{"id":1519,"date":"2024-11-05T08:02:29","date_gmt":"2024-11-04T23:02:29","guid":{"rendered":"https:\/\/info.zanet.biz\/?p=1519"},"modified":"2024-11-05T08:37:06","modified_gmt":"2024-11-04T23:37:06","slug":"rismed%e3%82%92%e7%94%a8%e3%81%84%e3%81%9fpubmed%e6%a4%9c%e7%b4%a2","status":"publish","type":"post","link":"https:\/\/info.zanet.biz\/?p=1519","title":{"rendered":"RISmed\u3092\u7528\u3044\u305fPubMed\u691c\u7d22"},"content":{"rendered":"\n

RISmed\u306fPubMed\u691c\u7d22\u306e\u305f\u3081\u306eR\u306e\u30d1\u30c3\u30b1\u30fc\u30b8\u3067\u3059\u3002\u4f5c\u8005\u306fStephanie Kovalchik\u6c0f\u3067\u3059\u3002ASReview https:\/\/asreview.nl\/<\/a> \u3092\u7528\u3044\u305f\u6587\u732e\u9078\u5b9a\u306e\u969b\u306b\u306f\u3001Title, Abstract\u306e\u30c7\u30fc\u30bf\u3092\u7528\u3044\u307e\u3059\u3002\u66f8\u8a8c\u60c5\u5831\u3068\u5408\u308f\u305b\u3066\u3001\u3053\u308c\u3089\u306e\u30c7\u30fc\u30bf\u3092\u542b\u3080Excel\u30d5\u30a1\u30a4\u30eb\u3001\u307e\u305f\u306fCSV\u3042\u308b\u3044\u306fRIS\u30d5\u30a1\u30a4\u30eb\u3092\u7528\u610f\u3059\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002\u305d\u306e\u969b\u306b\u3001RISmed\u3092\u4f7f\u3046\u306e\u304c\u3072\u3068\u3064\u306e\u65b9\u6cd5\u3067\u3059\u3002<\/p>\n\n\n\n

PubMed\u3067\u306fGET\u30e1\u30bd\u30c3\u30c9\u3067\u76f4\u63a5\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306b\u30a2\u30af\u30bb\u30b9\u3057\u3066\u3001\u691c\u7d22\u7d50\u679c\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3067\u304d\u308be-utilities\u3068\u3044\u3046\u30b5\u30fc\u30d3\u30b9\u304c\u3042\u308a\u307e\u3059\u3002MeSH\u3078\u306eAutomatic Term Mapping\u306f\u9069\u7528\u3055\u308c\u307e\u305b\u3093\u3002https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK25501\/<\/a><\/p>\n\n\n\n

\u305d\u308c\u3092\u5229\u7528\u3059\u308bR\u306e\u30d1\u30c3\u30b1\u30fc\u30b8\u3067\u3059\u3002pmSearch<\/a>\u3082\u540c\u3058\u30b5\u30fc\u30d3\u30b9\u3092\u5229\u7528\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n

RISmed\u3068tcltk2\u306e\u30d1\u30c3\u30b1\u30fc\u30b8\u3092The Comprehensive R Archive Network (CRAN)\uff08https:\/\/cran.r-project.org\/<\/a>\uff09\u304b\u3089R\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u304a\u304d\u307e\u3059\u3002tcltk2\u306f\u691c\u7d22\u7d50\u679c\u3092CSV\u30d5\u30a1\u30a4\u30eb\u3068\u3057\u3066\u4fdd\u5b58\u3059\u308b\u969b\u306e\u30a4\u30f3\u30bf\u30fc\u30d5\u30a7\u30fc\u30b9\u3068\u3057\u3066\u7528\u3044\u307e\u3059\u3002
Stephanie Kovalchik: RISmed https:\/\/cran.r-project.org\/web\/packages\/RISmed\/index.html<\/a>
Philippe Grosjean: tcltk2 https:\/\/cran.r-project.org\/web\/packages\/tcltk2\/index.html<\/a><\/p>\n\n\n\n

\u30d1\u30c3\u30b1\u30fc\u30b8\u304c\u307e\u3060\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u3066\u3044\u306a\u3044\u5834\u5408\u306f\u3001\u4ee5\u4e0b\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3092R\u3067\u5b9f\u884c\u3057\u3066\u304f\u3060\u3055\u3044\u3002
#Install the packages.
packneed=c(“RISmed”,”tcltk2″);current=installed.packages();addpack=setdiff(packneed,rownames(current));url=”https:\/\/ftp.yz.yamagata-u.ac.jp\/pub\/cran\/”;if(length(addpack)>0){install.packages(addpack,repos=url)};if(length(addpack)==0){print(“Already installed.”)}<\/p>\n\n\n\n

\u4ee5\u4e0b\u306eR\u3067\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u5b9f\u884c\u3059\u308b\u3068\u691c\u7d22\u7d50\u679c\u3092CSV\u30d5\u30a1\u30a4\u30eb\u3068\u3057\u3066\u4fdd\u5b58\u3067\u304d\u307e\u3059\u3002SearchWords\u3068\u8a00\u3046\u5909\u6570\u306b\u691c\u7d22\u5f0fsearch query\u3092\u683c\u7d0d\u3057\u307e\u3059\u306e\u3067\u3001””\u3067\u56f2\u3093\u3067\u3042\u308b\u3068\u3053\u308d\u3092\u66f8\u304d\u63db\u3048\u3066\u4f7f\u7528\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u3059\u3079\u3066\u3092\u9078\u629e\u3057\u3066\u3001\u5b9f\u884c\u3059\u308b\u3068\u3001\u30d5\u30a1\u30a4\u30eb\u4fdd\u5b58\u306e\u30c0\u30a4\u30a2\u30ed\u30b0\u307e\u3067\u5b9f\u884c\u3055\u308c\u307e\u3059\u3002ResultsData=EUtilsGet(Results, type=”efetch”, db=”pubmed”)\u306e\u5b9f\u884c\u306b\u6642\u9593\u304c\u304b\u304b\u308a\u307e\u3059\u3002<\/p>\n\n\n\n

\u4fdd\u5b58\u3057\u305fCSV\u30d5\u30a1\u30a4\u30eb\u3092\u76f4\u63a5\u958b\u304f\u306e\u3067\u306f\u306a\u304f\u3001Excel\u3092\u8d77\u52d5\u3057\u3066\u3001\u30c7\u30fc\u30bf\u30e1\u30cb\u30e5\u30fc\u304b\u3089\u30c6\u30ad\u30b9\u30c8\u307e\u305f\u306fCSV\u30d5\u30a1\u30a4\u30eb\u304b\u3089\u30a4\u30f3\u30dd\u30fc\u30c8\u3057\u307e\u3059\u3002\u5143\u306e\u30d5\u30a1\u30a4\u30eb\u306fUTF-8\u3067\u30a8\u30f3\u30b3\u30fc\u30c9\u3055\u308c\u3066\u304a\u308a\u3001Shift JIS\u304c\u30c7\u30d5\u30a9\u30eb\u30c8\u306eExcel\u3067\u306f\u6587\u5b57\u5316\u3051\u3059\u308b\u306e\u3067\u3001\u305d\u306e\u3088\u3046\u306a\u624b\u9806\u3092\u53d6\u308a\u307e\u3059\u3002\u30d5\u30a1\u30a4\u30eb\u4fdd\u5b58\u306e\u969b\u306f.xlsx\u306b\u3059\u308b\u3053\u3068\u3082\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n

\u307e\u305f\u3001CSV\u30d5\u30a1\u30a4\u30eb\u306f\u30c6\u30ad\u30b9\u30c8\u30d5\u30a1\u30a4\u30eb\u306a\u306e\u3067\u3001Notepad\uff0b\uff0b https:\/\/notepad-plus-plus.org\/<\/a> \u306a\u3069\u3067\u4e00\u5ea6\u958b\u3044\u3066\u3001\u30a8\u30f3\u30b3\u30fc\u30c7\u30a3\u30f3\u30b0\u3092UTF-8-BOM\u306b\u5909\u63db\u3059\u308b\u3068Excle\u3067\u76f4\u63a5\u958b\u3044\u3066\u3082\u6587\u5b57\u5316\u3051\u3057\u307e\u305b\u3093\u3002<\/p>\n\n\n\n

\"\"
\u56f3 Excle\u3067\u53d6\u308a\u8fbc\u3093\u3067.x.sx\u30d5\u30a1\u30a4\u30eb\u3068\u3057\u3066\u4fdd\u5b58\u3057\u305fPubMed\u691c\u7d22\u7d50\u679c\u3002<\/figcaption><\/figure>\n\n\n\n

\u4ee5\u4e0b\u306bR\u7528\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u793a\u3057\u307e\u3059\u3002
library(“RISmed”)
library(“tcltk2”)

#Make a search query for PubMed. Write your query in ” “.<\/p>\n\n\n\n

SearchWords=”(junior doctor OR young doctor OR resident physician OR intern) AND mindfulness AND humans[mh] AND (english[la] OR japanese[la]) AND hasabstract[tw] AND 2024[dp]”

#Connect and retrieve a list of PubMed IDs. You can change retmax and set years asmindate=2000, maxdate=2024, retmax=2000<\/p>\n\n\n\n

Results=EUtilsSummary(SearchWords, type=”esearch”, db=”pubmed”, retmax=2000)

#Show the number of citations retrieved and get title, abstract and other data. This step takes time.<\/p>\n\n\n\n

QueryCount(Results)
ResultsData=EUtilsGet(Results, type=”efetch”, db=”pubmed”)

#Make publication year list.<\/p>\n\n\n\n

year=YearEntrez(ResultsData)

#Make a list of authors (Last name + initials) for each citation and a list of reference id (first author + year).<\/p>\n\n\n\n

au=Author(ResultsData)
refn=length(au)
auv=rep(“”,refn)
refidv=rep(“”,refn)
for(i in 1:refn){
authors=cbind(au[[i]]$LastName,au[[i]]$Initials)
ma=nrow(authors)
authors[1,]
paste(authors[1,1],authors[1,2])<\/p>\n\n\n\n

aul=””
for(j in 1:ma){
aut=paste(authors[j,1],authors[j,2])
aul=paste(aul,aut,sep=”, “)
}
aul=substr(aul,3,nchar(aul))
auv[i]=aul
refidv[i]=paste(authors[1,1],authors[1,2],year[i])
}

#Make citation list. No formatting. Including DOI information.
refer=Citations(ResultsData)

cite=rep(“”,refn)
for(i in 1:refn){
cite[i]=refer[[2]][[i]]
}

#Create a data frame of PMID, Reference_ID,Citation,Year, Title,Abstract. Citation format is not modified.

pubmed_data=data.frame(‘PMID’=PMID(ResultsData),’Reference_ID’=refidv,’Citation’=cite, ‘Year’=YearEntrez(ResultsData), ‘Title’=ArticleTitle(ResultsData), ‘Abstract’=AbstractText(ResultsData))

#Save the frame work as a CSV file with a save file dialogue. Add file extension “.csv”.

filnam=tclvalue(tkgetSaveFile(initialfile=”export.csv”,filetypes=”{{CSV Files} {.csv}} {{All files} *}”));if(filnam!=”.csv”){write.csv(pubmed_data,filnam,row.names=FALSE)}

#Do not open the file directly to avoid character encoding trouble. Launch Excel, then from Data menu use import text\/csv file.
#The saved file is a text file with UTF-8. You can change encoding from UTF-8 to UTF-8-BOM using Notpad++, and you can directly open the file with Excel without garbles.<\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

RISmed\u306fPubMed\u691c\u7d22\u306e\u305f\u3081\u306eR\u306e\u30d1\u30c3\u30b1\u30fc\u30b8\u3067\u3059\u3002\u4f5c\u8005\u306fStephanie Kovalchik\u6c0f\u3067\u3059\u3002ASReview https:\/\/asreview.nl\/ \u3092\u7528\u3044\u305f\u6587\u732e\u9078\u5b9a\u306e\u969b\u306b\u306f\u3001Title, Abstr … “RISmed\u3092\u7528\u3044\u305fPubMed\u691c\u7d22” \u306e<\/span>\u7d9a\u304d\u3092\u8aad\u3080<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[23,2],"tags":[],"class_list":["post-1519","post","type-post","status-publish","format-standard","hentry","category-literature-search","category-sr"],"_links":{"self":[{"href":"https:\/\/info.zanet.biz\/index.php?rest_route=\/wp\/v2\/posts\/1519","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.zanet.biz\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.zanet.biz\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.zanet.biz\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/info.zanet.biz\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1519"}],"version-history":[{"count":6,"href":"https:\/\/info.zanet.biz\/index.php?rest_route=\/wp\/v2\/posts\/1519\/revisions"}],"predecessor-version":[{"id":1526,"href":"https:\/\/info.zanet.biz\/index.php?rest_route=\/wp\/v2\/posts\/1519\/revisions\/1526"}],"wp:attachment":[{"href":"https:\/\/info.zanet.biz\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1519"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.zanet.biz\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1519"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.zanet.biz\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1519"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}