Biodiversity data: From collection to publication

FRB-CESAB / PNDB / GBIF France training course

Authors
Affiliations

Nicolas Casajus

FRB-CESAB

Camille Coux

FRB-CESAB

Yvan Le Bras

PNDB

Olivier Norvez

PNDB

Anne-Sophie Archambeau

GBIF France

Sophie Pamerlon

GBIF France

Published

October 29, 2026

Welcome

NoteRegistration 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

  Monday

Session Material
9:00 Welcome and icebreaker
9:30

General context

  • Current challenges in biodiversity data
  • The Data ecosystem
  • What is data/metadata?
  • Major types of biodiversity data
  • Frameworks and good practices
11:30 Data management plan
12:30 Lunch
14:00 Speed dating
14:30 Procotols vs. methods
15:30 Sampling and collections (Practice)
17:00 End of the day


  Tuesday

Session Material
9:00 Biodiversity databases
9:30 GBIF overview
10:30 Environment databases
11:00

Data acquisition

  • Web portals
  • Scripting
  • API
  • Practice: Data acquisition
  • Web scraping
12:30 Lunch
14:00 Data formats
14:30

Data cleaning

  • Raw vs. derived data
  • Data cleaning
  • Working w/ taxonomy
  • Practice: Data cleaning
16:00 OpenRefine (Practice)
17:30 End of the day


  Wednesday

Session Material
9:00 DataSHARE projects
10:30 Legal and ethical aspects
11:00 Virtual Research Environments
12:30 Lunch
14:00 (Meta)data standards
15:30 GBIF tools
16:00 Integrated Publishing Toolkit (Practice)
17:30 End of the day


  Thursday

Session Material
9:00 Storage and archiving
9:30 Dissemination and sharing
10:30 Data paper
11:30 Software paper
12:00 Group formation
12:30 Lunch
14:00 Group projects
18:00 End of the day


  Friday

Session Material
9:00 Group projects
12:30 Lunch
14:00 Project Presentations
16:00 End of the day


Prerequisites

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

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 (2026) Biodiversity data: From 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.

See also

Discover the other training courses provided by the FRB-CESAB and its partners: https://frbcesab.github.io/training-courses/