Biodiversity data: From data collection to publication

FRB-CESAB / PNDB / GBIF France training course

Published

November 8, 2024

Welcome

Registrations for the 2024 session are closed.

Registrations open each spring and the training course takes place during the fall.

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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 cycle, 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 cycle.

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 cycle, FAIR, etc.)

Data acquisition

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

Data management

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

DataSHARE projects

  • FRB-CESAB DataSHARE call
  • Zoom on Islets & PhenoFish groups

Legal aspects

  • Sharing, licensing, etc.

Opening data

  • Data management plan
  • (Meta)data: standards
  • Storage and archiving
  • Dissemination and sharing
  • Enhancing value: data paper & software paper

Prerequisites

  Please follow this tutorial to install your working environment before attending the training course. Note that you just need to install R, RStudio IDE (optional) and Rtools (for Windows users).

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 (2024) 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.

See also

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