Search and format bibliographic data • bibou

library(bibou)
library(tidyverse)
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#> ✔ ggplot2   3.4.2     ✔ tibble    3.2.1
#> ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
#> ✔ purrr     1.0.1     
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#> ✖ dplyr::filter() masks stats::filter()
#> ✖ dplyr::lag()    masks stats::lag()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Get bibliographic data from Web of Science

Let’s imagine we wanted to obtain bibliographic data from Web of Science about the Rhone river. We searched keywords “Rhone” and “river” (or “basin” or “catchment”) either in title or topic field.

Fig.1 An example of search in Web of Science

Here we obtained a bit more than 2000 references, which is too much for a single export. Indeed, in case one wants to export the full references, including cited references, the maximum number of references one can export at once is 500. We’re going to export bibliographic references in several batches, according to years of publication.

Fig.2 Refine the search to certain years

Here, we’re going to repeat this process for periods going to

1957 to 1999,
2000 to 2007,
2008 to 2014,
2015 to 2020,
2021 to 2024

Fig.3 Export as bibtex

Fig.4 Export full reference and all results

We hence obtain 5 .bib export files, which are provided with the package (you can find their path once the bibou package is installed with function system.file()).

We merge these files into a single file using bibou’s function bib_merge_files():

bibtex_file_1=system.file("savedrecs(1).bib",package="bibou")
bibtex_files=purrr::map_chr(as.character(1:5),~stringr::str_replace(bibtex_file_1,"1(?=\\).bib)",.x))
bibtex_files
#> [1] "/tmp/RtmpWs9RVN/temp_libpath84cc28429a80/bibou/savedrecs(1).bib"
#> [2] "/tmp/RtmpWs9RVN/temp_libpath84cc28429a80/bibou/savedrecs(2).bib"
#> [3] "/tmp/RtmpWs9RVN/temp_libpath84cc28429a80/bibou/savedrecs(3).bib"
#> [4] "/tmp/RtmpWs9RVN/temp_libpath84cc28429a80/bibou/savedrecs(4).bib"
#> [5] "/tmp/RtmpWs9RVN/temp_libpath84cc28429a80/bibou/savedrecs(5).bib"
bib_merge_files(bibtex_files,
                to="data/savedrecs_merged.bib")

When exporting from Web of Science in several batches, one can mistakenly export the same references several times. The function bib_remove_duplicates() can clean the merged files by removing duplicated references (detected based on their common identifier).

bib_remove_duplicates(from_file="data/savedrecs_merged.bib",
                      to_file="data/savedrecs_clean.bib")

We can now import these references as a table using function bib_tib_doc(). This import relies on the bibliometrix package import method and, as such, formats descriptors in the same way. The complete list of descriptors is available here.

The most important fields are:

Variable	Description
AU	Authors’ Names
TI	Document Title
SO	Journal Name (or Source)
JI	ISO Source Abbreviation
DT	Document Type
DE	Authors’ Keywords
ID	Keywords associated by WoS database
AB	Abstract
C1	Authors’ Affiliations
CR	Cited References
TC	Times Cited
PY	Publication Year
SC	Subject Category
UT	Unique Article Identifier

library(bibliometrix)
tib_doc=bib_tib_doc("data/savedrecs_clean.bib")
#> 
#> Converting your isi collection into a bibliographic dataframe
#> 
#> Done!
#> 
#> 
#> Generating affiliation field tag AU_UN from C1:  Done!
dim(tib_doc)
#> [1] 2097   60
colnames(tib_doc)
#>  [1] "id_doc"                     "AU"                        
#>  [3] "DE"                         "ID"                        
#>  [5] "C1"                         "CR"                        
#>  [7] "AB"                         "PA"                        
#>  [9] "affiliations"               "AR"                        
#> [11] "EM"                         "book.author"               
#> [13] "book.group.author"          "BO"                        
#> [15] "da"                         "DI"                        
#> [17] "GA"                         "eissn"                     
#> [19] "esi.highly.cited.paper"     "esi.hot.paper"             
#> [21] "earlyaccessdate"            "BE"                        
#> [23] "FU"                         "FX"                        
#> [25] "BN"                         "SN"                        
#> [27] "JI"                         "SO"                        
#> [29] "LA"                         "meeting"                   
#> [31] "month"                      "note"                      
#> [33] "NR"                         "PN"                        
#> [35] "oa"                         "orcid.numbers"             
#> [37] "organization"               "PP"                        
#> [39] "PU"                         "SC"                        
#> [41] "researcherid.numbers"       "SE"                        
#> [43] "TC"                         "TI"                        
#> [45] "DT"                         "UT"                        
#> [47] "usage.count.last.180.days"  "U2"                        
#> [49] "VL"                         "web.of.science.categories."
#> [51] "web.of.science.index"       "PY"                        
#> [53] "RP"                         "DB"                        
#> [55] "J9"                         "AU_UN"                     
#> [57] "AU1_UN"                     "AU_UN_NR"                  
#> [59] "SR_FULL"                    "SR"

tib_doc %>% 
  select(AU,TI,SO,DT,DE,TC,PY) %>% 
  head(10) %>% 
  knitr::kable()

AU	TI	SO	DT	DE	TC	PY
GOLLMANN G;BOUVET Y;KARAKOUSIS Y;TRIANTAPHYLLIDIS C	GENETIC VARIABILITY IN CHONDROSTOMA FROM AUSTRIAN, FRENCH AND GREEK RIVERS (TELEOSTEI, CYPRINIDAE)	JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH	ARTICLE	ALLOZYMES; GENETIC VARIATION; RANGE EXPANSION; RIVER CAPTURE; CYPRINIDAE; CHONDROSTOMA	17	1997
FRUGET JF;CENTOFANTI M;OLIVIER JM	THE FISH FAUNA OF THE DOUBS RIVER PRIOR TO COMPLETION OF THE RHINE-RHONE CONNECTION	ENVIRONMENTAL MANAGEMENT	ARTICLE	FISH COMMUNITIES; REGULATION; RESTORATION; FLOODPLAIN; LARGE SHIP CANAL; DOUBS RIVER	2	1998
BRAVARD JP	TECTONICS AND FLUVIODYNAMICS AT THE SAONE-RHONE CONFLUENCE FROM THE WURM TO THE HOLOCENE (FRANCE).	GEOGRAPHIE PHYSIQUE ET QUATERNAIRE	ARTICLE; PROCEEDINGS PAPER	NA	11	1997
HUGHES FMR	FLOODPLAIN BIOGEOMORPHOLOGY	PROGRESS IN PHYSICAL GEOGRAPHY-EARTH AND ENVIRONMENT	REVIEW	FLOODS; FLOODPLAIN VEGETATION; RESTORATION; SOIL MOISTURE; REGENERATION	212	1997
VINSON MR;HAWKINS CP	BIODIVERSITY OF STREAM INSECTS: VARIATION AT LOCAL, BASIN, AND REGIONAL SCALES	ANNUAL REVIEW OF ENTOMOLOGY	REVIEW	BIODIVERSITY; AQUATIC INSECTS; MAYFLIES; STONEFLIES; CADDISFLIES	349	1998
FERNANDES MB;SICRE MA;BOIREAU A;TRONCZYNSKI J	POLYAROMATIC HYDROCARBON (PAH) DISTRIBUTIONS IN THE SEINE RIVER AND ITS ESTUARY	MARINE POLLUTION BULLETIN	ARTICLE	NA	298	1997
LOIZEAU JL;DOMINIK J;LUZZI T;VERNET JP	SEDIMENT CORE CORRELATION AND MAPPING OF SEDIMENT ACCUMULATION RATES IN LAKE GENEVA (SWITZERLAND, FRANCE) USING VOLUME MAGNETIC SUSCEPTIBILITY	JOURNAL OF GREAT LAKES RESEARCH	ARTICLE	VOLUME MAGNETIC SUSCEPTIBILITY; CORE CORRELATION; CS-137; SEDIMENT; ACCUMULATION RATE; SEDIMENT SUPPLY; LAKE GENEVA	23	1997
MARSALEIX P;ESTOURNEL C;KONDRACHOFF V;VEHIL R	A NUMERICAL STUDY OF THE FORMATION OF THE RHONE RIVER PLUME	JOURNAL OF MARINE SYSTEMS	ARTICLE	RIVER PLUME; NORTHWESTERN MEDITERRANEAN; THE RHONE; JEBAR EFFECT; TWOFOLD SIGMA COORDINATE	66	1998
COLLINA-GIRARD J	SUBMARINE SKETCHED PROFILES ANALYSIS ALONG PROVENCE COAST, USING SCUBA-DIVING, EUSTATICS AND NEOTECTONICS RESULTS	COMPTES RENDUS DE L ACADEMIE DES SCIENCES SERIE II FASCICULE A-SCIENCES DE LA TERRE ET DES PLANETES	ARTICLE	NEOTECTONIC; EUSTATISM; PROVENCE; FRANCE; SUBMARINE PROFILES; SCUBADIVING; HOLOCENE; COVE OF COSQUER	10	1997
GALASSI DMP;DE LAURENTIIS P	TWO NEW SPECIES OF NITOCRELLA FROM GROUNDWATERS OF ITALY (CRUSTACEA, COPEPODA, HARPACTICOIDA)	ITALIAN JOURNAL OF ZOOLOGY	ARTICLE	HARPACTICOIDA; NITOCRELLA; SPRINGWATERS; STYGOBIONT	11	1997