natagora-occurrences's Introduction

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.

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

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

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:

These are shared with the waarnemingen.be datasets.

Published data can be validated with whip:

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