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abbrever包，快速批量获取期刊缩写信息
The following article is from BioparaMeta Author 凯凯何
利用abbrevr包批量输出期刊缩写
有时候用endnote导入文献后显示的是期刊全称，而用到缩写时候就需要去一些网站上一个个搜索，比如CASSI[1], LetPub[2]、Pubumed等网站，或者Y叔公号里直接回复，而逛Github时候突然发现abbrevr[3]这小R包中可以很快批量实现这个需求，在此记录一下。
安装
# install.packages("remotes")
remotes::install_github("patrickbarks/abbrevr")
查询期刊缩写
library(abbrevr)
AbbrevTitle("Transactions of the American Fisheries Society")
#> [1] "Trans. Am. Fish. Soc."
AbbrevTitle("Deutsche Medizinische Wochenschrift")
#> [1] "Dtsch. Med. Wochenschr."
AbbrevTitle("L'Intermédiaire des Mathématiciens")
#> [1] "Interméd. Math."
根据doi号批量获取
这里就需要结合另一个R包rcrossref[4], 这个包主要功能就是利用API接口根据doi号提取文献信息(具体原理可自行摸索)，然后提取出文献全称再批量转化为缩写，一步到位，示例如下：
# load rcrossref
library(rcrossref)
# DOIs for a set of scientific publications
dois <- c(
"10.1577/T09-174.1",
"10.1371/journal.pone.007585",
"10.1111/1365-2435.1235",
"10.1111/jeb.12823",
"10.1111/1365-2745.12937"
)
# use rcrossref::cr_cn() to get citation info for DOIs
citations <- rcrossref::cr_cn(dois, format = "citeproc-json")
# extract journal titles from citation info
titles <- sapply(citations, function(x) x$`container-title`, USE.NAMES = FALSE)
# use abbrevr::AbbrevTitle() to abbreviate titles
titles_short <- sapply(titles, abbrevr::AbbrevTitle, USE.NAMES = FALSE)
# print data.frame
data.frame(
doi = dois,
title = titles,
title_short = titles_short,
stringsAsFactors = FALSE
)
附当前版本说明：
The current version…
only handles common articles, prepositions, and conjunctions in English, German, and French (ISO 4 dictates that these classes should generally be ommitted, with exceptions noted in the document linked above) omits all punctuation except for hyphens (ISO 4 dictates all punctuation except commas should be retained, but periods should be replaced with commas) does not omit generic identifiers such as “Section”, “Series”, or “Part” (ISO 4 dictates such generics should be ommitted unless required for identification) may not retain all diacritic marks (ISO 4 dictates that all diacritic marks should be retained)
Also beware of abbreviation rules that are difficult to implement algorithmically, e.g.:
names of persons should not be abbreviated prepositions and articles should be retained if they are integral parts of proper names (e.g. “Los Alamos”) or locutions (e.g. “in vivo”)
参考资料
CASSI: https://cassi.cas.org/search.jsp
[2]LetPub: https://www.letpub.com/index.php?page=journalapp&view=search
[3]abbrevr: https://github.com/patrickbarks/abbrevr/
[4]rcrossref: https://github.com/ropensci/rcrossref