Bibliography Report

Author
Affiliation

Rainer M. Krug

University of Zürich

Abstract

Reports analysing the IPBES Libraries on Zotero.

Introduction

This report assesses the ILK Bibliography in regards to different measures and shows some information of the content. It does not assess the content of the sources but rather the bibliometric data.

Bibliographic analysis

In most cases, the bibliographic analysis is done on the OpenAlex library. In some cases, we can also do it using the Zenodo data. This is mentioned in the beginning of each subsection

Publication types

Analysis: Zenodo and OpenAlex

OpenAlex and Zotero use different tyoes. These are not directly compable, which is whu=y both are shown.

Show the code 
bib_data$figure_types_data |>
  dplyr::arrange(
    from,
    desc(count)
  ) |>
  knitr::kable(
    caption = "Types of documents from the Zotero bibliography as well as from OpenApex."
  )
Types of documents from the Zotero bibliography as well as from OpenApex.
type count from
article 2899 OpenAlex
review 54 OpenAlex
book-chapter 10 OpenAlex
book 6 OpenAlex
preprint 6 OpenAlex
erratum 2 OpenAlex
dataset 1 OpenAlex
other 1 OpenAlex
report 1 OpenAlex
journalArticle 4036 Zotero
book 481 Zotero
report 321 Zotero
document 285 Zotero
bookSection 208 Zotero
videoRecording 48 Zotero
webpage 43 Zotero
conferencePaper 31 Zotero
thesis 29 Zotero
newspaperArticle 22 Zotero
blogPost 20 Zotero
manuscript 15 Zotero
annotation 11 Zotero
presentation 11 Zotero
artwork 8 Zotero
statute 6 Zotero
magazineArticle 4 Zotero
map 4 Zotero
letter 2 Zotero
dataset 1 Zotero
forumPost 1 Zotero
hearing 1 Zotero
Show the code 
bib_data$figure_types

Zenodo versus OpenAlex Types

Analysis: Zenodo and OpenAlex

The types entered in the Zenodo library and the types as retrieved from OpenAlex are not linked, therefore they can differ. This can indicate faulty data entering in Zenodo but not necessarily has to. These cases need to be carefully evaluated and here only given as a starting point.

NA in OpenAlex is likely caused by the doi not found in OpenAlex (not in there, not valid, non-standard DOI in Zenodo). NA in Zotero is linked to non-standard DOI entries (i.e. with http) which can therefore not be linked to OpenAlex data. If all DOIs are in standard format, there should be no NAs in this Table in the column Ferom Zenodo.

TODO: Improvements should be done after feedback.

Show the code 
bib_data$metrics$types$comparison |>
  knitr::kable(
    col.names = c("Type from Zenodo", "Type from [OpenAlex](https://OpenAlex.org){target='_blank'}", "count"),
    caption = "Table giving the combination of types from Zenodo as well as [OpenAlex](https://OpenAlex.org){target='_blank'} and their frequency"
  )
Table giving the combination of types from Zenodo as well as OpenAlex and their frequency
Type from Zenodo Type from OpenAlex count
journalArticle article 2360
journalArticle NA 1613
NA article 535
book NA 481
report NA 321
document NA 285
bookSection NA 208
videoRecording NA 48
webpage NA 43
journalArticle review 43
thesis NA 29
conferencePaper NA 27
newspaperArticle NA 22
blogPost NA 20
manuscript NA 15
presentation NA 11
annotation NA 11
NA review 11
artwork NA 8
journalArticle book-chapter 6
journalArticle book 6
statute NA 6
journalArticle preprint 5
conferencePaper article 4
map NA 4
magazineArticle NA 4
NA book-chapter 4
letter NA 2
journalArticle erratum 2
forumPost NA 1
hearing NA 1
journalArticle other 1
dataset NA 1
NA report 1
NA preprint 1
NA dataset 1

Year of Publication

Analysis: Zenodo and OpenAlex

The following ranges of publication years can be found in the data.

Show the code 
bib_data$figure_pub_year_data |>
  dplyr::summarize(
    min = min(publication_year, na.rm = TRUE),
    max = max(publication_year, na.rm = TRUE),
    .by = c(from)
  ) |>
  knitr::kable()
from min max
Zenodo 1616 2023
OpenAlex 1947 2023
Show the code 
bib_data$figure_pub_year
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_col()`).

Access Status of References

Analysis: OpenAlex

Show the code 
bib_data$figure_oa_status

50 Most often cited Journals

Analysis: Zenodo

TODO: OpenAlex should be added

Show the code 
bib_data$figure_top_journals

This table contains all Journals as specified in the Zotero database.

Show the code 
bib_data$figure_top_journals_data |>
  IPBES.R::table_dt("cited_journals")

Coutries of Institutes of all authors

Analysis: OpenAlex

In this section we will take a closer look at the countries from which ih the authors ot the publication come. THe data includes all authoirs without weighting.

Show the code 
#|
#| fig-height: 10
#| fig-width: 10

bib_data$figure_top_country_map

This plot only contains the countries with more than 10 references.

Show the code 
#|
#| fig-height: 10
#| fig-width: 10

bib_data$figure_top_country

This table contains all countries and the number of authorship.

Show the code 
bib_data$figure_top_country_data |>
  IPBES.R::table_dt("top_countries")

Cleanliness of the Bibliography

Cleanliness of a bibliography is defined here as the quality of the bibliografic data in the bibliography. It does not concern any topical measures, only measures related to the bibliografic data in the bibliography.

The analysis is at the moment only done for DOIs as corresponding measures are not available at the moment for ISBNs and ISSNs and duplicate ISBNs and ISSNs can be rcorrect as different chapters of a book might be in the bibliography.

Entries with DOIs, ISBNs or ISSNs in Zotero

To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.

To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead to duplicates.

  • DOIs: 3091 (55.31%) - 6 duplicates
  • ISBNss: 291 (5.21%)
  • ISBNss: 2525 (45.19%)

DOIs in Zotero

The following sections provide some more detailed analysis of the bibliography in Zenodo. The tables all contain clickable links which, shwen clicked, show the respective article in the Zotero bibliograpohy.

Duplicates

The following DOIs are duplicates in the bibliography. This table should be empty.

Show the code 
if (length(bib_data$metrics$zotero_dois$duplicate) > 0) {
  data.frame(
    doi = bib_data$metrics$zotero_dois$duplicate,
    link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$duplicate))
  ) |>
    dplyr::mutate(
      sort = doi,
      doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
    ) |>
    dplyr::arrange(
      sort
    ) |>
    dplyr::mutate(
      sort = NULL
    ) |>
    knitr::kable(
      caption = "DOIs in Zenodo which are duplicated",
      escape = FALSE
    )
}
DOIs in Zenodo which are duplicated
doi link
G4HZECZ5 10.1007/s00267-021-01485-8 https://www.zotero.org/groups/2344322/items/G4HZECZ5
Z8Q7D8PK 10.1007/s00267-021-01485-8 https://www.zotero.org/groups/2344322/items/Z8Q7D8PK
VQUQJDV3 10.1016/j.envsci.2014.05.007 https://www.zotero.org/groups/2344322/items/VQUQJDV3
EZPMR6G6 10.1016/j.envsci.2014.05.007 https://www.zotero.org/groups/2344322/items/EZPMR6G6
57KGGG4P 10.5751/ES-04342-160406 https://www.zotero.org/groups/2344322/items/57KGGG4P
7JQIASG8 10.5751/ES-04342-160406 https://www.zotero.org/groups/2344322/items/7JQIASG8

Non Standard

All DOIs should be given as only the DOI without the resolver, i.e. not starting with http. The following table shows all entries which do have a non-conform DOI:

Show the code 
#|

http <- grep("http", bib_data$metrics$zotero_dois$id_raw)
data.frame(
  doi = bib_data$metrics$zotero_dois$id_raw[http],
  link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$id_raw)[http])
) |>
  dplyr::mutate(
    doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
    link = NULL
  ) |>
  knitr::kable(
    caption = "DOIs in Zenodo which include a `http`",
    escape = FALSE
  )
DOIs in Zenodo which include a http
doi
H95DAVAC http://dx.doi.org/10.1016/j.envsci.2014.12.002
TYKQU2NV http://dx.doi.org/10.1016/j.ecolind.2015.10.019
LJTKR785 http://dx.doi.org/10.1016/j.jaridenv.2015.02.017
SPB4QTK2 http://dx.doi.org/10.1016/j.agee.2006.12.018
RYJEZRFY http://dx.doi.org/10.1071/RJ11002
VQUQJDV3 http://dx.doi.org/10.1016/j.envsci.2014.05.007
QR4YGR6I https://doi.org/10.1186/1746-4269-9-2
ZGNGJD3M http://dx.doi.org/10.1016/j.catena.2015.04.010
PXN5R7LF http://dx.doi.org/10.1098/rstb.2013.0164
ZNPSLAXD http://dx.doi.org/10.1057/dev.2008.48
A6Z38IBA http://dx.doi.org/10.1016/j.jhydrol.2013.02.051
PHYI85JL http://dx.doi.org/10.1016/j.ecss.2016.02.014
WU2DSDDQ http://dx.doi.org/10.1016/j.biocon.2015.10.008
57KGGG4P http://dx.doi.org/10.5751/ES-04342-160406
7JQIASG8 http://dx.doi.org/10.5751/ES-04342-160406
FQNXF5RC http://dx.doi.org/10.2111/REM-D-11-00155.1
C2CAB2VS http://dx.doi.org/10.1108/17506200710779521
5DCFXR2I http://nopr.niscpr.res.in/handle/123456789/2968
R4JZGI25 https://doi.org/10.1017/S2047102520000217
4XUACSMK https://doi. org/10.1111/tran.12538
VEUNA782 https://doi.org/10.1787/bf4514b6-en.
UH4SKBHB https://doi.org/10.1787/8036b14d-en
8N4J6X4X https://doi.org/10.1787/57b8c6e5-en.
RJIV2GEE https://doi.org/10.1787/ac7a11be-en.
4N55MZTV https://doi.org/10.1787/177906e7-en.
E7CX6G33 https://doi.org/10.1080/21513732.2017.1285814
RFTHTVHC https://doi.org/10.1038/s43247-022-00543-1
XUK9KDC4 https://doi.org/10.1007/s10460-022-10312-7
2PQC3A3S http://dx.doi.org/10.4337/jhre.2016.02.01
YEEKU77C https://doi.org/10.1007/BF01189660
9C7TC9F8 https://doi.org/10.2307/3673866
L4J2V5LM https://doi.org/10.1111/dpr.12545
5V54M5HX https://doi:10.3362/2041-7136.2010.014
3DMUG2QT https://hdl.handle.net/10289/5705
L9LCDPFL https://doi.org/10.1002/sd.240
GGEJZ5HR https://doi.org/10.1234/4.2010.1884
I3AIU35X https://doi.org/10.1023/A:1013151709605
SZEJSV5G https://doi.org/10.1659/0276-4741(2003)023[0278:TNSOIP]2.0.CO;2
Z8Q7D8PK https://doi.org/10.1007/s00267-021-01485-8

Not Valid

Here we do acheck for the structural validity of the dois. This check needs to be improved. Of these 662 are not valid. These are:

Show the code 
#|

if (length(bib_data$metrics$zotero_dois$not_valid) > 0) {
  data.frame(
    doi = bib_data$metrics$zotero_dois$not_valid,
    link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$not_valid))
  ) |>
    dplyr::mutate(
      doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
      link = NULL
    ) |>
    knitr::kable(
      caption = "DOIs in Zenodo which ar not valid",
      escape = FALSE
    )
} else {
  print("All DOIs in Zenodo are valid.")
}
DOIs in Zenodo which ar not valid
doi
MQWDLYCL 10.1111/gcb.13153
S927GC6A 12
MY39QJXC 10.1006
GA8V649I Doi 10.1644/13-Mamm-S-169
R8LWS6M4 10.1890/1051-0761(2000)010[1263:TKOIAL]2.0.CO;2
56N8LZNM 10.145/3/aitex.1603161
7IAZLE8P 27
GFGJSIUR 10.1146/
VKJ9AUHJ 10.1663/0013-0001(2006)60[374:CTOEKI]2.0.CO;2
GFT6RWIR 10.1639/0044-7447(2005)034[0131:imwqbm]2.0.co;2
BSVVZ6FA 10.14350
9ZJSEXYH 10.1890/1051-0761(2000)010[1249:TEKESA]2.0.CO;2
S9Z6IE7Q 10.1051/
6QL9BGS2 18
UWB57S8K 10.1890/1051-0761(2000)010[1251:ROTEKA]2.0.CO;2
Z5FU36ZN 10.1890/1051-0761(1997)007[0218:EORDOS]2.0.CO;2
5DCFXR2I http://nopr.niscpr.res.in/handle/123456789/2968
NNKYYLFZ 10.1663/0013-0001(2005)059[0356:FIMIKA]2.0.CO;2
7E7U2NQH 1746-4269-3-27 [pii]0.1186/1746-4269-3-27
4XUACSMK https://doi. org/10.1111/tran.12538
GBC62TBC DOI: 10.1038/NPLANTS.2014.21
LCLFQBXY :10.1016/j.biocon.2008.11.007
D2I8WNNU Policy Matters
VAEGCPHM 10.2192/1537-6176(2005)016[0222:DPHAFT]2.0.CO;2
5U65GPWK 10.1002/1099-145X(200011/12)11:6<523::AID-LDR411>3.0.CO;2-V
5V54M5HX https://doi:10.3362/2041-7136.2010.014
ADAXI7DG 10.1614/0043-1745(2003)051[0271:KNAATE]2.0.CO;2
3DMUG2QT 10289/5705
CC2WQCCV 10.100
X9JM5D5K 10.14506/
SA4Z3MTF 10.1577/1548-8446(2004)29[10:acssit]2.0.co;2
JE42LMWS 10.1080/09500690903203135>
D9SJLJJQ 10.3402/
SZEJSV5G 10.1659/0276-4741(2003)023[0278:TNSOIP]2.0.CO;2
SHUBFYDS : 10.3917/riss.187.0039
ZV48GSW9 10.1130/0091-7613(2000)28<843:OTHOHA>2.0.CO;2
3BRM3AVK Article

Not in OpenAlex

To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.

Of the 3091 unique DOIs in the library, 662 (21.42%) are in not in OpenAlex. This includes the non-valid DOIS, which are filtered out in the table below.

Show the code 
data.frame(
  doi = bib_data$metrics$zotero_dois$not_in_oa,
  link = paste0(bib_data$bibliography$url, "/items/", names(bib_data$metrics$zotero_dois$not_in_oa))
) |>
  dplyr::mutate(
    doi = paste0('<a href="', link, '" target="_blank">', doi, "</a>"),
    link = NULL
  ) |>
  knitr::kable(
    caption = "DOIs in Zenodo which ar not in [OpenAlex](https://OpenAlex.org){target='_blank'}",
    escape = FALSE
  )
DOIs in Zenodo which ar not in OpenAlex
doi
GKEASDQL 10.1006/BCON.2001.0937
4HSJT82I 10.1134/S2079970516030060
H95DAVAC 10.1016/j.envsci.2014.12.002
22D4LY93 10.5751/ES-04597-170222
F2G39GB8 10.1023/A:1025023906459
P9TJGQ79 10.5751/ES-05494-180410
KGT56WMI 10.1016/S0959-3780(00)00044-3
2BZQW6ND 10.1071/RJ14025
MQWDLYCL 10.1111/gcb.13153
DJ4L2HWP 10.1007/s13398-014-0173-7.2
TYKQU2NV 10.1016/j.ecolind.2015.10.019
LJTKR785 10.1016/j.jaridenv.2015.02.017
9LKR7XRM 10.1016/j.jhydrol.2009.02.030
VXNCIUCL 10.5751/ES-10747-240226
MY2CCP33 10.1017/S0030605316001228
SPB4QTK2 10.1016/j.agee.2006.12.018
KEPQ7573 10.1046/j.1466-822X.2003.00327.x
DTPMAKAD 10.3390/SU10124502
X79LVMCQ 10.14237/ebl.6.1.2015.420.
GGINTQ6D 10.1016/S0167-8809(00)00178-X
W9LK6SFG 10.1111/j.1365-294X.2012.05589.x
RYJEZRFY 10.1071/RJ11002
S7NWLJDI 10.1590/1983-084X/15_142
4N6FJHFP 10.1071/RJ14094
R3YBBN76 10.5751/ES-05501-180318
5HNLC5VD 10.1590/S1519-69842008000500004
FT8Y9JJG 10.1111/j.1755-263X.2011.00181.x
FE8D55RM 10.5751/ES-05981-180429
RNEUK5S9 10.1111/j.1526-100X.2006.00160.x
M2SLYMNH 10.1016/S0016-3287(03)00054-5
5XZ2BY43 10.5751/ES-09176-220215
BGKVB52W 10.11609/jot.2967.9.6.10307-10313
DSJVQ973 10.1017/S0376892997000325
AMZIQNMX 10.1081/PAD-120019247
YWJ39T8V 10.1007/s11258-004-1413-2
5FK5ZKEN 10.1108/IJLBE-10-2016-0016
DALWZWWE 10.4067/S0716-078X2006000200010
ZR5I5UV8 10.3986/AGS.4674
3Q7PGJI4 10.1111/j.1654-109X.2010.01120.x
IRWEUXEZ 10.1002/aqc
FB3IFASK 10.1505/ifor.10.2.292
5RMGY2KD 10.1017/S1479262108923789
DH2TVQBU 10.1023/A:1015584202121
VC8XRAJF 10.5751/ES-06163-190243
427BCALT 10.5751/ES-06896-190426
YCNEPEJ8 10.1017/S0376892915000089
Z68JQEN9 10.1590/S1020-49892004000300014
EX4C4WT7 10.5751/ES-07733-200333
B673L9YS 10.5751/ES-05867-180412
P4YEIRLL 10.17660/ActaHortic.2017.1158.39
AM6RHMFW 10.1007/BF00017672
9578ULNE 10.5751/ES-05563-180317
83DIIAFF 10.1007/BF00004802
MVUHVZJX 10.13140/2.1.5140.5444
TJQWTP9H 10.1175/WCAS-D-17-0064.1
DK7HDWA3 10.1134/S2075111710020116
W59CRSNA 10.1016/S0044-8486(03)00474-5
LA8AWS4N 10.5751/ES-08482-210325
S927GC6A 12
YAYKTGAK 10.1659/MRD-JOURNAL-D-14-00033.1
5AQWFEQY 10.1175/JAMC-D-17-0012.1
BCV3BQ4L 10.1016/S0378-8741(02)00052-1
MY39QJXC 10.1006
XD9NEKKN 10.5593/SGEM2014/B52/S20.105
MZ5VTRVB 10.1016/S0378-1127(09)00221-7
8MLWP4XT 10.1111/j.1755-263X.2009.00049.x
APVUVR6M 10.5751/ES-05597-180333
HKV653PB 10.1017/S0376892910000561
X2IJWHBW 10.1016/S0075-9511(04)80028-8
3HMSHNW5 10.1142/S0218127406014587
YAYV597D 10.1659/MRD-JOURNAL-D-09-00040.1
Q9K5WSDE 10.2307/23616572
RTXCNQXZ 10.1111/j.1755-263X.2012.00309.x
GA8V649I Doi 10.1644/13-Mamm-S-169
26LCE6QF 10.1023/A:1007680726231
GHFXQ3BF 10.5751/ES-00675-090302
I4J7P77A 10.1023/B:AGFO.0000028995.13227.ca
RGJEY7LF 10.5751/ES-06937-190444
92A65NR3 10.1023/B:BINV.0000041562.31023.42
RFBDZDAE 10.1017/S1368980009005783
LDMQJXC8 10.5751/ES-09867-230132
7EILUJ4U 10.5751/ES-06741-190339
R8LWS6M4 10.1890/1051-0761(2000)010[1263:TKOIAL]2.0.CO;2
56N8LZNM 10.145/3/aitex.1603161
7IAZLE8P 27
E7C7CSDK 10.1017/S0376892907004067
3UDJ7HG9 10.1080/1088937X.2016.1184721
J3R9W9YC 10.1134/S2075111710030070
ZVLEIUY8 10.1016/J.ECOLIND.2007.01.008
SXBGRQES 10.5897/AJEST08.173
GFGJSIUR 10.1146/
UB2FWELQ 10.5751/ES-07988-210122
EHUR78UW 10.1017/S2047102512000064
QR4YGR6I 10.1186/1746-4269-9-2
VKJ9AUHJ 10.1663/0013-0001(2006)60[374:CTOEKI]2.0.CO;2
PXTHMDXK 10.5751/ES-10041-230210
GG4PIB2U 10.1016/S0016-7185(01)00027-6
NE9Z8ZEC 10.5751/ES-05873-180226
3S9CY4KX 10.1615/IntJMedMushr.v15.i6.10
GFT6RWIR 10.1639/0044-7447(2005)034[0131:imwqbm]2.0.co;2
V7NM2ARR 10.1017/S0022216X17000414
Y8GEX7LH 10.5751/ES-04531-170109
JFSIX9DT 10.1300/J064v26n01
5V8FRMLI 10.5751/ES-06527-200112
PSNNBZFN 10.1017/S0376892909990385
2ZUAWJKM 10.1017/S0014479716000168
9259BCKE 10.15451/ec2017
GY58T8MI 10.1016/J.LINDIF.2013.04.002
6DBLMFVX 10.3390/rs40401046
FG53QUM9 10.1590/S0102-33062013000100002
ESQEJVGE 10.1017/PHN2006987
D82NFTNN 10.1108/JEC-01-2015-0010
NEVA9FQS 10.1023/B:AHUM.0000029403.91466.21
6BW2HBQU 10.1163/187471611X600369
ZGNGJD3M 10.1016/j.catena.2015.04.010
W8BRKBKD 10.1071/RJ15047
DEUSRFPP 10.1071/PC140206
IS6BNYRC 10.5751/ES-08140-210112
L98FXEJ9 10.1029/2006WR005584
9M83ICTW 10.2305/IUCN.CH.2017.PARKS-23-2HDJ.en
8JLFQW6K 10.5751/ES-05874-190143
BSVVZ6FA 10.14350
HKX4RTFG 10.2307/25094583
6KKT8F62 10.5751/ES-05843-180403
2SLJ9P4K 10.1007/s10745-005-2432-X
9D2DVHPD 10.1023/A:1009698717015
FNGTKPKG 10.5751/ES-04587-170123
3586RKVV 10.1080/2154896X.2014.913917
ZIX9MV3F 10.1890/100017
FWYLL2JF 10.1179/0430877814Z.00000000031
B83VP53N 10.1016/S0277-9536(98)00181-6
KRHIYJPM 10.1163/187197309X401406
JTEXTDNF 10.5751/ES-06915-190432
QRMUEEXF 10.1017/S0376892906283371
ZVHJUQTM 10.1017/S0030605312001457
EWBBTQJV 10.1659/MRD-JOURNAL-D-17-00093.1
QBD6X2JH 10.5751/ES-05414-180215
ZAKVTI7H 10.4238/2015.March.20.8
NHB64KXY 10.1525/AA.2007.109.3.529.530
GF9NGZCB 10.2305/IUCN.CH.2017.PARKS-23-2PG.en
MJ9LWQH6 10.7930/J0Q81B0T
PXN5R7LF 10.1098/rstb.2013.0164
XLKJPWF8 10.1017/CBO9781107415324.004
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TODO Do Exist

TODO Finally we check, if these dois exist but are not ingested into OpenAlex. This is done using the doi.org resolver This is disabled at the moment and still needs to be implemented.

Reuse

Citation

BibTeX citation:
@report{krug,
  author = {Krug, Rainer M.},
  title = {Bibliography {Report}},
  langid = {en},
  abstract = {Reports analysing the IPBES Libraries on Zotero.}
}
For attribution, please cite this work as:
Krug, Rainer M. n.d. “Bibliography Report.”