Bibliography Report

Author

Affiliation

Rainer M. Krug

University of Zürich

Abstract

Reports analysing the IPBES Libraries on Zotero.

• NFF Bibliography
• This Report
• Github repository

Introduction

This report assesses the NFF 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.

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	60	OpenAlex
preprint	3	OpenAlex
review	3	OpenAlex
editorial	1	OpenAlex
journalArticle	76	Zotero
presentation	35	Zotero
report	23	Zotero
bookSection	5	Zotero
thesis	4	Zotero
magazineArticle	2	Zotero
preprint	2	Zotero
webpage	2	Zotero
conferencePaper	1	Zotero
document	1	Zotero

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.

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	57
presentation	NA	35
report	NA	23
journalArticle	NA	14
bookSection	NA	5
thesis	NA	4
journalArticle	review	3
NA	article	3
preprint	preprint	2
magazineArticle	NA	2
webpage	NA	2
journalArticle	preprint	1
conferencePaper	NA	1
document	NA	1
journalArticle	editorial	1

Year of Publication

Analysis: Zenodo and OpenAlex

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

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	2017	2024
OpenAlex	2020	2024

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

bib_data$figure_oa_status

50 Most often cited Journals

Analysis: Zenodo

TODO: OpenAlex should be added

bib_data$figure_top_journals

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

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.

#|
#| fig-height: 10
#| fig-width: 10

bib_data$figure_top_country_map

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

#|
#| fig-height: 10
#| fig-width: 10

bib_data$figure_top_country

This table contains all countries and the number of authorship.

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: 72 (47.68%) - 2 duplicates
• ISBNss: 5 (3.31%)
• ISBNss: 64 (42.38%)

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.

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
QBFZA5XW	10.1007/s11625-023-01411-3	https://www.zotero.org/groups/4937409/items/QBFZA5XW
K6XP4GZK	10.1007/s11625-023-01411-3	https://www.zotero.org/groups/4937409/items/K6XP4GZK

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:

#|

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
9P8ILX2I	https://doi.org/10.5281/zenodo.8286255
QBFZA5XW	https://doi.org/10.1007/s11625-023-01411-3
T2X7FRRX	https://doi.org/10.1016/j.marpol.2023.105644
LPTVHBNM	https://doi.org/10.1016/j.envsci.2023.03.015

Not Valid

Here we do acheck for the structural validity of the dois. This check needs to be improved. Of these 7 are not valid. These are:

#|

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.")
}

[1] "All DOIs in Zenodo are valid."

Not in OpenAlex

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

Of the 72 unique DOIs in the library, 7 (9.72%) are in not in OpenAlex. This includes the non-valid DOIS, which are filtered out in the table below.

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
GXDB95GY	10.1017/S0376892924000067
9P8ILX2I	10.5281/zenodo.8286255
T2X7FRRX	10.1016/j.marpol.2023.105644
DIP3XCJM	10.19741/j.issn.1673-4831.2021.0237
LPTVHBNM	10.1016/j.envsci.2023.03.015
XQJ5RL6X	10.5751/ES-13393-270340
S59BTLGC	10.22920/PNIE.2021.2.2.82

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.