution: Volume IV: The Human Condition
5 24983032                                            The Role of Human Factors in Home Health Care: Workshop Summary

Answer 2

NCBI下面的XML路径有助于从abstracts，PubmedArticle以及那些文章PubmedBookArticle中提取without abstracts (NA)。

<!-- language: lang-r -->
abstracts <- xpathSApply(fetch.pubmed, c('//PubmedArticle//Article',
         '//PubmedBookArticle//Abstract'), function(x) {
xmlValue(xmlChildren(x)$Abstract) })
abstracts <- data.frame(abstracts,stringsAsFactors = F)
dim(abstracts)
rownames(abstracts) <- PM.ID

如何在XML文件中访问具有不同名称的子节点（子）的值？

2 个答案: