从网页检索标题和ID数据并将其保存在Excel文件中

问题描述

我正在寻找从网页检索标题和PMID（PubMed ID）记录，并将其保存在MS excel文件中。我尝试使用R中的easyPubMed库进行提取，但是我无法获得相同的结果。是否有任何库或软件包获取此文件。请协助我。

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 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))

解决方法

您需要收集并解析查询结果。我认为应该这样做

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]])}
    )