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html - 从网页中检索标题和 ID 数据并保存在 excel 文件中

问题描述

我正在寻找从网页中检索标题和 PMID (PubMed ID) 记录并将其保存在 MS excel 文件中。我尝试使用easyPubMedR 中的库进行提取，但是，我无法获得相同的内容。是否有任何库或包获得这个。请帮我解决这个问题。

下面提供了输入数据和预期输出数据的示例：

代码：

    library(easyPubMed)
    my_query <- '"ACSL1" [ti] OR "Acyl-CoA Synthetase Long Chain Family Member 1" [ti] OR "Acyl-CoA Synthetase Long Chain Family Member 1" [ti] OR "Fatty-Acid-Coenzyme A Ligase, Long-Chain 2" [ti] OR "Long-Chain Fatty-Acid-Coenzyme A Ligase 1" [ti] OR "Long-Chain-Fatty-Acid–CoA Ligase 1" [ti] OR "Long-Chain Fatty Acid-CoA Ligase 2" [ti] OR "Long-Chain Acyl-CoA Synthetase" [ti] OR "Long-Chain Acyl-CoA Synthetase 1" [ti] OR "Long-Chain Acyl-CoA Synthetase 2" [ti] OR "Lignoceroyl-CoA Synthase" [ti] OR "Palmitoyl-CoA Ligase 1" [ti] OR "Palmitoyl-CoA Ligase 2" [ti] OR "Acyl-CoA Synthetase 1" [ti] OR "LACS 1" [ti] OR "LACS 2" [ti] OR "LACS-1" [ti] OR "LACS-2" [ti] OR "FACL2" [ti] OR "FACL1" [ti] OR "LACS1" [ti] OR "LACS2" [ti] OR "ACS1" [ti] OR "LACS" [ti] OR "Fatty-Acid-Coenzyme A Ligase, Long-Chain 1" [ti] OR "Palmitoyl-CoA Ligase 1" [ti] AND (acyl [ti] OR CoA [ti] OR fatty [ti] OR synthetase [ti] OR Palmitoyl [ti] OR ligase [ti] OR ACSL1 [ti]'
#### To count the number of PubMed IDs####
    my_entrez_id <- get_pubmed_ids(my_query)
    my_entrez_id$Count

输入

Webpage: https://pubmed.ncbi.nlm.nih.gov/
Search String: "ACSL1" [ti] OR "Acyl-CoA Synthetase Long Chain Family Member 1" [ti] OR "Acyl-CoA Synthetase Long Chain Family Member 1" [ti] OR "Fatty-Acid-Coenzyme A Ligase, Long-Chain 2" [ti] OR "Long-Chain Fatty-Acid-Coenzyme A Ligase 1" [ti] OR "Long-Chain-Fatty-Acid–CoA Ligase 1" [ti] OR "Long-Chain Fatty Acid-CoA Ligase 2" [ti] OR "Long-Chain Acyl-CoA Synthetase" [ti] OR "Long-Chain Acyl-CoA Synthetase 1" [ti] OR "Long-Chain Acyl-CoA Synthetase 2" [ti] OR "Lignoceroyl-CoA Synthase" [ti] OR "Palmitoyl-CoA Ligase 1" [ti] OR "Palmitoyl-CoA Ligase 2" [ti] OR "Acyl-CoA Synthetase 1" [ti] OR "LACS 1" [ti] OR "LACS 2" [ti] OR "LACS-1" [ti] OR "LACS-2" [ti] OR "FACL2" [ti] OR "FACL1" [ti] OR "LACS1" [ti] OR "LACS2" [ti] OR "ACS1" [ti] OR "LACS" [ti] OR "Fatty-Acid-Coenzyme A Ligase, Long-Chain 1" [ti] OR "Palmitoyl-CoA Ligase 1" [ti] AND (acyl [ti] OR CoA [ti] OR fatty [ti] OR synthetase [ti] OR Palmitoyl [ti] OR ligase [ti] OR ACSL1 [ti]

预期输出：

dput(Output)
structure(list(Title = c("The 3-ketoacyl-CoA thiolase: an engineered enzyme for carbon chain elongation of chemical compounds.", 
"Potential influence of miR-192 on the efficacy of saxagliptin treatment in T2DM complicated with non-alcoholic fatty liver disease.", 
"Myosteatosis in nonalcoholic fatty liver disease: An exploratory study."
), PMID = c(32830293L, 32829627L, 32828745L)), class = "data.frame", row.names = c(NA, 
-3L))

标签： htmlrextractexport-to-excel

解决方案

您需要收集和解析查询结果。我认为这样的事情应该做

my_entrez_id <- get_pubmed_ids(my_query)
my_entrez_data <- fetch_pubmed_data(my_entrez_id)
my_entrez_list <- my_entrez_data %>% 
  XML::xmlParse() %>% 
  XML::xmlToList() #turn the xml int an R List thats is easier to handle
my_entrez_df <- my_entrez_list %>% 
  purrr::map_df(function(x){ # use the map function from the package purrr to select the attributes that we need
    tibble(
      Title = x$MedlineCitation$Article$ArticleTitle[[1]], 
      PMID = x$MedlineCitation$PMID[[1]])}
    )

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