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# Welcome {.unnumbered}

::: {.callout-note}
## 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](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/develop-skills/la_donnee_en_biodiversite/).

{{< fa hand-point-right >}}&nbsp; Subscribe to the 
[FRB-CESAB newsletter](https://www.fondationbiodiversite.fr/en/newsletter/) 
to stay informed. 
:::



This five-day training course, co-organized by the [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/), the [PNDB](https://www.pndb.fr/), and [GBIF France](http://www.gbif.fr/) 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.

![](images/data-lifecycle-0.png){width=50% fig-align="center"}

## Program {.unnumbered}

**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 {.unnumbered}

{{< fa hand-point-right >}}&nbsp; Please follow this [tutorial](https://frbcesab.github.io/rsetup/) to install 
your working environment **before attending the training course**. 

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## Installation notes

For this training course, you just need to install [**R**](https://cran.r-project.org/), [**RStudio IDE**](https://posit.co/download/rstudio-desktop/) (optional) and [**Rtools**](https://cran.r-project.org/bin/windows/Rtools/) (for Windows users only). **Do not install** git, Quarto, Pandoc or Docker.
And do not forget to **configure RStudio IDE** as explaining [here](https://frbcesab.github.io/rsetup/chapters/rstudio.html).
:::

## Material {.unnumbered}

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



## Citation {.unnumbered}

> 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 {.unnumbered}

If you see mistakes or want to suggest changes, please [create an issue](https://github.com/biodiversitydata/biodiversitydata.github.io/issues/new) on the source repository.


## Reuse {.unnumbered}

Text and figures are licensed under Creative Commons Attribution [CC By 4.0](https://creativecommons.org/licenses/by/4.0/), unless otherwise noted.


## See also {.unnumbered}


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