Building and exporting a reference set • scopusflow

library(scopusflow)

A retrieval becomes useful once it leaves the package, as a reading list in a reference manager or as input to a science-mapping tool. This article covers that export end of the workflow. Every step runs without an API key, on the bundled example_records, a corpus of 138 real journal articles that stands in for a harvest of your own because Scopus records may not be redistributed. The article vignette("scopusflow") describes where it comes from.

Take stock first

Before exporting anything, it helps to see what the set contains. summary() reports the size, the span of years, the number of distinct sources, the citation spread and the most-cited record.

summary(example_records)

 [34m<scopus_records> [39m summary

138 records, from 2015 to 2024.

90 sources, 127 with a DOI.

Cited 7015 times in total, median 24 per record.

Most frequent source: ACS Applied Materials & Interfaces.

Most cited:  [3mGraphene for batteries, supercapacitors and beyond [23m.

Eleven of those 138 records arrived without a DOI, which is why the summary counts 127 with one. That is ordinary in a real harvest, and the sections below show how each export handles it.

A record set is an ordinary tibble underneath, so it drops straight into tidyverse or base workflows. as_tibble() and as.data.frame() make that explicit when a downstream tool expects a plain frame.

head(tibble::as_tibble(example_records))

entry_number	scopus_id	doi	title	authors	year	date	publication	citations	query
1	NA	10.15541/jim20140527	Enhanced Capacitive Properties of All-solid-state Symmetric Graphene Supercapacitors by Incorporating Nitrogen-doping and SnO2 Nanoparticles	Jianhua Yu	2015	2015-01-01	Journal of Inorganic Materials	1	graphene supercapacitor
2	NA	NA	Fabrication and Characterization of a Vertically-Oriented Graphene Supercapacitor	Patrick R Rice	2015	2015-01-01	DigitalCommons - CalPoly (California State Polytechnic University)	0	graphene supercapacitor
3	NA	10.1021/am509065d	Flexible and Stackable Laser-Induced Graphene Supercapacitors	Zhiwei Peng	2015	2015-01-13	ACS Applied Materials & Interfaces	469	graphene supercapacitor
4	NA	10.1016/j.electacta.2015.02.019	Heavily nitrogen doped, graphene supercapacitor from silk cocoon	Vikrant Sahu	2015	2015-02-04	Electrochimica Acta	195	graphene supercapacitor
5	NA	10.1002/smll.201403383	Graphene-Based Integrated Photovoltaic Energy Harvesting/Storage Device	Chih-Tao Chien	2015	2015-02-19	Small	108	graphene supercapacitor
6	NA	10.1016/j.jpowsour.2015.03.015	Nanoporous graphene materials by low-temperature vacuum-assisted thermal process for electrochemical energy storage	Hao Yang	2015	2015-03-05	Journal of Power Sources	47	graphene supercapacitor

as.data.frame(example_records)[1:3, c("title", "year")]

title	year
Enhanced Capacitive Properties of All-solid-state Symmetric Graphene Supercapacitors by Incorporating Nitrogen-doping and SnO2 Nanoparticles	2015
Fabrication and Characterization of a Vertically-Oriented Graphene Supercapacitor	2015
Flexible and Stackable Laser-Induced Graphene Supercapacitors	2015

A clean, deduplicated DOI list

Reference managers such as Zotero import most reliably from DOIs. scopus_extract_dois() pulls them out, normalises them and removes duplicates, so the same article imports once even when its DOI was stored with a resolver prefix or in a different case.

dois <- scopus_extract_dois(example_records)
length(dois)

[1] 127

head(dois, 6)

[1] "10.15541/jim20140527"            "10.1021/am509065d"              
[3] "10.1016/j.electacta.2015.02.019" "10.1002/smll.201403383"         
[5] "10.1016/j.jpowsour.2015.03.015"  "10.1103/physrevb.91.125415"

The same cleaning applies to a plain vector of DOIs from any source, so the first two entries below collapse to one because comparison ignores case and resolver prefixes, while dedupe = FALSE keeps every occurrence, for instance to count how often a DOI recurs across retrievals.

scopus_extract_dois(c("https://doi.org/10.1/A", "doi: 10.1/a", "10.2/B"))

[1] "10.1/A" "10.2/B"

scopus_extract_dois(c("https://doi.org/10.1/A", "doi: 10.1/a", "10.2/B"),
                    dedupe = FALSE)

[1] "10.1/A" "10.1/a" "10.2/B"

The list can be written to a single-column CSV at a path you choose. Nothing is written unless a path is given. Here are the first few lines of the file, which holds a header and one DOI per line.

out <- file.path(tempdir(), "reference-set.csv")
scopus_extract_dois(example_records, file = out)
writeLines(head(readLines(out), 6))

"doi"
"10.15541/jim20140527"
"10.1021/am509065d"
"10.1016/j.electacta.2015.02.019"
"10.1002/smll.201403383"
"10.1016/j.jpowsour.2015.03.015"

Into a reference manager

A DOI list is enough for an import-by-identifier, but a full record carries more. as_ris() and as_bibtex() render the set in the two interchange formats that reference managers read, so a search moves straight into Zotero, EndNote or a LaTeX bibliography. Each record becomes one entry, with its authors split out.

cat(substr(as_ris(example_records), 1, 470))

TY  - JOUR
TI  - Enhanced Capacitive Properties of All-solid-state Symmetric Graphene Supercapacitors by Incorporating Nitrogen-doping and SnO2 Nanoparticles
AU  - Jianhua Yu
PY  - 2015
JO  - Journal of Inorganic Materials
DO  - 10.15541/jim20140527
ER  - 

TY  - JOUR
TI  - Fabrication and Characterization of a Vertically-Oriented Graphene Supercapacitor
AU  - Patrick R Rice
PY  - 2015
JO  - DigitalCommons - CalPoly (California State Polytechnic University)
ER  -

The first two entries of 138 are shown. The second has no DOI, so its DO line is simply absent rather than empty, and the entry still imports on its title, author and year.

Pass a file to write the whole set. Nothing is written without one.

bib <- file.path(tempdir(), "reference-set.bib")
as_bibtex(example_records, file = bib)

Handing off to science mapping

as_bibliometrix() re-maps the records to the tagged column layout that the bibliometrix package and the wider ISI convention expect.

m <- as_bibliometrix(example_records)
head(m[, c("AU", "TI", "PY", "SO", "TC", "DB")])

AU	TI	PY	SO	TC	DB
JIANHUA YU	ENHANCED CAPACITIVE PROPERTIES OF ALL-SOLID-STATE SYMMETRIC GRAPHENE SUPERCAPACITORS BY INCORPORATING NITROGEN-DOPING AND SNO2 NANOPARTICLES	2015	JOURNAL OF INORGANIC MATERIALS	1	SCOPUS
PATRICK R RICE	FABRICATION AND CHARACTERIZATION OF A VERTICALLY-ORIENTED GRAPHENE SUPERCAPACITOR	2015	DIGITALCOMMONS - CALPOLY (CALIFORNIA STATE POLYTECHNIC UNIVERSITY)	0	SCOPUS
ZHIWEI PENG	FLEXIBLE AND STACKABLE LASER-INDUCED GRAPHENE SUPERCAPACITORS	2015	ACS APPLIED MATERIALS & INTERFACES	469	SCOPUS
VIKRANT SAHU	HEAVILY NITROGEN DOPED, GRAPHENE SUPERCAPACITOR FROM SILK COCOON	2015	ELECTROCHIMICA ACTA	195	SCOPUS
CHIH-TAO CHIEN	GRAPHENE-BASED INTEGRATED PHOTOVOLTAIC ENERGY HARVESTING/STORAGE DEVICE	2015	SMALL	108	SCOPUS
HAO YANG	NANOPOROUS GRAPHENE MATERIALS BY LOW-TEMPERATURE VACUUM-ASSISTED THERMAL PROCESS FOR ELECTROCHEMICAL ENERGY STORAGE	2015	JOURNAL OF POWER SOURCES	47	SCOPUS

From there the usual bibliometrix entry points apply. This step needs that package, so it is shown but not run.

if (requireNamespace("bibliometrix", quietly = TRUE)) {
  results <- bibliometrix::biblioAnalysis(m)
  summary(results, k = 10)
}

As noted on the as_bibliometrix() help page, this reconstructs the core descriptive fields only. Analyses that need full affiliations or cited references still call for a complete ‘Scopus’ CSV or BibTeX export read with bibliometrix::convert2df().

Saving the working set

To pick the work up in a later session, save the records and read them back. The .rds form preserves the types and class exactly, while .csv is portable plain text.

path <- file.path(tempdir(), "records.rds")
write_scopus_records(example_records, path)
identical(read_scopus_records(path), example_records)

[1] TRUE