Registration to the training course

Registrations open each spring and the training course takes place during fall. More information is available on the FRB-CESAB website.

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This five-day training course, co-organized by the FRB-CESAB, the PNDB, and GBIF France aims to work on the different stages of the data lifecycle, from acquisition to opening, including management, storage and the drafting of data papers.

We will 1) contextualize the issues surrounding the understanding, sharing and (re)use of biodiversity data and metadata, and 2) enhance the skills of communities involved in one or more stages of the data lifecycle.

Program

General context

Current challenges in biodiversity data
The data ecosystem
Reproducibility concepts
What is data/metadata?
Major types of biodiversity data
Framework and good practices (data lifecycle, FAIR, etc.)
Data management plan

Data acquisition

Best practices for data collection
Major biodiversity databases
Major environmental databases
Data acquisition: Web portals, API & web scraping

Data management

Structure, formats & files
Processing & cleansing data
Introduction to OpenRefine
Virtual Research Environments

DataSHARE projects

FRB-CESAB DataSHARE projects
Zoom on Islets & PhenoFish groups

Legal aspects

Sharing, licensing, etc.

Opening data

(Meta)data: standards
Storage and archiving
Dissemination and sharing
Data & software paper

Prerequisites

Please follow this tutorial to install your working environment before attending the training course.

Installation notes

For this training course, you just need to install R, RStudio IDE (optional) and Rtools (for Windows users only). Do not install git, Quarto, Pandoc or Docker. And do not forget to configure RStudio IDE as explaining here.

Material

All the material used in this training course (slides, data, exercises) is available at: https://github.com/biodiversitydata/

Citation

Casajus N, Coux C, Le Bras Y, Norvez O, Archambeau A-S & Pamerlon S (2025) Biodiversity data: From data collection to publication. An FRB-CESAB, PNDB & GBIF France training course. URL: https://biodiversitydata.github.io/

Contributions

If you see mistakes or want to suggest changes, please create an issue on the source repository.

Reuse

Text and figures are licensed under Creative Commons Attribution CC By 4.0, unless otherwise noted.

Welcome

Program

Prerequisites

Material

Citation

Contributions

Reuse

See also