NCBI 提供的 E-utilities API 可以很方便的从 NCBI 的数据库中提取信息。对于其 PubMed 数据库， pubmedR 封装了 E-utilities API（内部基于底层 rentrez 包），用户可以更为直接的从 PubMed 数据库提取相应的数据。
本文将展示如何获取来自某一学术期刊的所有论文，通过分析作者，获取在此学术期刊上发表论文最高的作者。
批量从 PubMed 上获取数据需要提供 NCBI 的 API key。可以免费获得，具体步骤为：登录 NCBI -> Account Settings -> API Key Management。
library(pubmedR)
api_key =
对 PubMed 数据库进行查询时，我们需要提供格式化的查询字串，详见 https://pubmed.ncbi.nlm.nih.gov/help/#using-search-field-tags 。如果不知道如何编写查询字串，可先在网页版上输入查询内容，PubMed 的搜索功能会自动将其格式化成标准查询字串，然后再 按照自己的需求略加修改即可。
注意通过 NCBI API 最多一次只能获取一万条记录，如果超过一万条，需要分次获取。在下面的例子中，我们将所有2014年至2025年 Bioinformatics 期刊上的所有论文分两次获取。
期刊的标准名字可以在 https://ftp.ncbi.nlm.nih.gov/pubmed/J_Medline.txt 查询获得。
query = '("Bioinformatics (Oxford, England)"[Journal]) AND (("1998"[Date - Publication] : "2014"[Date - Publication]))'
res = pmQueryTotalCount(query = query, api_key = api_key)
D1 = pmApiRequest(query = query, limit = res$total_count, api_key = NULL)
query = '("Bioinformatics (Oxford, England)"[Journal]) AND (("2015"[Date - Publication] : "2025"[Date - Publication]))'
res = pmQueryTotalCount(query = query, api_key = api_key)
D2 = pmApiRequest(query = query, limit = res$total_count, api_key = NULL)
D1 = pmApi2df(D1)
D2 = pmApi2df(D2)
df = rbind(D1, D2)
df = df[df$DT == "JOURNAL ARTICLE", ]
现在所有的论文信息均存储在df数据框中，其中作者列表在AF列中。
以第一作者最高发文量前十名：
first_authors = gsub(";.*$", "", df$AF)
first_authors = first_authors[first_authors != ""]
sort(table(first_authors), decreasing = TRUE)[1:10]
## first_authors
## LI, HENG FOGG, CHRISTIANA N CHEN, LI DEOROWICZ, SEBASTIAN
## 21 17 12 11
## SAVOJARDO, CASTRENSE LIU, BIN GU, ZUGUANG HÄKKINEN, ANTTI
## 10 9 8 8
## LI, YANG CHEN, WEI
## 8 7
以最后作者最高发文量前十名：
last_authors = gsub("^.*;", "", df$AF)
last_authors = last_authors[last_authors != ""]
sort(table(last_authors), decreasing = TRUE)[1:10]
## last_authors
## WANG, JIANXIN DEANE, CHARLOTTE M GAO, XIN BALDI, PIERRE CHENG, JIANLIN
## 41 30 28 27 25
## DOUGHERTY, EDWARD R ASAI, KIYOSHI BAR-JOSEPH, ZIV RAPHAEL, BENJAMIN J ZHANG, YANG
## 25 24 24 24 24
我们可以让代码变得略微聪明一点，我们可以将总记录按年逐份提取，可以编写如下函数 top_authors().
library(GetoptLong)
cache = new.env()
cache$data = list()
top_authors = function(journal, year_start = 2000, remove_single_author = FALSE) {
year_end = as.integer(gsub("-.*$", "", as.character(Sys.Date())))
df = NULL
for(y in seq(year_start, year_end)) {
query = qq('("@{journal}"[Journal]) AND (("@{y}/01/01"[Date - Publication] : "@{y}/12/31"[Date - Publication]))')
cat(query, "\n")
res = pmQueryTotalCount(query = query, api_key = api_key)
if(res$total_count > 1) {
if(!is.null(cache$data[[qq("@{journal}/@{y}")]])) {
cat(" read from cache\n")
m1 = cache$data[[qq("@{journal}/@{y}")]]
} else {
if(res$total_count > 8000) {
query = qq('("@{journal}"[Journal]) AND (("@{y}/01/01"[Date - Publication] : "@{y}/06/30"[Date - Publication]))')
cat(" ", query, "\n")
res = pmQueryTotalCount(query = query, api_key = api_key)
D1 = pmApiRequest(query = query, limit = res$total_count, api_key = api_key)
m1 = pmApi2df(D1)
query = qq('("@{journal}"[Journal]) AND (("@{y}/07/01"[Date - Publication] : "@{y}/12/31"[Date - Publication]))')
cat(" ", query, "\n")
res = pmQueryTotalCount(query = query, api_key = api_key)
D1 = pmApiRequest(query = query, limit = res$total_count, api_key = api_key)
m1 = rbind(m1, pmApi2df(D1))
} else {
D1 = pmApiRequest(query = query, limit = res$total_count, api_key = api_key)
m1 = pmApi2df(D1)
}
cache$data[[qq("@{journal}/@{y}")]] = m1
}
df = rbind(df, m1)
}
}
df = df[df$DT == "JOURNAL ARTICLE", ]
author_list = df$AF
author_list = strsplit(author_list, ";")
author_list = lapply(author_list, function(x) x[!grepl("^\\d*$", x)])
author_list = author_list[sapply(author_list, length) > 0]
# 某些期刊会有editor's letter，在pubmed中也算journal article
# 一般来说，这种文章只有一个作者
if(remove_single_author) {
author_list = author_list[sapply(author_list, length) > 1]
}
authors = sapply(author_list, function(x) x[1])
cat("top 10 first authors:\n")
print(as.data.frame(sort(table(authors), decreasing = TRUE)[1:10]))
# last author
authors = sapply(author_list, function(x) x[length(x)])
cat("top 10 last authors:\n")
print(as.data.frame(sort(table(authors), decreasing = TRUE)[1:10]))
# all authors
authors = unlist(author_list)
cat("top 10 all authors:\n")
print(as.data.frame(sort(table(authors), decreasing = TRUE)[1:10]))
return(invisible(df))
}
我们来试验一下近十年的：
top_authors("BMC bioinformatics", year_start = 2015)
## top 10 first authors:
## authors Freq
## 1 DENG, LEI 7
## 2 PENG, JIAJIE 6
## 3 FIANNACA, ANTONINO 5
## 4 TAGUCHI, Y-H 5
## 5 ZHANG, JUNPENG 5
## 6 ADHIKARI, BADRI 4
## 7 BONNICI, VINCENZO 4
## 8 CHEN, YAO-MEI 4
## 9 EZAWA, KIYOSHI 4
## 10 FAN, YONGXIAN 4
## top 10 last authors:
## authors Freq
## 1 CHENG, JIANLIN 15
## 2 SHANG, XUEQUN 13
## 3 WANG, YADONG 12
## 4 PAPPALARDO, FRANCESCO 11
## 5 ROST, BURKHARD 10
## 6 LI, JINYAN 9
## 7 WANG, LEI 9
## 8 ZHENG, CHUN-HOU 9
## 9 BOUTROS, PAUL C 7
## 10 KAHVECI, TAMER 7
## top 10 all authors:
## authors Freq
## 1 WANG, LEI 20
## 2 WANG, YADONG 20
## 3 WANG, JIAN 17
## 4 WANG, JIANXIN 16
## 5 CHENG, JIANLIN 15
## 6 LIU, JIN-XING 15
## 7 LIN, HONGFEI 14
## 8 PAPPALARDO, FRANCESCO 14
## 9 SHANG, XUEQUN 14
## 10 DENG, LEI 13
top_authors("Genome biology", year_start = 2015)
## top 10 first authors:
## authors Freq
## 1 MARINOV, GEORGI K 4
## 2 ARAN, DVIR 3
## 3 DAVIDSON, NADIA M 3
## 4 HUANG, YUANHUA 3
## 5 LIPINSKA, AGNIESZKA P 3
## 6 MCCARTNEY, DANIEL L 3
## 7 MURAT, PIERRE 3
## 8 RUBIN, ALAN F 3
## 9 SONG, QINGXIN 3
## 10 TESCHENDORFF, ANDREW E 3
## top 10 last authors:
## authors Freq
## 1 STEGLE, OLIVER 9
## 2 YUAN, GUO-CHENG 9
## 3 BALASUBRAMANIAN, SHANKAR 8
## 4 ERNST, JASON 8
## 5 GERSTEIN, MARK 8
## 6 ALKURAYA, FOWZAN S 7
## 7 LANGMEAD, BEN 7
## 8 LI, JINGYI JESSICA 7
## 9 ROBINSON, MARK D 7
## 10 SCHLÖTTERER, CHRISTIAN 7
## top 10 all authors:
## authors Freq
## 1 LI, WEI 16
## 2 STEGLE, OLIVER 16
## 3 MARIONI, JOHN C 15
## 4 REIK, WOLF 13
## 5 HE, CHUAN 12
## 6 LI, JINGYI JESSICA 12
## 7 MASON, CHRISTOPHER E 12
## 8 SHI, LEMING 12
## 9 CHEN, WEI 11
## 10 FLICEK, PAUL 11
top_authors("Nature communications", year_start = 2015)
## top 10 first authors:
## authors Freq
## 1 LIU, YANG 25
## 2 YANG, YANG 25
## 3 LIU, WEI 23
## 4 WANG, WEI 22
## 5 ZHANG, LEI 22
## 6 LI, XIN 20
## 7 LI, YANG 19
## 8 LIU, CHANG 19
## 9 ZHANG, TAO 19
## 10 WANG, YU 18
## top 10 last authors:
## authors Freq
## 1 HUANG, WEI 42
## 2 TANG, BEN ZHONG 40
## 3 WANG, ZHONG LIN 38
## 4 SARGENT, EDWARD H 35
## 5 STEFANSSON, KARI 33
## 6 CHEN, WEI 31
## 7 YANG, YANG 29
## 8 CHEN, JUN 28
## 9 WANG, LEI 28
## 10 NUREKI, OSAMU 27
## top 10 all authors:
## authors Freq
## 1 TANIGUCHI, TAKASHI 249
## 2 WATANABE, KENJI 249
## 3 LI, WEI 222
## 4 LIU, YANG 218
## 5 WANG, WEI 199
## 6 ZHANG, WEI 189
## 7 WANG, JING 175
## 8 WANG, LEI 175
## 9 YANG, YANG 168
## 10 CHEN, WEI 165
top_authors("Nature", year_start = 2015, remove_single_author = TRUE)
## top 10 first authors:
## authors Freq
## 1 LIU, YANG 11
## 2 AHMADI, M 8
## 3 DONG, XIAO 6
## 4 WANG, LI 6
## 5 COORENS, TIM H H 5
## 6 EVARISTO, JAIVIME 5
## 7 LIU, PENG 5
## 8 ROGELJ, JOERI 5
## 9 ABBOSH, CHRISTOPHER 4
## 10 BLUVSTEIN, DOLEV 4
## top 10 last authors:
## authors Freq
## 1 BAKER, DAVID 36
## 2 MACMILLAN, DAVID W C 16
## 3 DUAN, XIANGFENG 15
## 4 PAN, JIAN-WEI 15
## 5 SARGENT, EDWARD H 15
## 6 GOUAUX, ERIC 14
## 7 LUKIN, MIKHAIL D 14
## 8 BARAN, PHIL S 13
## 9 CRAMER, PATRICK 13
## 10 DIXIT, VISHVA M 13
## top 10 all authors:
## authors Freq
## 1 WATANABE, KENJI 132
## 2 TANIGUCHI, TAKASHI 130
## 3 BAKER, DAVID 51
## 4 LIU, YANG 44
## 5 REGEV, AVIV 41
## 6 CAMPBELL, PETER J 39
## 7 WANG, WEI 35
## 8 CHANG, HOWARD Y 30
## 9 ZHANG, YU 30
## 10 REN, BING 29
top_authors("Science", year_start = 2015, remove_single_author = TRUE)
## top 10 first authors:
## authors Freq
## 1 VIGNIERI, SACHA 44
## 2 LOPEZ, BIANCA 29
## 3 SMITH, JESSE 16
## 4 SMITH, KEITH T 16
## 5 ASH, CAROLINE 13
## 6 SIMONTI, CORINNE 12
## 7 GROCHOLSKI, BRENT 11
## 8 SMITH, H JESSE 11
## 9 JIANG, DI 10
## 10 STERN, PETER 9
## top 10 last authors:
## authors Freq
## 1 BAKER, DAVID 29
## 2 OLINGY, CLAIRE 25
## 3 ZHANG, FENG 19
## 4 SHI, YIGONG 18
## 5 DOUDNA, JENNIFER A 15
## 6 BARAN, PHIL S 14
## 7 MALO, COURTNEY 14
## 8 PAN, JIAN-WEI 14
## 9 SABATINI, DAVID M 14
## 10 ASH, CAROLINE 13
## top 10 all authors:
## authors Freq
## 1 JIANG, DI 135
## 2 VIGNIERI, SACHA 135
## 3 LAVINE, MARC S 129
## 4 SZUROMI, PHIL 125
## 5 ASH, CAROLINE 118
## 6 FUNK, MICHAEL A 115
## 7 LOPEZ, BIANCA 104
## 8 STAJIC, JELENA 104
## 9 MAROSO, MATTIA 98
## 10 GROCHOLSKI, BRENT 97
top_authors("Cell", year_start = 2015, remove_single_author = TRUE)
## top 10 first authors:
## authors Freq
## 1 GRUBAUGH, NATHAN D 6
## 2 WALLS, ALEXANDRA C 5
## 3 WU, JUN 5
## 4 YAN, LIMING 5
## 5 CHEN, YUN 4
## 6 GARCIA-BELTRAN, WILFREDO F 4
## 7 HOFFMANN, MARKUS 4
## 8 LE, TUNG T 4
## 9 LÓPEZ-OTÍN, CARLOS 4
## 10 VATANEN, TOMMI 4
## top 10 last authors:
## authors Freq
## 1 DIAMOND, MICHAEL S 18
## 2 AMIT, IDO 15
## 3 CLEVERS, HANS 12
## 4 LUO, LIQUN 12
## 5 COLONNA, MARCO 11
## 6 DEISSEROTH, KARL 11
## 7 DILLIN, ANDREW 11
## 8 GINTY, DAVID D 11
## 9 IZPISUA BELMONTE, JUAN CARLOS 11
## 10 FUCHS, ELAINE 10
## top 10 all authors:
## authors Freq
## 1 REGEV, AVIV 45
## 2 DIAMOND, MICHAEL S 29
## 3 LI, WEI 27
## 4 AMIT, IDO 26
## 5 DEISSEROTH, KARL 25
## 6 GYGI, STEVEN P 25
## 7 GINHOUX, FLORENT 23
## 8 ZHANG, BING 23
## 9 CLEVERS, HANS 22
## 10 COLONNA, MARCO 22
Session Info：
sessionInfo()
## R version 4.4.2 (2024-10-31)
## Platform: aarch64-apple-darwin20
## Running under: macOS 26.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## locale:
## [1] C.UTF-8/UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8
##
## time zone: Europe/Berlin
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] GetoptLong_1.0.5 pubmedR_0.0.3 knitr_1.50 colorout_1.3-2
##
## loaded via a namespace (and not attached):
## [1] crayon_1.5.3 httr_1.4.7 cli_3.6.4 rlang_1.1.5
## [5] xfun_0.51 jsonlite_1.9.0 rjson_0.2.23 htmltools_0.5.8.1
## [9] GlobalOptions_0.1.4 XML_3.99-0.18 sass_0.4.9 rmarkdown_2.29
## [13] evaluate_1.0.3 jquerylib_0.1.4 fastmap_1.2.0 yaml_2.3.10
## [17] lifecycle_1.0.4 bookdown_0.44 compiler_4.4.2 rentrez_1.2.4
## [21] blogdown_1.19 digest_0.6.37 R6_2.6.1 curl_6.2.1
## [25] bslib_0.9.0 tools_4.4.2 cachem_1.1.0