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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 an open and reproducible data publication and data processing pipeline developed for the TrIAS project. The data publication pipeline is based on the Checklist recipe and consists of the publication of a selection of authoritative (inter)national checklists as standardized Darwin Core Archives to GBIF. These are:

  1. Verloove et al. (2018) based on Verloove (2018) for plants
  2. Boets et al. (2018) based on Boets et al. (2016) for macroinvertebrates
  3. Verreycken et al. (2018a) based on Verreycken et al. (2018b) for fishes
  4. Vanderweyen et al. (2018) based on Vanderweyen & Fraiture (2007, 2008, 2011) for rust fungi
  5. Reyserhove et al. (2018) for various species
  6. Zieritz et al. (2018) based on Zieritz et al. (2017) for pathways.

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. The data processing consists of the extraction of all Belgian non-native taxa from these checklists and the unification of their taxonomy (using the GBIF Backbone Taxonomy) and related information. This automated process is implemented and documented at https://trias-project.github.io/unified-checklist/

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.