Citing GBIF Data

Preamble, Package-Loading, and GBIF API Credential Registering (click here):
## Custom install & load function
install.load.package <- function(x) {
  if (!require(x, character.only = TRUE)) {
    install.packages(x, repos = "")
  require(x, character.only = TRUE)
## names of packages we want installed (if not installed yet) and loaded
package_vec <- c(
  "ggplot2" # for visualisation
## executing install & load for each package
sapply(package_vec, install.load.package)
##   rgbif ggplot2 
##    TRUE    TRUE
options(gbif_user = "my gbif username")
options(gbif_email = "my registred gbif e-mail")
options(gbif_pwd = "my gbif password")

First, we obtain and load the data use for our publication like such:

# Download query
res <- occ_download(
  pred("taxonKey", sp_key),
  pred_in("basisOfRecord", c("HUMAN_OBSERVATION")),
  pred("country", "NO"),
  pred("hasCoordinate", TRUE),
  pred_gte("year", 2000),
  pred_lte("year", 2022)
# Downloading and Loading
res_meta <- occ_download_wait(res, status_ping = 5, curlopts = list(), quiet = FALSE)
res_get <- occ_download_get(res)
res_data <- occ_download_import(res_get)
# Limiting data according to quality control
preci_data <- res_data[which(res_data$coordinateUncertaintyInMeters < 10), ]
# Subsetting data for desired variables and data markers
data_subset <- preci_data[
  c("scientificName", "decimalLongitude", "decimalLatitude", "basisOfRecord", "year", "month", "day", "eventDate", "countryCode", "municipality", "taxonKey", "species", "catalogNumber", "hasGeospatialIssues", "hasCoordinate", "datasetKey")

Now all we need to worry about is properly accrediting data sources to make our data usage fair and reproducible.

Finding Download Citation

Much like previous steps of this workshop, identifying the correct citation for a given download from GBIF can be done via:

  1. GBIF Portal
  2. rgbif functionality

GBIF Portal

To figure out how to reference a GBIF mediated set of data records you may head to the download tab of the GBIF portal where, once in the detailed overview of an individual download job, you will find proper accrediation instructions right at the top:

I would like to caution against this practise as the download tab can become a bit cluttered when having a long history of asking GBIF for similar downloads.


This is the preferred way of figuring out correct GBIF mediated data citation.

To avoid the pitfalls of manual data citation discovery, rgbif download metadata make available to us directly a DOI which can be used for refrencing our data:

paste("GBIF Occurrence Download", occ_download_meta(res)$doi, "accessed via on", Sys.Date())
## [1] "GBIF Occurrence Download 10.15468/dl.awgk9s accessed via on 2023-05-22"

With this, you are ready to reference the data you use.

Derived Datasets

When additionally (heavily) filtering or subsetting a GBIF download locally, it is best to not cite the download itself, but rather a derived data set.

Derived datasets are citable records of GBIF-mediated occurrence data derived either from:

  • a download that has been filtered/reduced significantly, or
  • data accessed through a cloud service, e.g. Microsoft AI for Earth (Azure), or
  • data obtained by any means for which no DOI was assigned, but one is required (e.g. third-party tools accessing the GBIF search API)

For our purposes, we have used a heavily subsetted data download - just look at the number of records in the original and the subsetted data:

  Records = c(nrow(data_subset), nrow(res_data)),
  Data = c("Subset", "Original")
), aes(y = Data, x = Records)) +
  geom_bar(stat = "identity", fill = "#4f004e") +
  theme_bw(base_size = 12)

To correctly reference the underlying data sets mediated by GBIF and contributing to our final dataset, we should register a derived data set. When created, a derived dataset is assigned a unique DOI that can be used to cite the data. To create a derived dataset you will need to authenticate using a account and provide:

  • a title of the dataset,
  • a list of the GBIF datasets (by DOI or datasetKey) from which the data originated, ideally with counts of how many records each dataset contributed,
  • a persistent URL of where the extracted dataset can be accessed,
  • a description of how the dataset was prepared,
  • (optional) the GBIF download DOI, if the dataset is derived from an existing download , and
  • (optional) a date for when the derived dataset should be registered if not immediately .

Arguably, the most important aspect here is the list of GBIF datasets and the counts of data used per dataset. First, let’s isolate how many datasets contributed to our original data and the subsetted, final data:

## Original
## [1] 47
## Subsetted
## [1] 14

There is a signifcant decrease in number of datasets which make up our final data product post-subsetting. Let us visualise how the data records are spread across the individual datasets per data product we have handled:

## Originally downloaded abundances per dataset
plot_data <- data.frame(table(res_data$datasetKey))
    x = factor(Var1, levels = plot_data$Var1[order(plot_data$Freq, decreasing = TRUE)]),
    y = Freq
) +
  geom_col(color = "black", fill = "forestgreen") +
    y = "Abundance", x = "Dataset",
    title = paste0("Originally downloaded abundances per dataset (", occ_download_meta(res)$doi, ")")
  ) +
  theme_bw(base_size = 21) +
  theme(axis.text.x = element_blank(), axis.ticks.x = element_blank())

## Subsetted abundances per dataset
plot_subset <- data.frame(table(data_subset$datasetKey))
    x = factor(Var1, levels = plot_subset$Var1[order(plot_subset$Freq, decreasing = TRUE)]),
    y = Freq
) +
  geom_col(color = "black", fill = "darkred") +
  labs(y = "Abundance", x = "Dataset", title = "Subsetted abundances per dataset") +
  theme_bw(base_size = 21) +
  theme(axis.text.x = element_blank(), axis.ticks.x = element_blank())

Subsequently, to prepare a potential query to GBIF to establish a derived data set for us, we can tabulate the counts of records per dataset key as follows:

Var1 Freq
09c38deb-8674-446e-8be8-3347f6c094ef 133
0efbb3b3-6473-414a-af91-cdbcbcd8aba1 1
14d5676a-2c54-4f94-9023-1e8dcd822aa0 71
3fdf4093-6cb4-4ca6-b329-b12e96d57342 3
50c9509d-22c7-4a22-a47d-8c48425ef4a7 214
520909f1-dbca-411e-996c-448d87c6a700 1
78ab5416-bf56-4714-a2bf-096b16f0e1d8 231
7a3679ef-5582-4aaa-81f0-8c2545cafc81 7
88ea9eca-96ad-4a5a-8a01-99a4acabe050 4
8a863029-f435-446a-821e-275f4f641165 67
9678e1a6-b1c4-4e86-9d26-ebb169338655 503
a12cba4c-c620-4e76-aa22-0ec988824b6d 12
ae77cf87-0f7f-4a08-91cc-5d55230fb421 12
b124e1e0-4755-430f-9eab-894f25a9b59c 5543

Finally, we can head to the registration for derived data sets at GBIF and supply our information:

You are finished - you should now be able to find relevant data for your requirements on GBIF, download said data, handle and subset it according to your needs, and now how to reference back to the data obtained and used in your final report.

Session Info

## R version 4.3.1 (2023-06-16)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS Sonoma 14.0
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## time zone: Europe/Oslo
## tzcode source: internal
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## other attached packages:
## [1] ggplot2_3.4.3 rgbif_3.7.7  
## loaded via a namespace (and not attached):
##  [1] styler_1.9.1      sass_0.4.6        utf8_1.2.3        generics_0.1.3   
##  [5] xml2_1.3.4        blogdown_1.16     stringi_1.7.12    httpcode_0.3.0   
##  [9] digest_0.6.31     magrittr_2.0.3    evaluate_0.20     grid_4.3.1       
## [13] bookdown_0.34     fastmap_1.1.1     R.oo_1.25.0       R.cache_0.16.0   
## [17] plyr_1.8.8        jsonlite_1.8.7    R.utils_2.12.2    whisker_0.4.1    
## [21] crul_1.4.0        urltools_1.7.3    httr_1.4.7        purrr_1.0.1      
## [25] fansi_1.0.4       scales_1.2.1      oai_0.4.0         lazyeval_0.2.2   
## [29] jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1       triebeard_0.4.1  
## [33] R.methodsS3_1.8.2 bit64_4.0.5       munsell_0.5.0     withr_2.5.1      
## [37] cachem_1.0.8      yaml_2.3.7        tools_4.3.1       dplyr_1.1.2      
## [41] colorspace_2.1-0  curl_5.0.2        vctrs_0.6.3       R6_2.5.1         
## [45] lifecycle_1.0.3   stringr_1.5.0     bit_4.0.5         pkgconfig_2.0.3  
## [49] pillar_1.9.0      bslib_0.4.2       gtable_0.3.4      data.table_1.14.8
## [53] glue_1.6.2        Rcpp_1.0.11       highr_0.10        xfun_0.39        
## [57] tibble_3.2.1      tidyselect_1.2.0  rstudioapi_0.15.0 knitr_1.43       
## [61] farver_2.1.1      htmltools_0.5.5   labeling_0.4.3    rmarkdown_2.21   
## [65] compiler_4.3.1