如何用R语言优雅地玩转PubMed-RISmed包的使用

news2024/11/18 0:39:14

PubMed是最大的生命科学文献数据库之一，在开展课题使用关键词搜索时，会检索出大量文献。如何对这些文献进行筛选，出了巧妙使用关键词组合外，还可以使用R将相关文献信息一键提取，实现文献的快速浏览。RISmed是一个用于从PubMed数据库获取和分析医学文献数据的R包。它可以帮助你进行文献检索、下载文献摘要、获取作者信息等操作。其具体应用如下。

# 安装加载包
#install.packages("RISmed") #未安装的需要首先安装RISmed包
library(RISmed)

## Warning: package 'RISmed' was built under R version 4.2.3

#查看使用说明
help(package="RISmed")

# 限定检索主题，如“gestational diabetes"
search_topic<-"gestational diabetes"
search_query<-EUtilsSummary(search_topic,db="pubmed",type="esearch",mindate=2018,maxdate=2023)

## Warning in any(is.na(WhichArgs)) || sapply(WhichArgs, length) > 1: 'length(x) =
## 2 > 1' in coercion to 'logical(1)'

这将检索包含关键词”diabetes”的文献记录。

#查看检索内容
summary(search_query)

## Query:
## ("diabetes, gestational"[MeSH Terms] OR ("diabetes"[All Fields] AND "gestational"[All Fields]) OR "gestational diabetes"[All Fields] OR ("gestational"[All Fields] AND "diabetes"[All Fields])) AND 2018/01/01:2023/12/31[Date - Entry] 
## 
## Result count:  12775

#获取摘要信息
records<- EUtilsGet(search_query)

class(records)

## [1] "Medline"
## attr(,"package")
## [1] "RISmed"

#str(records)

# 获取作者信息
authors <- Author(records)

这将提取文献摘要中的作者信息。

##提取检索结果
pubmed_data <- data.frame('Title'=ArticleTitle(records),

                           'Year'=YearAccepted(records),

                          'journal'=ISOAbbreviation(records))



head(pubmed_data)

##                                                                                                                                                                                          Title
## 1                                                   Preconceptional and prenatal exposure to air pollutants and risk of gestational diabetes in the MADRES prospective pregnancy cohort study.
## 2                                                                                                                                   Mechanism and recent updates on insulin-related disorders.
## 3                                                                         Environmental tobacco smoke increased risk of gestational diabetes mellitus: A birth cohort study in Sichuan, China.
## 4 Development and feasibility of a theory-guided and evidence-based physical activity intervention in pregnant women with high risk for gestational diabetes mellitus: a pilot clinical trial.
## 5                                                                       Association between serum copper level and reproductive health of Women in the United States: a cross-sectional study.
## 6                                                          Prediction of large-for-gestational age at 36 weeks' gestation: two-dimensional vs three-Dimensional vs magnetic resonance imaging.
##   Year                   journal
## 1 2023      Lancet Reg Health Am
## 2 2023        World J Clin Cases
## 3 2023    Diabetes Metab Res Rev
## 4 2023  BMC Pregnancy Childbirth
## 5   NA  Int J Environ Health Res
## 6 2023 Ultrasound Obstet Gynecol

pubmed_data[1:3,1]

## [1] "Preconceptional and prenatal exposure to air pollutants and risk of gestational diabetes in the MADRES prospective pregnancy cohort study."
## [2] "Mechanism and recent updates on insulin-related disorders."                                                                                
## [3] "Environmental tobacco smoke increased risk of gestational diabetes mellitus: A birth cohort study in Sichuan, China."

write.csv(pubmed_data,file='diabetes.csv')

##可视化一下

library(ggplot2)

## Warning: package 'ggplot2' was built under R version 4.2.3

# 提取发表年份和文章数
pub_years <- YearPubmed(records)
article_counts <- table(pub_years)

# 创建数据框
data_df <- data.frame(Year = as.factor(names(article_counts)), Counts = as.integer(article_counts))

p<-ggplot(data=data_df, aes(x=Year, y=Counts,fill=Year)) +

  geom_bar(stat="identity", width=0.5)+

  labs(y = "Number of articles",title="PubMed articles containing diabetes"

       )+

  scale_fill_brewer(palette="Dark2")

p