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trias-project / unified-checklist

🇧🇪 Global Register of Introduced and Invasive Species - Belgium
https://trias-project.github.io/unified-checklist/
MIT License
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checklist dataset gbif invasive-species oscibio r rstats

readme

Global Register of Introduced and Invasive Species - Belgium

Rationale

This repository contains the functionality to create and standardize the Global Register of Introduced and Invasive Species - Belgium to a Darwin Core checklist that can be harvested by GBIF.

This unified checklist is the result of two open and reproducible data pipelines developed for the TrIAS project (http://trias-project.be). In the data publication pipeline, we use the Checklist recipe to standardize and publish a selection of authoritative species checklists as Darwin Core Archives to GBIF. Predominantly, these checklists record the presence of alien species in Belgium for a specific taxon group or habitat and are maintained by their respective authors. In the data processing pipeline, we extract all Belgian non-native taxa from these checklists and unify their taxonomy using the GBIF Backbone Taxonomy. This automated process is implemented and documented at https://trias-project.github.io/unified-checklist/ The sources used for the unified checklist are:

  1. Manual of the Alien Plants of Belgium (Verloove et al. 2018)
  2. Checklist of alien birds of Belgium (Preda et al. 2019)
  3. Checklist of non-native freshwater fishes in Flanders, Belgium (Verreycken et al. 2018)
  4. Checklist of alien herpetofauna of Belgium (van Doorn et al. 2021)
  5. Inventory of alien macroinvertebrates in Flanders, Belgium (Boets et al. 2018)
  6. Registry of introduced terrestrial molluscs in Belgium (Backeljau et al. 2019)
  7. Checklist of alien species in the Scheldt estuary in Flanders, Belgium (Soors et al. 2021)
  8. Catalogue of the Rust Fungi of Belgium (Vanderweyen et al. 2018)
  9. WRiMS: World Register of Introduced Marine Species (Rius et al. 2023)
  10. Waarnemingen.be / observations.be - List of species observed in Belgium (Swinnen et al. 2022)
  11. Ad hoc checklist of alien species in Belgium (Reyserhove et al. 2018)
  12. RINSE - Pathways and vectors of biological invasions in Northwest Europe (Zieritz et al. 2018)

Workflow

See https://trias-project.github.io/unified-checklist/

Published dataset

Repo structure

The repository structure is based on Cookiecutter Data Science and the Checklist recipe. Files and directories indicated with GENERATED should not be edited manually.

├── README.md              : Description of this repository
├── LICENSE                : Repository license
├── unified-checklist.Rproj : RStudio project file
├── .gitignore             : Files and directories to be ignored by git
│
├── data
│   ├── raw                : Source data as downloaded from GBIF GENERATED
│   ├── interim            : Unified data GENERATED
│   └── processed          : Darwin Core output of mapping script GENERATED
│
├── references
│   └── verification.tsv   : Verification file (for synonyms). Generated by 
│                            3_verify_taxa.Rmd and then manually annotated
│
├── docs                   : Repository website GENERATED
│
├── index.Rmd              : Website homepage
├── _bookdown.yml          : Settings to build website in docs/
│
└── src
    ├── 1_get_taxa.Rmd     : Script to get taxa from checklists
    ├── 2_get_information.Rmd : Script to get related information
    ├── 3_verify_taxa.Rmd  : Script to verify taxa
    ├── 4_unify_taxa.Rmd   : Script to unify taxa
    ├── 5_unify_information.Rmd : Script to unify related information
    ├── 6_dwc_mapping.Rmd  : Script to map to Darwin Core
    └── 7_griis_mapping.Rmd : Script to map to create Excel file for GRIIS

Installation

  1. Clone this repository to your computer
  2. Open the RStudio project file
  3. Open the index.Rmd R Markdown file in RStudio
  4. Install any required packages
  5. Click Build > Build Book to generate the processed data and build the website in docs/

Publication

To publish an update of the dataset:

  1. Open the resource in the IPT (login required)
  2. Source data: upload the newly generated data files from data/processed
  3. Darwin Core mappings: does not require updates, unless terms were added/removed in the pipeline
  4. Metadata: does not require updates, except for:
    • Basic metadata: in description, check if number of taxa (2.500+) still applies
    • Taxonomic coverage: in description, update numbers per kingdom based on new data
    • Temporal coverage: update End date if need be
  5. Publish: click Publish, add a short description and publish
  6. Check if dataset is updated at GBIF (can take a couple of hours)

Contributors

List of contributors

License

MIT License for the code and documentation in this repository. The included data is released under another license.