diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index bbae1bd..b2bd17b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,6 +1,6 @@ -# Contributing to quarto-template +# Contributing to general-context -First off, thanks for taking the time to contribute to `quarto-template`! +First off, thanks for taking the time to contribute to `general-context`! All types of contributions are encouraged and valued. See the [Table of contents](#table-of-contents) for different ways to help and details @@ -24,13 +24,13 @@ maintainers and smooth out the experience for all involved. ## Code of conduct -This project is released with a [Contributor Code of Conduct](https://github.com/biodiversitydata/quarto-template/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to . +This project is released with a [Contributor Code of Conduct](https://github.com/biodiversitydata/general-context/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to . ## Style guide -We use the [Tidyverse style guide](https://style.tidyverse.org/) for writing R code. Functions are documented with the [roxygen2](https://roxygen2.r-lib.org/articles/roxygen2.html) syntax. `quarto-template` uses the `lower_snake_case`. +We use the [Tidyverse style guide](https://style.tidyverse.org/) for writing R code. Functions are documented with the [roxygen2](https://roxygen2.r-lib.org/articles/roxygen2.html) syntax. `general-context` uses the `lower_snake_case`. @@ -42,12 +42,12 @@ If you want to contribute by commiting changes, please try to use the [Conventio ## Asking questions -Before you ask a question, it is best to search for existing [Issues](https://github.com/biodiversitydata/quarto-template/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. +Before you ask a question, it is best to search for existing [Issues](https://github.com/biodiversitydata/general-context/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. If you then still feel the need to ask a question and need clarification, we recommend the following: -- Open a new [Issue](https://github.com/biodiversitydata/quarto-template/issues/new). -- Use the template [other_issue.md](https://github.com/biodiversitydata/quarto-template/blob/main/.github/ISSUE_TEMPLATE/other_issue.md). +- Open a new [Issue](https://github.com/biodiversitydata/general-context/issues/new). +- Use the template [other_issue.md](https://github.com/biodiversitydata/general-context/blob/main/.github/ISSUE_TEMPLATE/other_issue.md). - Provide as much context as you can about what you're running into. - Provide project and platform versions (paste the output of `sessionInfo()`). @@ -63,19 +63,19 @@ We will then take care of the issue as soon as possible. A good bug report shouldn't leave others needing to chase you up for more information. Therefore, we ask you to investigate carefully, collect information and describe the issue in detail in your report. Please complete the following steps in advance to help us fix any potential bug as fast as possible. -- Make sure that you are using the latest version of `quarto-template`. +- Make sure that you are using the latest version of `general-context`. - Determine if your bug is really a bug and not an error on your side. -- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/biodiversitydata/quarto-template/issues?q=label%3Abug). +- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/biodiversitydata/general-context/issues?q=label%3Abug). ### How do I submit a bug report? -We use [GitHub Issues](https://github.com/biodiversitydata/quarto-template/issues) to +We use [GitHub Issues](https://github.com/biodiversitydata/general-context/issues) to track bugs and errors. If you run into an issue with the project: -- Open a new [Issue](https://github.com/biodiversitydata/quarto-template/issues/new). -- Use the template [bug_report.md](https://github.com/biodiversitydata/quarto-template/blob/main/.github/ISSUE_TEMPLATE/bug_report.md). +- Open a new [Issue](https://github.com/biodiversitydata/general-context/issues/new). +- Use the template [bug_report.md](https://github.com/biodiversitydata/general-context/blob/main/.github/ISSUE_TEMPLATE/bug_report.md). - Explain the behavior you would expect and the actual behavior. - Please provide as much context as possible and describe the *reproduction steps* that someone else can follow to recreate the issue on @@ -91,21 +91,21 @@ We will then take care of the issue as soon as possible. ### Before requesting a feature -- Make sure that you are using the latest version of `quarto-template`. -- Read the [documentation](https://github.com/biodiversitydata/quarto-template/) and the [wiki](https://github.com/biodiversitydata/quarto-template/wiki) carefully and find out if the functionality is already covered. -- Perform a [search](https://github.com/biodiversitydata/quarto-template/issues) to see if this enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one. +- Make sure that you are using the latest version of `general-context`. +- Read the [documentation](https://github.com/biodiversitydata/general-context/) and the [wiki](https://github.com/biodiversitydata/general-context/wiki) carefully and find out if the functionality is already covered. +- Perform a [search](https://github.com/biodiversitydata/general-context/issues) to see if this enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one. ### How do I submit a feature request? -Feature requests are tracked as [GitHub Issues](https://github.com/biodiversitydata/quarto-template/issues). +Feature requests are tracked as [GitHub Issues](https://github.com/biodiversitydata/general-context/issues). -- Open a new [Issue](https://github.com/biodiversitydata/quarto-template/issues/new). -- Use the template [feature_request.md](https://github.com/biodiversitydata/quarto-template/blob/main/.github/ISSUE_TEMPLATE/feature_request.md). +- Open a new [Issue](https://github.com/biodiversitydata/general-context/issues/new). +- Use the template [feature_request.md](https://github.com/biodiversitydata/general-context/blob/main/.github/ISSUE_TEMPLATE/feature_request.md). - Provide a clear and descriptive title for the issue to identify the suggestion. - Provide a step-by-step description of the suggested enhancement in as many details as possible. -- Explain why this enhancement would be useful to most `quarto-template` users. +- Explain why this enhancement would be useful to most `general-context` users. We will then take care of the issue as soon as possible. @@ -122,7 +122,7 @@ We use the [GitHub flow](https://docs.github.com/en/get-started/quickstart/githu 1. Make your contribution. 1. Stage (`git add`) and commit (`git commit`) your changes as often as necessary 1. Push your changes to GitHub w/ `git push origin branch-name`. -3. Submit a [Pull Request](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request) on the [original repo](https://github.com/biodiversitydata/quarto-template/compare). +3. Submit a [Pull Request](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request) on the [original repo](https://github.com/biodiversitydata/general-context/compare). We will then review the PR as soon as possible. diff --git a/README.md b/README.md index 37bcf16..882a068 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,9 @@
Logo
- Quarto template + Biodiversity data: General context
- HTML presentation w/ RevealJS + Open science, complex landscape & reproducibility
@@ -15,7 +15,7 @@

- View presentation + View presentation


@@ -37,13 +37,13 @@
- - GHA render + + GHA render - - GHA deploy + + GHA deploy

@@ -52,57 +52,46 @@

Overview • - FeaturesUsageCitationContributingAcknowledgments

-![](images/readme/title-slide-screenshot.png) -
## Overview -This repository contains files and folders required to setup a minimal [Quarto HTML Presentation](https://quarto.org/docs/presentations/) based on the [RevealJS](https://quarto.org/docs/presentations/revealjs/) framework with a custom CSS theme. -This is a [Template Repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-template-repository) and you can generate a new repository from this template with the same directory structure, branches, and files. - +This repository contains files used to generate the online presentation [Biodiversity data: General context](https://biodiversitydata.github.io/general-context) based on [Quarto](https://quarto.org/) and the [RevealJS](https://quarto.org/docs/presentations/revealjs/) framework. -## Features +## Usage -- Basics of Quarto presentation (title slide, two column slides, code block, images and tables) -- Custom CSS style -- Emoji support -- [Fontawesome](https://github.com/quarto-ext/fontawesome) & [Academicons](https://github.com/schochastics/academicons) extensions -- Complete repository structure -- GitHub Action to automatically render `index.qmd` -- Website deployment on `gh-pages` branch +If you want to render the slides locally, you need to install the following tools: +- [`R`](https://cran.r-project.org/) and [`RStudio Desktop`](https://posit.co/download/rstudio-desktop/) +- [`Quarto CLI`](https://quarto.org/docs/get-started/) -## Usage +[Fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo) this repository and [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) your copy. -A dedicated Wiki is available [**here**](https://github.com/biodiversitydata/quarto-template/wiki/). +Then, open the `index.qmd` in RStudio and click on the button **Render**. This will create an `index.html` containing your presentation. Open this `index.html` in your favorite web browser to access slides. -- Read the [Installation](https://github.com/biodiversitydata/quarto-template/wiki/Installation) page to learn how to use this template. -- Read the [Content](https://github.com/biodiversitydata/quarto-template/wiki/Content) page to discover the role of each file. -- Read the [Usage](https://github.com/biodiversitydata/quarto-template/wiki/Usage) page to start writing your own presentation. +To understand the file organisation of this repository, please read this [Wiki](https://github.com/biodiversitydata/quarto-template/wiki). ## Citation -Casajus N (2024) _A Quarto template for HTML presentation with RevealJS framework_. . +Norvez O, Pamerlon S & Casajus N (2024) Biodiversity data: General context. Online presentation available at . ## Contributing -All types of contributions are encouraged and valued. For more information, check out our [Contributor Guidelines](https://github.com/biodiversitydata/quarto-template/blob/main/CONTRIBUTING.md). +All types of contributions are encouraged and valued. For more information, check out our [Contributor Guidelines](https://github.com/biodiversitydata/general-context/blob/main/CONTRIBUTING.md). -Please note that the `quarto-template` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms. +Please note that the `general-context` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms. ## Acknowledgments -This project has been developed for the [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) training courses [program](https://frbcesab.github.io/content/courses.html). +This project has been developed for the [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) training courses [program](https://frbcesab.github.io/content/courses.html) and it's part of the training course [Biodiversity data management](https://biodiversitydata.github.io). diff --git a/_quarto.yml b/_quarto.yml index f5a5b51..c43ac89 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -1,2 +1,4 @@ project: - title: "index" + title: "General context" + +pagetitle: "General context" diff --git a/images/image-PaysageBD_Roche2023-2.png b/images/image-PaysageBD_Roche2023-2.png new file mode 100644 index 0000000..9c02fa5 Binary files /dev/null and b/images/image-PaysageBD_Roche2023-2.png differ diff --git a/index.qmd b/index.qmd index f638f3b..82866b5 100644 --- a/index.qmd +++ b/index.qmd @@ -3,12 +3,15 @@ from: markdown+emoji format: revealjs: logo: images/logo-affiliation.png - footer: "{{< fa brands github >}}  " + footer: "{{< fa brands github >}}  [`biodiversitydata/general-context`](https://github.com/biodiversitydata/general-context)   •   {{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}}  [`cc-by-4.0`](https://creativecommons.org/licenses/by/4.0/deed.en)" smaller: true auto-stretch: false chalkboard: true toc-depth: 1 theme: [default, "styles/main.scss"] +knitr: + opts_chunk: + comment: "##" engine: knitr --- diff --git a/sections/slides.qmd b/sections/slides.qmd index f45e2a6..f9d6b79 100644 --- a/sections/slides.qmd +++ b/sections/slides.qmd @@ -1,262 +1,255 @@ -# Current challenges in biodiversity data and ecoinformatics +# Current challenges in biodiversity data -## Current challenges in biodiversity data and ecoinformatics : *Open Science* +## Open Science -«La France s’engage pour que les résultats de la recherche scientifique soient ouverts à tous, chercheurs, entreprises et citoyens, sans entrave, sans délai, sans paiement». -
-*France is committed to ensuring that the results of scientific research are open to all, researchers, businesses and citizens, without hindrance, without delay, without payment.* +**Second French Plan for Open Science**[^1] -[Ouvrir la science](https://www.ouvrirlascience.fr/deuxieme-plan-national-pour-la-science-ouverte-pnso/) +> France is committed to ensuring that the results of scientific research are open to all, researchers, companies and citizens, without hindrance, without delay, without payment. -
+[^1]: [Second French Plan for Open Science](https://www.ouvrirlascience.fr/deuxieme-plan-national-pour-la-science-ouverte-pnso/) :::: {.columns} -::: {.column width=50%} - -**Axe 1**: Généraliser l’accès ouvert aux publications *Generalize open access to publications*. -
-**Axe 2** : Structurer, partager et ouvrir les données de la recherche *Structure, share and open research data*. -
-**Axe 3** : Ouvrir et promouvoir les codes sources produits par la recherche *Open and promote source codes produced by research*. -
-**Axe 4** : Transformer les pratiques pour faire de la science ouverte le principe par défaut *Transforming practices to make open science the default principle*. -
+::: {.column width=40%} +![](images/logo-PNSO2.png){width=60%} ::: -::: {.column .center width=50%} +::: {.column width=60%} +


-![](images/logo-PNSO2.png){width=50%} +- **Axe 1 :** Generalize open access to publications +- **Axe 2 :** Structure, share and open research data +- **Axe 3 :** Open and promote source codes produced by research +- **Axe 4 :** Transforming practices to make open science the default principle ::: :::: -::: -## Current challenges in biodiversity data and ecoinformatics : *heterogeneity and loss of informations* - +## Heterogeneity and loss of informations :::: {.columns} -::: {.column width=50%} - +::: {.column .center width=50%} ![](images/image-Page2016.png){width=80%} -
-**Heterogeneity (data types, origin, standards) & diversity of “objects” to be linked together** -
-[R. Page, 2016](https://riojournal.com/article/8767) -
+::: +::: {.column .center width=50%} +![](images/image-Michener1997.jpg){width=80%} ::: -::: {.column width=50%} +:::: -![](images/image-Michener1997.jpg){width=80%} -
-**Loss of information over time** -
-[W.K. Michener et al., 1997](https://doi.org/10.1890/1051-0761(1997)007[0330:NMFTES]2.0.CO;2) -
+:::: {.columns} +::: {.column .center width=50%} +**Heterogeneity (data types, origin, standards) &
Diversity of "objects" to be linked together**[^2] +::: + +::: {.column .center width=50%} +**Loss of information over time**[^3] ::: :::: -::: + +[^2]: [Page (2016)](https://riojournal.com/article/8767) +[^3]: [Michener _et al._ (1997)](https://doi.org/10.1890/1051-0761(1997)007[0330:NMFTES]2.0.CO;2) + -::: -## Current challenges in biodiversity data and ecoinformatics : *a complex landscape* +## A complex landscape :::: {.columns} -::: {.column width=25%} +::: {.column width=30%} +
-- Diversity of tools and practices Historical practices. -- Different supervision. -- Flow and storage of data and metadata. -- Difficulty for data producers to identify the right information systems to deposit their data according to the scopes and themes. -- Difficulty for users to know where and how to search for data. +- Diversity of tools and practices (historical practices) +- Different supervisions +- Flow and storage of data and metadata +- Difficulty for data producers to identify the right information systems to deposit their data according to the scopes and themes +- Difficulty for users to know where and how to search for data ::: -::: {.column .center width=75%} -![](images/image-PaysageBD_Roche2023.png){width=100%} - +::: {.column .center width=70%} +![](images/image-PaysageBD_Roche2023-2.png){width=100%} ::: :::: -::: -::: - -## Current challenges in biodiversity data and ecoinformatics : *a complex landscape* +## A complex landscape :::: {.columns} -::: {.column width=50%} +::: {.column width=60%}
-The objectives of this note are to support producers and reusers of biodiversity data and metadata in: - -- Understanding the landscape (actors, who does what, who is who...), -- Sharing data/metadata (where to deposit, what types of data...) -- And using the latter via the complementary of information systems according to the themes and/or target audiences. +A note are to support producers and reusers of biodiversity data and metadata in: -The targets of this note are above all researchers, managers, engineers and data technicians -
+- Understanding the landscape (actors, who does what, who is who, etc.) +- Sharing (meta)data (where to deposit, what types of data, etc.) +- Using the latter via the complementary of information systems according to the themes and/or target audiences -*Nota Bene* +
-- *The V1 is available [here](https://mnhn.hal.science/mnhn-04296424/)* -- *The V2 will be available soon (December 2024 or January 2025)* -
+The targets of this note are above all researchers, managers, engineers and data technicians ::: -::: {.column .center width=50%} +::: {.column .center width=40%} -![](images/image-noteflux2023.jpg){width=70%} +![](images/image-noteflux2023.jpg){width=60%} ::: - +:::: -::: +
-## Current challenges in biodiversity data and ecoinformatics : *a complex landscape* +- Version 1 is available [here](https://mnhn.hal.science/mnhn-04296424/) +- Version 2 will be available soon (December 2024 or January 2025) +
-![](images/image-Flux_dispositifs_SI.png){width=70%} -::: - -## Current challenges in biodiversity data and ecoinformatics : *a complex landscape* + -![](images/image-logigrammeFluxSI.png){width=70%} -::: - -## Current challenges in biodiversity data and ecoinformatics : *reproductibility* +## A complex landscape -:::: {.columns} +![](images/image-Flux_dispositifs_SI.png){width=70% fig-align='center'} -::: {.column width=50%} -*"Computational reproducibility frequently refers to the ability to generate equivalent analytical outcomes from the same data set using the same code and software"* -[Powers & Hampton, 2018](https://doi.org/10.1002/eap.1822) -![](images/image-Powers2018.jpg){width=100%} + -::: +## A complex landscape -::: {.column .center width=50%} +![](images/image-logigrammeFluxSI.png){width=70% fig-align='center'} -*"all raw data and metadata, code, programming scripts, and bespoke software necessary for fully replicating any analyses that lead to inferences made in a published study."* -[Genkins *et al.,* 2016](https://doi.org/10.1002/ece3.9961) +# Reproducibility concepts -![](images/image-JenkinsReproductibility.png){width=100%} + -::: +## Reproducibility -:::: +:::: {.columns} +::: {.column width=50%} +![](images/image-Powers2018.jpg){width=100%} ::: - +::: {.column width=50%} +![](images/image-JenkinsReproductibility.png){width=100%} +::: -## Current challenges in biodiversity data and ecoinformatics : *reproductibility* +:::: :::: {.columns} ::: {.column width=50%} +> Computational reproducibility frequently refers to the ability to generate equivalent analytical outcomes from the same data set using the same code and software[^4]. +::: -*"example 1"* - +::: {.column width=50%} +> [...] all raw data and metadata, code, programming scripts, and bespoke software necessary for fully replicating any analyses that lead to inferences made in a published study[^5]. ::: -::: {.column .center width=50%} +:::: -*"example 2* +[^4]: [Powers & Hampton (2018)](https://doi.org/10.1002/eap.1822) +[^5]: [Genkins _et al._ (2016)](https://doi.org/10.1002/ece3.9961) -::: -:::: + -::: +## Reproducibility +Coming soon... + + +# Data vs. metadata -## Data & Metadata : *about you?* +## Data vs. metadata -**What kind of data and/or metadata are you using for your research ?** +**What kind of data and/or metadata are you using for your research?** + +
:::: {.columns} ::: {.column width=50%} - **DATA** +::: -::: {.column .center width=50%} - +::: {.column width=50%} **METADATA** ::: :::: -::: -## Data & Metadata : *definition* +## Definitions :::: {.columns} ::: {.column width=33%} -*"Research data are defined as factual records in the form of figures, texts, images and sounds which are used as the main sources for scientific research and which the scientific community generally recognizes as being necessary to validate research results."* - -[OECD, 2007 : Principles and Guidelines for Access to Research Data from Public Funding](https://www.oecd-ilibrary.org/science-and-technology/oecd-principles-and-guidelines-for-access-to-research-data-from-public-funding_9789264034020-en-fr) - -![](images/image-OECD-Data2007.jpg){width=50%} - +"_Research_ **data** _are defined as factual records in the form of figures, texts, images and sounds which are used as the main sources for scientific research and which the scientific community generally recognizes as being necessary to validate research results_"[^6]. ::: ::: {.column .center width=33%} - ![](images/image_DataMetadata.png){width=100%} - ::: ::: {.column width=33%} +"**Metadata**, _which can be simply defined as “data about data,” is a way of naming things and representing data and their relationships [...] Metadata is structured information that describes, explains, locates, or otherwise makes it easier to retrieve, use or manage an information resource_"[^7]. +::: -*"Metadata, which can be simply defined as “data about data,” is a way of naming things and representing data and their relationships [...] Metadata is structured information that describes, explains, locates, or otherwise makes it easier to retrieve, use or manage an information resource"* +:::: -[Christine L. Borgman, 2015 & 2020](https://books.openedition.org/oep/14692) -![](images/image_Borgman2015.jpg){width=50%} +:::: {.columns} +::: {.column .center width=33%} +![](images/image-OECD-Data2007.jpg){width=45%} ::: -:::: +::: {.column width=33%} +::: +::: {.column .center width=33%} +![](images/image_Borgman2015.jpg){width=40%} ::: +:::: + + +[^6]: [OECD (2007)](https://www.oecd-ilibrary.org/science-and-technology/oecd-principles-and-guidelines-for-access-to-research-data-from-public-funding_9789264034020-en-fr) + +[^7]: [Borgman CL (2020)](https://books.openedition.org/oep/14692) + -::: -## Data & Metadata : *definition* +## Definitions + +
:::: {.columns} @@ -274,95 +267,194 @@ The targets of this note are above all researchers, managers, engineers and data :::: -::: + +# Data classification(s) + + -## Data categories : *definition* +## Data classification(s) -**What kind of data and/or metadata are you using for your research ?** +**What kind of data and/or metadata are you using for your research?** + +
:::: {.columns} ::: {.column width=50%} - **DATA** +::: +::: {.column width=50%} +**METADATA** ::: -::: {.column .center width=50%} +:::: -**METADATA** + + + +## Characterizing data + +
+ +:::: {.columns} + +::: {.column width=50%} + +![](images/image_DataMetadata.png){width=80%} ::: -:::: +::: {.column .center width=50%} + +




+{{< fa circle-right>}}   **Link this information with your biodiversity research projects** + +Imagine : you're wondering about the distribution of a given species. ::: +:::: - -## Data categories : *questions to ask and characterization of data* + + +## Characterizing data + +
:::: {.columns} ::: {.column width=50%} -Characterization of data: +![](images/image_DataMetadata.png){width=80%} -- Temporal information (e.g. longitudinal data / time series (LTS)) -- Spatial information (spatial data (GIS, occurrences, remote sensing, etc.) -- Textual data (csv, DNA, …) -- Taxonomic data -- Trait data -- ... +::: + +::: {.column width=50%} + +- **what ** species ? --> observation data: presence/absence, abundance, density, biomass ? + +> but also: what are the intra-population variations ? DNA, trait measurements ? phylogeny ? + +- **where** are they spatially ? in which proportions ? + +- **when** were they observed or sampled ? repeated measures ? time stamp or global period ? + +- **how** were they collected ? biases ? pseudoreplication ? true absences ? + +- **why** and **who** : citizen science ? opportunistic ? funding ? + +::: +:::: + + + +## Classifying data by... + +
+ +:::: {.columns} + +::: {.column width=33%} + +**Format**[^8] +- Data Table +- Spatial raster +- Spatial vector +- Databases +- Other entities ::: -::: {.column .center width=50%} +::: {.column width=33%} + + +::: + +::: {.column width=33%} -**Link these informations with your biodiversity research projects** -![](images/image_DataMetadata.png){width=100%} ::: :::: +[^8]: According to the [Ecological Metadata Language (EML)](https://eml.ecoinformatics.org/eml-schema) classification + -## Data categories : *classification* +## Classifying data by... +
:::: {.columns} ::: {.column width=33%} -**By format** (Ecological Metadata Language - EML - classification) : - -- data Table -- spatial raster -- spatial vector -- databases -- other Entity +**Format**[^8] +- Data Table +- Spatial raster +- Spatial vector +- Databases +- Other entities ::: -::: {.column .center width=33%} +::: {.column width=33%} -**By type**: +**Type** - Citizen science - Sensors - DNA-based techniques - Satellite remote sensing - Others (simulated data) +::: + +::: {.column width=33%} + ::: +:::: + + +[^8]: According to the [Ecological Metadata Language (EML)](https://eml.ecoinformatics.org/eml-schema) classification + + +## Classifying data by... + +
+ +:::: {.columns} + ::: {.column width=33%} -**Others classifications:** +**Format**[^8] + +- Data Table +- Spatial raster +- Spatial vector +- Databases +- Other entities +::: + +::: {.column width=33%} + +**Type** + +- Citizen science +- Sensors +- DNA-based techniques +- Satellite remote sensing +- Others (simulated data) +::: + +::: {.column width=33%} + +**Other classifications** - Temporal information (e.g. longitudinal data / time series (LTS)) - Spatial information (spatial data (GIS, occurrences, remote sensing, etc.) @@ -370,50 +462,62 @@ Characterization of data: - Taxonomic - Trait data - Non-exhaustive - ::: :::: +[^8]: According to the [Ecological Metadata Language (EML)](https://eml.ecoinformatics.org/eml-schema) classification + + + -## Data categories : *by formats* +## Data categories: *by format* :::: {.columns} ::: {.column width=50%} -By format (classification EML classification) : - -- data Table -- spatial raster -- spatial vector -- databases -- other Entity +According to the EML classification[^9] +- Data Table +- Spatial raster +- Spatial vector +- Databases +- Other entities ::: ::: {.column .center width=50%} - ![](images/image-eml-semantics.png){width=100%} ::: :::: -![](images/image-logo-eml.jpg){width=10%} -[Matthew B. Jones, *et al.,* 2019. Ecological Metadata Language version 2.2.0. KNB Data Repository.](https://eml.ecoinformatics.org/eml-schema) +:::: {.columns} +::: {.column width=50%} +![](images/image-logo-eml.jpg){width=30% fig-align='center'} +::: + +::: {.column width=50%} ::: +:::: +[^9]: [Matthew B _et al._ (2019)](https://eml.ecoinformatics.org/eml-schema) + + -## Data categories : *by types* +## Data categories: *by type* :::: {.columns} -::: {.column width=25%} +::: {.column width=30%} +
+ +According to [Kissling WD _et al._ (2018)](https://doi.org/10.1111/brv.12359) - Citizen science - Sensors @@ -423,127 +527,161 @@ By format (classification EML classification) : ::: -::: {.column .center width=75%} - +::: {.column .center width=70%} ![](images/image-dataType-Kissing2018.jpg){width=100%} -[Kissling W.D. et al., 2018](https://doi.org/10.1111/brv.12359) ::: :::: -::: -## Data categories : *others classifications* +## Data categories: *other classifications* + +- **Longitudinal data** + +Repeated measures, such as long term surveys, allowing to look at evolution (of abundances, biomass, etc) over time. + +> Time series analyses + + +- **Spatial data** + +Generic term that starts whenever there are spatial coordinates (long/lat) associated with an observation. May also refer to remote sensing images, GIS. + +
+ +- **Textual data** + +Again a very generic term, ranges from spreadsheets of data occurrences to DNA sequences, and text mining (systematic reviews, web scrapping, etc). + + + +# Frameworks and Good practices -- Longitudinal data / time series (LTS) -- Spatial data (GIS, occurrences, remote sensing, etc.) -- Textual data (csv, DNA, …) -## Good practises and frameworks +## Frameworks and Good practices + +
:::: {.columns} -::: {.column width=33%} +::: {.column .center width=33%} -the Data life cycle +**Data life cycle** -![](images/image-datalifecycle.png){width=100%} +
+![](images/image-datalifecycle.png){width=100%} ::: ::: {.column .center width=33%} +**FAIR Principles** -the FAIR Principles +


![](images/image-FAIR.png){width=100%} - ::: -::: {.column width=33%} +::: {.column .center width=33%} -Flux and stocks of data +**Flux and stocks of data** -![](images/image-Flux_dispositifs_SI.png){width=100%} +
+![](images/image-Flux_dispositifs_SI.png){width=100%} ::: :::: -::: + -## Good practises and frameworks : *the data life cycle* +## Data life cycle :::: {.columns} -::: {.column width=25%} +::: {.column width=60%} -The data lifecycle is the set of stages of management, conservation and dissemination of research data, associated with research activities. +![](images/image-datalifecycle.png){width=100%} +::: -*for more information : [PNDB web page](https://www.pndb.fr/fr/ressources/principes-fair-et-cycle-de-vie-des-donnees)* -::: +::: {.column width=40%} +


-::: {.column .center width=75%} +The data lifecycle is the set of stages of management, conservation and dissemination of research data, associated with research activities. + +
+ +{{< fa circle-right >}}  For more information: [PNDB](https://www.pndb.fr/fr/ressources/principes-fair-et-cycle-de-vie-des-donnees) -![](images/image-datalifecycle.png){width=100%} ::: :::: -::: + -## Good practises and frameworks : *the FAIR principles* + +## FAIR principles + :::: {.columns} ::: {.column width=60%} -A set of guiding principles for managing research data to make it findable, accessible, interoperable, and reusable by humans and machines. +

+ +A set of guiding principles for managing research data to make it **F**indable, **A**ccessible, **I**nteroperable, and **R**eusable by humans and machines[^10]. + + +**This is the way!** -**“This is the way!”** -![](images/image-FAIR.png){width=60%} +![](images/image-FAIR.png){width=50%} -![](images/image-GOFAIR.png){width=40%} +![](images/image-GOFAIR.png){width=30%} +{{< fa circle-right >}}  For more information: [PNDB](https://www.pndb.fr/fr/outils-services/outils-services-par-etapes/preservation#Standardisation%20des%20{m%C3%A9ta}donn%C3%A9es) ::: -::: {.column width=40%} +::: {.column .right width=40%} -![](images/image-FAIRprinciples.jpg){width=80%} -[Wilkinson M. D. et al., 2017](https://doi.org/10.1038/sdata.2016.18) +![](images/image-FAIRprinciples.jpg){width=70% fig-align='right'} ::: :::: -*for more information : [PNDB web page](https://www.pndb.fr/fr/outils-services/outils-services-par-etapes/preservation#Standardisation%20des%20{m%C3%A9ta}donn%C3%A9es)* -::: + +[^10]: [Wilkinson M. D. et al., 2017](https://doi.org/10.1038/sdata.2016.18) + -## Good practises and frameworks : *the FAIR principles* +## FAIR principles + + +![](images/image-Datastandardization.png){width=80% fig-align='center'} + +{{< fa circle-right >}}  For more information: [PNDB](https://www.pndb.fr/fr/ressources/principes-fair-et-cycle-de-vie-des-donnees) -![](images/image-Datastandardization.png){width=100%} -*for more information : [PNDB web page](https://www.pndb.fr/fr/ressources/principes-fair-et-cycle-de-vie-des-donnees)* -::: -## Good practises and frameworks : *flux and stocks* +## Flux and stocks + +![](images/image-Flux_dispositifs_SI.png){width=60% fig-align='center'} + + -![](images/image-Flux_dispositifs_SI.png){width=70%} -::: -## Good practises and frameworks : *flux and stocks* +## Flux and stocks :::: {.columns} @@ -551,16 +689,17 @@ A set of guiding principles for managing research data to make it findable, acce Sharing data from research activities requires making them available in repositories. -It is recommended to prioritize deposits in trusted thematic repositories, or failing that, in generic repositories such as Recherche data gouv. +It is recommended to prioritize deposits in trusted thematic repositories, or failing that, in generic repositories such as [Recherche Data Gouv](https://recherche.data.gouv.fr/en). +
-**Focus : the InDoRES repository** +**Focus: the InDoRES repository** Under the supervision of the CNRS Institute of Ecology and Environment and the National Museum of Natural History, the InDoRES portal offers: - to discover databases and datasets thanks to a description of the projects that produce them (standardized and interoperable metadata catalog that meets European directives). When they exist, links are provided to the data to download or to associated publications - to access the secure data.InDoRES warehouse to publish data -- to gather and link to a set of resources on practices that facilitate the sharing and reuse of data, in accordance with the recommendations of the FAIR principles (Easy to find, Accessible, Interoperable, Reusable +- to gather and link to a set of resources on practices that facilitate the sharing and reuse of data, in accordance with the recommendations of the FAIR principles ![](images/image-logo-INDORES.png){width=30%} ::: @@ -568,7 +707,8 @@ Under the supervision of the CNRS Institute of Ecology and Environment and the N ::: {.column width=30%} ![](images/image-selection-entrepot.jpg){width=80%} -[Ouvrir la science, 2024](https://www.ouvrirlascience.fr/selectionner-un-entrepot-thematique-de-confiance-pour-le-depot-de-donnees-methodologie-et-analyse-de-loffre-existante/) +
+[Ouvrir la science (2024)](https://www.ouvrirlascience.fr/selectionner-un-entrepot-thematique-de-confiance-pour-le-depot-de-donnees-methodologie-et-analyse-de-loffre-existante/) ::: :::: @@ -601,4 +741,4 @@ Under the supervision of the CNRS Institute of Ecology and Environment and the N ## Data & Metadata : *definition* -**coming soon** \ No newline at end of file +**coming soon** diff --git a/sections/table-of-contents.qmd b/sections/table-of-contents.qmd index 02f9ad3..ce7de72 100644 --- a/sections/table-of-contents.qmd +++ b/sections/table-of-contents.qmd @@ -4,14 +4,14 @@ ## Table of contents -![](images/image-PNDB.png){width=100%} +![](images/image-PNDB.png){width=90% fig-align='center'} :::: { .columns } ::: { .column .center width="25%"} {{< fa code size=2x >}}
-**Current challenges in biodiversity data and ecoinformatics** +**Current challenges** ::: ::: { .column .center width="25%"} @@ -29,7 +29,7 @@ ::: { .column .center width="25%"} {{< fa book size=2x >}}
-**Framework and good practises** +**Framework and good practices** ::: :::: diff --git a/sections/title-slide.qmd b/sections/title-slide.qmd index edb7420..c78f643 100644 --- a/sections/title-slide.qmd +++ b/sections/title-slide.qmd @@ -11,11 +11,11 @@ ::: {.column .information width="68%"} ::: {.title} -Biodiversity data context & introduction +Biodiversity data: General context ::: ::: {.subtitle} -Open science, complex landscape & reproductibility +Open science, complex landscape & reproducibility ::: ::: {.date} @@ -49,10 +49,11 @@ Sophie Pamerlon
::: {.column .author width="32%"} Nicolas Casajus
-[{{< fa envelope >}}](mailto:nicolas.casajus@fondationbiodiversite.fr) -[{{< fa globe >}}](https://nicolascasajus.fr/) +[{{< fa envelope >}}](mailto:rdev.nc@gmail.com) +[{{< fa globe >}}](https://nicolascasajus.fr) [{{< fa brands github >}}](https://github.com/ahasverus) [{{< fa brands orcid >}}](https://orcid.org/0000-0002-5537-5294) +[{{< ai google-scholar >}}](https://scholar.google.fr/citations?user=n1swa1UAAAAJ) ::: @@ -63,24 +64,31 @@ Nicolas Casajus
::: {.column .affiliation width="32%"} Animation coordinator
-@PNDB [{{< fa globe >}}](https://www.pndb.fr/) -  -@DATATERRA [{{< fa globe >}}](https://www.data-terra.org/) +@PNDB   +[{{< fa globe >}}](https://www.pndb.fr/)
- +@DataTerra +  +[{{< fa globe >}}](https://www.data-terra.org/) ::: ::: {.column .affiliation width="32%"} Data engineer
-{{< fa globe >}}  [GBIF France](http://www.gbif.fr/) +@GBIF-France +  +[{{< fa globe >}}](http://www.gbif.fr/) ::: ::: {.column .affiliation width="32%"} Data scientist
-{{< fa globe >}}  [CESAB-FRB](https://www.fondationbiodiversite.fr/la-fondation/le-cesab/) +@FRB-CESAB +  +[{{< fa globe >}}](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) +  +[{{< fa brands github >}}](https://github.com/frbcesab) ::: diff --git a/styles/main.scss b/styles/main.scss index 8185beb..dd0d9c9 100644 --- a/styles/main.scss +++ b/styles/main.scss @@ -142,3 +142,35 @@ aside { text-align: center; } + +.callout-title p { + font-size: 1.8em; +} + +.callout-content p { + font-size: 1.8em; +} + +blockquote { + border: 0 !important; + margin: 0.5em 0 !important; + margin-bottom: 2em !important; + padding: 0 !important; + margin-left: 2% !important; + margin-right: 2% !important; +} + + +blockquote p { + font-style: normal; + padding: 0.5em 1em; + border-left: 5px solid #cccccc; +} + +/* +blockquote p::before { + content: "\27A4"; + font-style: normal; + padding-right: 10px; +} +*/