从 R 中的 NCBI entrez 解析 xml

Question

我想从 NCBI 条目的特征部分提取一些信息，我正在使用此代码。下载数据

fetch2 <- entrez_fetch(db = "nucleotide", id = 1028916732, 
                       rettype = "gbc", retmode="xml", parsed = TRUE)

分析数据

xmltop = xmlRoot(fetch2) #gives content of root
class(xmltop)#"XMLInternalElementNode" "XMLInternalNode" "XMLAbstractNode"
xmlName(xmltop) 
xmlSize(xmltop)
xmlName(xmltop[[1]]) 
features <- xmltop[[1]][[20]][[1]][[4]]

我只对功能感兴趣

  <INSDFeature_quals>
      <INSDQualifier>
        <INSDQualifier_name>organism</INSDQualifier_name>
        <INSDQualifier_value>Alanphillipsia aloeigena</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>mol_type</INSDQualifier_name>
        <INSDQualifier_value>genomic DNA</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>strain</INSDQualifier_name>
        <INSDQualifier_value>CPC 21286</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>isolation_source</INSDQualifier_name>
        <INSDQualifier_value>leaves</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>host</INSDQualifier_name>
        <INSDQualifier_value>Aloe melanacantha</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>culture_collection</INSDQualifier_name>
        <INSDQualifier_value>CBS:136408</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>culture_collection</INSDQualifier_name>
        <INSDQualifier_value>CPC:21286</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>type_material</INSDQualifier_name>
        <INSDQualifier_value>culture from holotype of Alanphillipsia aloeigena</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>db_xref</INSDQualifier_name>
        <INSDQualifier_value>taxon:1414674</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>country</INSDQualifier_name>
        <INSDQualifier_value>South Africa: Namakwaland, Koegap Nature Reserve</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>collected_by</INSDQualifier_name>
        <INSDQualifier_value>M.J. Wingfield</INSDQualifier_value>
      </INSDQualifier>
      <INSDQualifier>
        <INSDQualifier_name>note</INSDQualifier_name>
        <INSDQualifier_value>ex-holotype culture of Alanphillipsia aloeigena</INSDQualifier_value>
      </INSDQualifier>
    </INSDFeature_quals>

我想创建一个table喜欢

Organism | culture_collection | host  
Alanphillipsia aloeigena | CBS:136408 | Aloe melanacantha

但是我不明白如何使用

检索数据

<INSDQualifier_name>
<INSDQualifier_value>

我看过 Pubmed 的一些教程，效果很好，但输出结构不同。最后，我想创建一个循环以从 ID 列表中提取数据，并且由于并非所有条目都具有相同的结构，所以我想使用 host organism 之类的标签来检索该信息。

Answer 1

由于您的 XML 相当平坦，请考虑 XML 的便捷处理程序，xmlToDataFrame:

library(XML)

fetch2 <- ...
doc <- xmlParse(fetch2)
df <- xmlToDataFrame(doc, nodes=getNodeSet(doc, "//INSDQualifier"))

df
#    INSDQualifier_name                               INSDQualifier_value
# 1            organism                          Alanphillipsia aloeigena
# 2            mol_type                                       genomic DNA
# 3              strain                                         CPC 21286
# 4    isolation_source                                            leaves
# 5                host                                 Aloe melanacantha
# 6  culture_collection                                        CBS:136408
# 7  culture_collection                                         CPC:21286
# 8       type_material culture from holotype of Alanphillipsia aloeigena
# 9             db_xref                                     taxon:1414674
# 10            country  South Africa: Namakwaland, Koegap Nature Reserve
# 11       collected_by                                    M.J. Wingfield
# 12               note   ex-holotype culture of Alanphillipsia aloeigena

然后运行如果上面的每一行都应该是具有相应值的列，则使用列名和行名清理转置

final_df <- data.frame(t(df), stringsAsFactors = FALSE)

colnames(final_df) <- as.character(final_df[1,])
final_df <- final_df[-1,]
rownames(final_df) <- NULL

final_df 
#                   organism    mol_type    strain isolation_source              host culture_collection culture_collection                                     type_material
# 1 Alanphillipsia aloeigena genomic DNA CPC 21286           leaves Aloe melanacantha         CBS:136408          CPC:21286 culture from holotype of Alanphillipsia aloeigena
#          db_xref                                          country   collected_by                                            note
#  1 taxon:1414674 South Africa: Namakwaland, Koegap Nature Reserve M.J. Wingfield ex-holotype culture of Alanphillipsia aloeigena

从 R 中的 NCBI entrez 解析 xml

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