Observations.be - Species occurrence datasets published by Natagora

Rationale

This repository contains the functionality to standardize datasets of observations.be to Darwin Core Occurrence datasets that can be harvested by GBIF. It was originally developed for the TrIAS project.

Workflow

observations.be database → Darwin Core SQL view → Direct connection with the IPT or CSV upload

Datasets

Title (and GitHub directory)	IPT	GBIF
Observations.be - Non-native species occurrences in Wallonia, Belgium	natagora-alien-occurrences	https://doi.org/10.15468/p58ip1
Observations.be - Orthoptera occurrences in Wallonia, Belgium	natagora-orthoptera-occurrences	https://doi.org/10.15468/r763pb

Repo structure

The structure for each dataset in datasets is based on Cookiecutter Data Science and the Checklist recipe. Files and directories indicated with GENERATED should not be edited manually.

├── sql                      : Darwin Core SQL queries
│
└── specs                    : Whip specifications for validation

references contains controlled vocabularies for:

• behavior
• lifeStage
• occurrenceRemarks
• reproductiveCondition
• samplingProtocol

These are shared with the waarnemingen.be datasets.

Validating with whip

Published data can be validated with whip:

1. Download the published DwC Archive from the IPT
2. Unzip the data in the directory data (git ignored), so data are available at data/data_file.txt
3. In terminal, start jupyter notebook from the repository root
4. Open notebooks/whip.ipynb
5. In the notebook, set the correct paths at the top of the file
6. Run the notebook
7. Update dataset or specifications until they align

Contributors

List of contributors

License

MIT License