update website (2025)

Author: ahasverus

_quarto.yml

@@ -77,29 +77,35 @@ book:
     - part: "Introduction"
       chapters: 
         - chapters/introduction.qmd
+        - chapters/dmp.qmd
     - part: "Data acquisition"
       chapters: 
         - chapters/protocols-methods.qmd
-        - chapters/databases.qmd
-        - chapters/env-databases.qmd
+        - chapters/sampling-collections.qmd
+        - chapters/biodiversity-databases.qmd
+        - chapters/gbif-overview.qmd
+        - chapters/environment-databases.qmd
+        - chapters/data-repositories.qmd
         - chapters/data-acquisition.qmd
     - part: "Data management"
       chapters: 
         - chapters/files-formats.qmd
         - chapters/data-cleaning.qmd
         - chapters/openrefine.qmd
         - chapters/vre.qmd
+    - part: "Legal concerns"
+      chapters: 
+        - chapters/legal-concerns.qmd
+    - part: "DataSHARE projects"
+      chapters: 
+        - chapters/datashare.qmd
     - part: "Opening data"
       chapters: 
-        - chapters/dmp.qmd
         - chapters/standards.qmd
         - chapters/storage-archiving.qmd
         - chapters/data-sharing.qmd
         - chapters/data-paper.qmd
         - chapters/software-paper.qmd
-    - part: "DataSHARE projects"
-      chapters: 
-        - chapters/datashare.qmd
     - chapters/resources.qmd
 
 format:

chapters/biodiversity-databases.qmd

@@ -0,0 +1,21 @@
+## Biodiversity databases {.unnumbered}
+
+
+::: {.callout-note icon=true appearance="simple"}
+## Biodiversity databases
+
+<br />
+_Most frequently used databases in biodiversity research_
+
+{{< fa user >}} &nbsp;**Authors:** [Olivier Norvez](https://scholar.google.fr/citations?user=0HfITX4AAAAJ&hl)<br/>
+{{< fa brands github >}} &nbsp;**Source:** <https://github.com/biodiversitydata/biodiversity-data/><br/>
+{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/biodiversity-data/><br/><br/>
+**License:** &nbsp;[Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/deed.en) &nbsp;{{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}
+:::
+
+
+<br />
+
+<div class="container">
+  <iframe class="responsive-iframe" src="https://biodiversitydata.github.io/biodiversity-data"></iframe>
+</div>

chapters/data-acquisition.qmd

@@ -5,9 +5,12 @@
 ## Data acquisition
 
 <br />
+_Web portals, scripting, API & Web scraping_
+
 {{< fa user >}} &nbsp;**Authors:** [Nicolas Casajus](https://nicolascasajus.fr) & [Camille Coux](https://www.fondationbiodiversite.fr/en/membre/camille-coux/)<br/>
 {{< fa brands github >}} &nbsp;**Source:** <https://github.com/biodiversitydata/data-access/><br/>
-{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-access/>
+{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-access/><br/><br/>
+**License:** &nbsp;[Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/deed.en) &nbsp;{{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}
 :::
 
 

chapters/data-cleaning.qmd

@@ -1,13 +1,15 @@
-## Processing & cleansing data {.unnumbered}
-
+## Data processing  {.unnumbered}
 
 ::: {.callout-note icon=true appearance="simple"}
-## Processing & cleansing data
+## Data processing
 
 <br />
+_Good practices, tools and homogenizing taxonomy_
+
 {{< fa user >}} &nbsp;**Authors:** [Nicolas Casajus](https://nicolascasajus.fr) & [Camille Coux](https://www.fondationbiodiversite.fr/en/membre/camille-coux/)<br/>
 {{< fa brands github >}} &nbsp;**Source:** <https://github.com/biodiversitydata/data-cleaning/><br/>
-{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-cleaning/>
+{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-cleaning/><br/><br/>
+**License:** &nbsp;[Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/deed.en) &nbsp;{{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}
 :::
 
 

chapters/data-paper.qmd

@@ -5,9 +5,12 @@
 ## Writing a data paper
 
 <br />
+_Describe and share your {meta}data_
+
 {{< fa user >}} &nbsp;**Authors:** [Sophie Pamerlon](https://www.patrinat.fr/fr/annuaire/sophie-pamerlon-6148), [Olivier Norvez](https://scholar.google.fr/citations?user=0HfITX4AAAAJ&hl) & [Yvan Le Bras](https://scholar.google.fr/citations?user=PVBOyvYAAAAJ&hl=fr)<br/>
 {{< fa brands github >}} &nbsp;**Source:** <https://github.com/biodiversitydata/data-paper/><br/>
-{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-paper/>
+{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-paper/><br/><br/>
+**License:** &nbsp;[Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/deed.en) &nbsp;{{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}
 :::
 
 

chapters/data-repositories.qmd

@@ -0,0 +1,21 @@
+## Biodiversity data repositories {.unnumbered}
+
+
+::: {.callout-note icon=true appearance="simple"}
+## Biodiversity data repositories
+
+<br />
+_Share and use data and metadata _
+
+{{< fa user >}} &nbsp;**Authors:** [Olivier Norvez](https://orcid.org/0000-0001-7696-3493) & [Yvan Le Bras](https://www.researchgate.net/profile/Yvan-Le-Bras)<br/>
+{{< fa brands github >}} &nbsp;**Source:** <https://github.com/biodiversitydata/data-repositories/><br/>
+{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-repositories/><br/><br/>
+**License:** &nbsp;[Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/deed.en) &nbsp;{{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}
+:::
+
+
+<br />
+
+<div class="container">
+  <iframe class="responsive-iframe" src="https://biodiversitydata.github.io/data-repositories"></iframe>
+</div>

chapters/data-sharing.qmd

@@ -5,9 +5,12 @@
 ## Data sharing
 
 <br />
+_Research compendium, R Package & Shiny App_
+
 {{< fa user >}} &nbsp;**Author:** [Nicolas Casajus](https://nicolascasajus.fr)<br/>
 {{< fa brands github >}} &nbsp;**Source:** <https://github.com/biodiversitydata/data-sharing/><br/>
-{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-sharing/>
+{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-sharing/><br/><br/>
+**License:** &nbsp;[Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/deed.en) &nbsp;{{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}
 :::
 
 

chapters/databases.qmd

@@ -5,9 +5,12 @@
 ## DataSHARE projects
 
 <br />
+_Sharing open-access and large scale biodiversity datasets_
+
 {{< fa user >}} &nbsp;**Author:** [Nicolas Casajus](https://nicolascasajus.fr)<br/>
 {{< fa brands github >}} &nbsp;**Source:** <https://github.com/biodiversitydata/datashare/><br/>
-{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/datashare/>
+{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/datashare/><br/><br/>
+**License:** &nbsp;[Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/deed.en) &nbsp;{{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}
 :::
 
 

chapters/datashare.qmd

@@ -5,9 +5,12 @@
 ## Data management plan
 
 <br />
+_How to plan your data lifecycle?_
+
 {{< fa user >}} &nbsp;**Authors:** [Yvan Le Bras](https://scholar.google.fr/citations?user=PVBOyvYAAAAJ&hl=fr) & [Olivier Norvez](https://scholar.google.fr/citations?user=0HfITX4AAAAJ&hl)<br/>
 {{< fa brands github >}} &nbsp;**Source:**  <https://github.com/biodiversitydata/data-management-plan/><br/>
-{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-management-plan/>
+{{< fa globe >}} &nbsp;**Slides:** <https://biodiversitydata.github.io/data-management-plan/><br/><br/>
+**License:** &nbsp;[Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/deed.en) &nbsp;{{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}
 :::